When do partonic 2-surfaces and string world sheets define large cognitive representations?

Cognitive representations are identified as points of space-time surface X⁴⊂ M⁴× CP₂ having imbedding space coordinates in the extension of of rationals defined by the polynomial defined by the M⁸ pre-image of X⁴ under M⁸-H correspondence. Cognitive representations have become key piece in the formulation of scattering amplitudes and in TGD view about consciousness and cognition. One might argue that number theoretic evolution as increase of the dimension of the extension of rationals favors space-time surfaces with especially large cognitive representations since the larger the number of points in the representation is, the more faithful the representation is.

Strong form of holography (SH) suggests that it is enough to consider cognitive representations restricted to partonic 2-surfaces and string world sheets. What kind of 2-surfaces are the cognitively fittest one? It would not be surprising if surfaces with large symmetries acting in extension were favored and elliptic curves with discrete 2-D translation group indeed turn out to be assigable string world sheets as singularities and string like objects.

See the article When do partonic 2-surfaces and string world sheets define large cognitive representations? or the chapter Does M⁸-H duality reduce classical TGD to octonionic algebraic geometry?: Part III.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

North Pole is moving

Norther Magnetic Pole is moving rather fast towards Siberia with rate between 55-60 km per year. On the other hand the magnetic field of Earth has been weakening. Could these phenomena relate to each other? There is also the long-standing mystery of the maintenance of the magnetic field B_E of Earth: one would expect that the dissipation for the currents generating B_E would lead to a rather rapid disappearance of B_E. A further mystery is that the orientation of B_E is different from the orientation of the rotation axis and can differ from it very much: this is not what one would expect if the rotational flow of liquid metal in the outer core is responsible for the entire B_E.

In TGD Universe B_E having nominal value .5 Gauss has two parts: monopole flux tube part and non-monopole part analogous to Maxwellian magnetic field. Monopole part is perhaps identifiable as the endogenous magnetic field B_end = 2B_E/5=.2 Gauss explaining Blackman's findings about quantal effects of ELF em fields on vertebrate brain in terms of the identification of dark matter as phases of the ordinary matter with effective Planck constant h_eff=n×h₀. No currents are needed to maintain the monopole part whereas the non-monopole requires current maintaining it. B_end corresponds to a flux tube radius of about L(169) then the minimal radius for flux tube would be about L(163) ≈ 640 nm.

Non-monopole part of B_E would be naturally parallel to the rotation axis of Earth since it is generated by the rotation of the outer core. Monopole part could correspond to the magnetic axis. The change of the direction of B_E would be induced by the change of the direction of the monopole part and induce currents changing the non-monopole part. Monopole part together with this refreshing mechanism would explain the maintenance of B_E (see this). The magnetic North pole is recently moving rather rapidly towards Siberia and the strength of B_E has been decreasing suggesting that the refreshing operation has been activated. This mechanism would force transfer of energy needed to refresh the current maintaining the non-monopole part.

See the article TGD inspired model for magneto-reception and circadian rhythm.
For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Very simple system showing brain like behaviours

The popular article "Human Brain-Like Functions Emerge in Neuromorphic Metallic Nanowire Network" published in Scitechdaily represents findings, which are very interesting from TGD point of view. The original article "Emergent dynamics of neuromorphic networks" by Diaz-Alvarez et al is published in Nature.

Consider first the findings.

1. One can say that the self-organization process corresponds to the system "struggling" to find optimal current pathways. This process involves fluctuations akin to those found in memorization, learning and forgetting processes of brain. The temporal flutuations also resemble the processes by which brain becomes alert or returns to calm.
   
   
2. The metallic Ag nanowires become coated with a polymer (PVP) insulating layer with about 1 nm thickness. Also metallic junctions between two nanowires acting as a resistive elements analogous to synapse are formed. The average diameter and length of nanowires was measured to be 360 +/- 110 nm and 14 +/- 5 μ m, respectively.
   

   Remark: These scales correspond to biological length scales (p-adic length scales (L(161) and L(172)).
   
   

3. There are suggestive connections with biology. PVP polymer is an organic compound with repetive active part which consist of two parts: CH₂ and aromatic Carbon 5-cycle with one C replaced with N and one CH₂ replaced with C =O. In TGD framework this could be relevant for the self-organization - maybe the magnetic bodies of PVP polymers are in an essential role.
   
   
4. The formation of low resistance pathways between probes contacting the networks induces a transition from low conductance state to high-conductance state at given voltage threshold usually below 10 V. This occurs even for millimeter distance between probes. The weak independence on voltage suggests that the current flow is almost dissipation free - could dark supra currents at magnetic flux tubes be involved?
   
   

TGD predicts several a lot of new physics possibly relevant to the findings (see this and and this ).

1. Magnetic flux tubes (magnetic body, MB) carrying dark matter as phases with effective Planck constant h_eff=n×h₀ .
   
   
2. Zero energy ontology allowing to formulate quantum measurement theory without paradoxes. The possibility of time reversal is one dramatic prediction. Basic mental functions like memory would be completely universal phenomena and possessed in principle evan by elementary particles.
   
   
3. Also universality of cognition described in terms of p-adic (adelic physics) is predicted. Number theoretic vision realized as adelic physics predicts evolution as increase of the dimension of extension of rationals characterizing basic building bricks of space-time as surface.
   

   Self-organization involves generation of coherence and requires energy feed. Same applies to life. Self-organization would be also universal: the self-assembly aspect of self organization would be simply due dissipation at reverse time direction at the level of dark matter at magnetic body controlling the dynamics at the level of ordinary matter as master.
   
   

4. Quantum criticality is essential element of self-organization and the observed 1/f fuctuations could be interpreted as their signature. Note that 1/f fluctuations are observed also in the ordinary electric circuits and since also these involve self-organization aspects, dark matter in TGD sense might be involved.
   

   At quantum criticality long range fluctuations take place and correspond to the creation of phases with large h_eff and therefore of large quantum coherence length. Energy feed is however required and serves as analog of metabolic energy. Freezing of water could a good example about quantum criticality at the level of MB inducing ordinary criticality and leading to generation of complex structures at the level of ordinary matter. Snowflakes and the patterns observed by Emoto as a response to stimuli like emotional voices provide examples of this.
   

Consider now a possible TGD based interpretation.

1. The voltage feeds metabolic energy to the system by making current flow possible. The transition to high conductance state above critical voltage could correspond to minimal metablic energy feed needed to induce a phase transition generating Cooper pairs of dark Ag ions with h_eff> h at magnetic flux tubes so that current would become partially dark and conductance would increase. Also electrons could become dark and form Cooper pairs. The preservation of dark phase requires energy feed but the reduction of dissipation makes this possible.
   
   
2. Ag⁺ have cyclotron frequency of 2.8 Hz in "endogenous" magnetic field B_end= .2 Gauss assigned with living systems identified tentatively as the dark monopole flux carrying part of the Earth's magnetic field with nominal value B_E= .5 Gauss. Are the Cooper pairs of these ions involved? Also electronic Cooper pairs might be involved. Could the Coulomb energy ZeV for Cooper pair in critical voltage correspond to the cyclotron energy of the dark Ag⁺Cooper pair or of electronic Cooper pairs?
   
   
3. EEG is basic aspect of brain function of vertebrates. Could it be that Ag⁺ ions and also
   the possible ionization of the aromatic cycles make possible analog of EEG around 2.8 Hz?
   
   

In this framework the findings discussed in the article could be assigned with system which are very simple life forms. To gain improved understanding a model for the magnetic body of the system would be needed.

See the short article article The emergence of human brain like functions in neuromorphic metallic nanowire network, the longer article Life-like properties observed in a very simple system, or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

A possible paradox related to zero energy ontology

ZEO provides a radically new view about time. If one proposes something radical it is better to invent all possible objections to it. lthough this is a considerable challenge to ego, it is also the best manner to develop the idea. Last night I discovered one really bad sounding objection against ZEO.

Consider first the basic ideas of ZEO (see this).

1. Causal diamond (CD) is essential piece of ZEO. CD is essentially intersection of future and past directed light-cones and defines imbedding space (M⁴× CP₂) correlate for self as conscious entity. CDs form a length scale hierachy. Zero energy states are pairs of states at the two boundaries of CD, the active and passive one.
   
   
2. During the sequence of unitary evolutions followed by "small" state functions (SSFRs) defining self as a conscious entity the passive boundary of CD is un-affected as also the members of state pairs defining zero energy state as their superposition. SSFRs as counterparts of "weak" measurements preserve the arrow of time and the sequence of unitary evolutions followed by SSFR gives rise to the life cycle of self as conscious entity.
   

   Active boundary and members of state pairs at it change during this sequence. In statistical sense the distance between the tips of CD increases and this corresponds to the "clock time" as correlate for the subjective time defined by the sequence of unitary evolutions followed by "small" state function reductions (SSFRs). The permanent part of self, "soul", corresponds to passive boundary and sensory input to active boundary.
   
   

3. The arrow of time changes in ordinary, "big", state function reductions (BSFRs). Self dies in BSFR and reincarnates with reverse arrow of time.
   
   
4. To make ZEO more precise one must specify what happens in BSFR for CD. Is CD replaced with CD which is bigger than it was before CD or whether the the formed passive boundary can shift so that the size of CD is reduced. The first option would mean that self starts where it was and the latter option that the reincarnated self experiences childhood. The option in which CD can increase without limit is couterintuive.
   

   If the size of CD is reduced then it can happen that the maximum size of CD increases very slowly and can remain bounded. Selves would continue the life in the geometric past re-incarnating again and again and becoming more complex and evolved. Kind of endless spiritual growth due to the statistical increase of "IQ" defined by the distribution of of effective Planck constats h_eff=n×h₀ -n is essentially dimension of extension of rationals assignable to particular sub-self.
   
   

ZEO has profound implications.

1. ZEO based view solves the basic paradox of quantum measurement theory and leads to a theory of consciousness (see this).
   
   
2. Thermodynamics must be generalized and one also ends up to a theory of self-organization in which self-assemly aspect of self-organization could be understood as dissipation in non-standard arrow of time (see this and this ). This would due to time reversal at the magnetic body (MB) containing dark matter as h_eff=nh₀ phases servig as master controlling ordinary matter (and lower onion like layers of MB) serving as slaves.
   
   
3. The evolutionary aspect of self-organization is due to the tendency of h_eff to increase: in adelic physics this follows from the unvoidable tendency of the dimension of extension of rationals to increase in BSFRs: the number of extensions with dimension larger than that for given extension is infinitely larger than those with smaller dimension (see this and this) .
   
   

Surprisingly, ZEO finds considerable support. Minev et al discovered that BSFR in atomic systems indeed has unexpected features understandable in ZEO (see this). There is evidence for time anomalies having explanation in terms of time reversal at the level of MB even in astrophysical scales. Earthquakes and volcanic eruptions are one example (see this). Cosmology also provides further evidence (see this).

One can however invent an objection.

1. Suppose that in biological death I indeed re-incarnate with opposite arrow of time and continue to live towards geometric past. Suppose also that I re-incarnate as more advanced human being - at least in statistical sense. Human beings have parents. But how can I have parents in the former geometric future, if my parents how have already died live in the former geometric past?
   
   
2. The only solution of the paradox seems to be that the MB - the boss - does not disappear in the death of biological body (BB). The MBs of my parents continue their existence and in my biological death means their separation in stanard time direction and meeting in the new time direction. They meet, fall in love, and give rise to my birth but all this in opposite time direction.
   

   This would provide an answer to a long-standing question about whether MBs are preserved in biological death or not. My view has been that biological death is more or less that MB loses interest in my BB and directs attention to something more interesting. One could however argue that also MB is generated in birth and genes code also for it so that it would die. If directing attention corresponds to BSFR MB would continue to exist after biological death. This particular reincarnation - CD - would be like vortex in the flow of time.
   
   

3. Can one find any support for this crazy looking proposal? TGD Universe is fractal and lower levels in the length scale hierarchies are slaves. In particular, bio-chemical level serves as the slave of MB expected to obey kind of shadow dynamics. If the proposed topological dynamics of MBs solving the above paradox has a miniature representation at the level of DNA, one could take the proposal with some seriousness.
   

   In meiosis (this) germ cells, whose chromosomes are coctails of paternal and maternal chromoses (PCs and MCs), are formed. In fertilization (this) - in some sense a (time?) reversal of meiosis - pairs of PCs and MCs are formed. The fusion of paternal and maternal germ cells could be indeed seen in topological sense as a time reversal of replication. The replication of soma cells involves mitosis (this) forming pairs of chromosomes of PCs and MCs.
   

   Could the chromosomal dynamics be a miniature version of the proposed dynamics at the level of MB even at the level of organisms? If so, mitosis at the level of MB would correspond to a loose pairing of paternal and maternal MBs - formation of a relationship. Our personal MBs as analogs of germ cells would be coctails of MBs of PCs and MCs formed by reconnection process.
   

   What about replication? In the case of asexual reproduction (this) one could speak about replication at the level of MB of the entire organism. Also cell - and DNA replication would represent examples of asexual reproduction and in meiosis sexual reproduction of also DNA would take place.
   
   

See the article Some comments related to Zero Energy Ontology (ZEO) or the chapter Life and Death and Consciousness.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Are the laws of physics inevitable?

article "Why the laws of physics are inevitable?" published in Quanta Magazine has received a lot of attention and for good reason. The claims of article are so hypeish that it is really surprising that a high standard journal like Quanta Magazine published it.

The key message of the article is that Bootstrap approach or S-matrix theory was fashionable approach to strong interaction at sixties before the emergence of standard model based on quantum field theory approach. QCD became the theory of strong interactions but the fact is that low energy hadron physics is still poorly understood.

After the fall-down of superstring models, the bootstrap approach has made a comeback and relies on the progress made in the understanding of scattering amplitudes of massless theories - in particular N=4 SUSY. These theories are unrealistic since most particles are massive and SUSY in the sense assumed has been excluded at LHC but twistor Grassmann approach and so called amplituhedron have led to the renaissance. Nima Arkani-Hamed is powerfully propagating this ideology. The bootstrap philosophy involves space-time symmetries Poincare invariance extended to conformal invariance in 4-D Minkowski space and in cosmological context restricted to special conformal invariance in de-Sitter space.

The article starts with an argument of Baumann. Particles with spin 1/2,2, 2 are highly unique in QFT context in the sense that higher spins do not allow QFT description. In super-string models the situation changes. What is argued that physics is inevitable. One can of of course ask "What about electroweak and color interactions?".

One can also ask what "inevitable" means. Every mathematical theory relies on axioms and those one cannot prove.
Sabine Hossenfelder talked about this in her blog . A more realistic notion would be inevitability forced by general mathematical conditions such as mathematical existence plus general ontological assumptions forced by empirical facts. For instance, the existence of space-time or of symmetries allowing a well-defined unique theory.

The spirit of bootstrap approach is technical. It is indeed nice to be able to calculate. It would be however much nicer is to start from problems and thought experiments and try to proceed to new principles. Calculations come when the time is ripe for them. General Relativity is wonderful example about this. The rise of superstring models followed by their fall-down should serve as a school example about what can happen when calculations replace thinking.

A. Renewed bootstrap program

The starting point idea is to look at cosmology from the point of view of particle physics where S-matrix is expressible in terms of correlation functions for fields. Now one would look for correlation functions for mass density. Non-vanishing correlation function would mean that the mass densities at different points do not reduce to constant density as in the standard model for cosmology.

Remark: What is somewhat ironic that there is flux of anomalies from cosmology and correlations between dynamics of galaxies are routinely observed in cosmological scales but theoreticians at the top of the academic hierarchy do not notice these findings at all! See for instance this.

There are a many assumptions. One might argue quite too many and not well-founded.

1. Inflation is assumed although there is no real empirical support for it and it has severe conceptual problems. Inflation would guarantee that the correlations in short scales are scaled up to long length scales.
   

   Remark: An alternative TGD based view would be that the long range correlations have much deeper content and related to quantum coherence of dark matter in arbitrarily long length sales.
   
   

2. De-Sitter spaces serves as initial and final state of cosmology. Special conformal symmetries in 4-D sense are realized. This means that translations not symmetries anymore. Four-momentum is lost. Poincare symmetry must be assumed as a mere tangent space symmetry as in GRT. This could be seen as the basic explanation for why GRT cannot be quantized: conserved energy would generate unitary S-matrix but does not exist mathematically. This problem was the starting point of TGD.
   

   Remark: De-Sitter space is not anti-de-Sitter space appearing AdS/CFT correspondence.
   

   One could assume conformal symmetries and M⁴ but now one would have only massless particles but the fact is that also massive particles exist.
   
   

3. Twistor Grassmann approach and amplituhedron are taken as starting point in the program of Nima Arkani-Hamed. The Starting point is applications of twistor Grassmann approach to massless theories in M⁴, in particular N=4 SUSY.
   

   The first problem of standard twistor approach has been already mentioned. Only massless particles are allowed. The generalization of masslessness would be needed.
   

   Remark: It seems that I am thinking negatively and just digging problems. My excuse is that becoming aware of a problem is the only manner to make progress.
   
   

4. The idea is also to get rid of space-time and replace it with amplituhedron. This means however forgetting the basic assumptions. Twistors are a concept relying essentially on 4-D Minkowski space. They allow an alternative field theoretic description of massless fields in M⁴. One cannot say that M⁴ is just a scaffolding, which can be forgotten when the house has been built.
   

   Second deep problem of he twistor Grassmann approach is that classical picture is missing. Amplitudes are not enough. One must perform also measurements and every measurement applies space-time picture: one does not measure just abstract momenta and spins of final states but their space-time correlates such as particle orbits, frequencies and wave vectors. The very existence of 4-momentum and spin require M⁴.
   
   

5. One could weaken the idea about getting rid of space-time. Get rid of time only. This approach is of course in blatant conflict with the very ida of special relativity, which is also the starting point of also twistor approach.
   

   Remark: Philosophically oriented physicist might wonder why one should get rid of time. Even worse, we have actually two times to get rid of: experienced time and geometric time. They are very different: the first one is irreversible, has no future and the moment "Now" is in preferred role. Geometric time is reversible, there is no distinction between past and future, and there is no preferred moment "Now". Why should we continue to identify them? The answer of an orthodox physicalistic theoretician is easy to guess: consciousness is a mere epiphenomenon and one can safely forget it when oen is trying to become conscious of theory of everything.
   

   The article contains very misty argument suggesting how the time might emerge. One considers singularities of n-point function emerging as two or more points fuse. The result of fusion must be an n-1-point function, and this is rather strong constraint on n-point function. What has been found that near the fusion point the n-point function oscillates. Oscillation is a dynamical phenomenon involving time. Heureka: time has emerged! The elementary mistake is that one has a homotopy depending on some parameter analogous to time and one actually thinks that there is some-one performing this homotopy! A little bit of consciousness theory would have helped to avoid the error.
   
   Remark: Holography suggests that S-matrix could allow construction in terms of 3-D n-point functions but also this requires the notion of space-time. In TGD framework this is indeed achieved in zero energy ontology (ZEO) solving the basic problem of quantum measurement theory and leading to a theory of consciousness by lifting the observer from an outsider to part of the system.
   

   As a matter of fact, number theoretic vision about TGD leads to a cognitive representation as a purely number theoretic unique discretization of space-time and n-point functions have as arguments points of cognitive representations as points of 8-D imbedding space. The condition that the limit for co-inciding arguments gives lower n-point function is an important constraint.
   
   

6. Super string theorists might also criticize the approach. 2-D conformal symmetry is an infinite-D symmetry and huge as compared to conformal symmetry of Minkowski space or de-Sitter space. It seems awkward to give up this symmetry also allowing massive particles as excitations of strings. Superstrings did not work but why not consider generalization of the 2-D conformal symmetry to 4-D one in some sense. The super-conformal symmetries find a huge extension to their 4-D analog in TGD framework. This is due to the fact that 3-D light-like surfaces allow extension of 2-D conformal symmetries so that light-like coordinate becomes a parameter of the 2-D conformal symmetry.
   
   

B. TGD could have been discovered for 4 decades ago!

It is interesting to see that TGD could have been discovered already 4 decades ago and by making certain very general either mathematical or physical assumptions TGD is indeed inevitable. To see this consider the theoretical situation around 1978.

1. Standard model and its symmetries had been discovered but not understood.
   
   
2. Spontaneous compactication was invented already in Kaluza-Klein theories but was highly non-unique and much later led to landscape catastrophe and after that to swampland catastrophe. One would give up 4-D space-time except as approximation. This does not look nice.
   
   
3. Super string model had been discovered and their huge 2-D conformal symmetries had been discovered. The possibility that particles are not point-like had been realized. The problem was that string world sheets are not 4-D and the higher-D space-time in which superstrings moved had to be 10-D. How to get 4-D space-time?
   

   Why not replace strings with 3-surfaces in some higher-D imbedding space H? This was the innocent question, which I made around 1978. Space-time would be 4-D surface representing orbit of 3-D particle. One would obtain 4-D space-time and would get rid of spontaneous compactification. But in what space H space-time surfaces would live?
   

   One wants Poincare symmetries so that one must have H= M⁴× S, S some compact space. This would solve the energy problem of GRT: this was actually second starting point of TGD. It is ironic that people still have failed to realize how deep this problem is. Space-time as surface would allow dynamical space-time since Poincare symmetry would be lifted to H.
   

   Gravitational field would be obtained from the induced metric. S has some symmetries and it has spinor connection. Could one geometrize gauge fields in terms of induced spinor connection. Could spinors of H have standard model quantum numbers.
   
   

4. What could be the choice of S? Could it have standard model symmetries and allow to realized standard model gauge fields as induced gauge fields?
   

   Hawking et al had already discovered CP₂. They had not realized that it has standard model symmetries: I had to discover this. Could one have S=CP₂? Theory would be unique.
   
   

5. But what about inevitability - at least in some sense? Is there something special in M⁴ and CP₂? Hitchin had already discovered that S⁴ and CP₂ are the only compact 4-D spaces having twistor space with Kähler structure. M⁴ has also twisor space with Kähler structure. See "Kählerian twistor spaces" of Hitchin. I learned about this article much later when I realized that TGD could allow twistor lift.
   
   
6. Could one find some use for the existence of the Kähler structure in the twistor spaces of M⁴ and CP₂? The existence of twistor space for general space-time surface is actually a problem of GRT. Could one imagine that one replaces space-time surfaces with 6-D surfaces in the 12-D product of twistor spaces of M⁴ and CP₂ as 12-D imbedding space?
   

   These 6-surfaces should have induced twistor structure as S² bundle over space-time surface. This would require dimensional reduction. The action would be 6-D Kähler action by conformal invariance and exist only for M⁴× CP₂! This action reduces to a sum of 4-D Kähler action and volume term in dimensional reduction required by twistor bundle property of 6-surfaces and volume term has interpretation as dynamically generated cosmological constant.
   

   The theory would would be unique just by its mathematical existence!
   
   

7. This would also solve the basic problem of the 4-D twistor approach: 8-D analog of masslessness allows 4-D massiveness.
   
   

To summarize, the twistor lift of TGD could have been born for four decades ago! Not only generalization of twistor approach at the level of amplitudes would have emerged but also the geometrization of twistor description of massless fields to a description of 6-D surfaces in 12-D twistor space. Theoretical physics develops slowly and the reasons often have very little to do with the lack of good ideas.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

TGD inspired model for magneto-reception and circadian rhythm

For few years ago I was contacted by a friend with whom we have had several interesting discussions about consciousness and neuroscience. She sent several links related to certain aspects of quantum biology about which I had not been aware and these links inspired this article.

Background

One of the proposals of quantum biology is a quantum mechanism for the mysterious looking ability of birds and fishes to find back to the place, where they were born. It is believed that navigation involves detection of the inclination of the local magnetic field of Earth but not its direction as in the ordinary ordinary compass. The alternative option states that birds have an analog of compass in their brain. The challenge is to understand what is the mechanism making possible to get the information about magnetic field and how this information is transformed to a chemical signal and eventually to a pattern of nerve pulses. In TGD framework one can challenge the assumption that the magnetic field of Earth is what makes possible the navigation and even what the navigation means.

Quantum biologists try to solve the problem using standard quantum physics. The formidable looking problem is that the energy scale for magnetic energies is extremely small. In the magnetic field of Earth the magnetic interaction cyclotron energy for electron is by factor of order one million below the thermal energy. If one believes of quantum physics in its standard form, one should understand how it is possible to generate a signal making possible non-trivial chemical effects. The proposal that has gained widest acceptance is known has as radical-pair mechanism (RPM) and has raised hopes about circumvent this problem.

The answer to the question whether RPM works is very important from the point of view of TGD based explanation for macroscopic quantum effects in living matter since TGD based model involves new quantum physics via the hypothesis that dark matter corresponds to h_eff=n× h₀ phases located at flux tubes of "magnetic body" (MB). If RPM fails, TGD based quantum biology would be the next natural trial (if science proceeded by trying first all options that fail).

I have already earlier proposed a TGD based model for various difficult-to-understand findings related to magneto-reception and pace-maker of circadian rhythym. The model discussed also photo-taxis and gravi-taxis. The improved model discussed here relies on essentially the same elements but does not assume RPM as the mechanism producing nuclear spin polarization as an analog of compass.

Improved TGD inpired model

Magnetic flux tubes are key objects of TGD based quantum biology able to act as sending and receiving antennas and if they contain cyclotron Bose-Einstein condensates they can act also as quantum compasses communicating the orientation of the external magnetic field by emission of Larmor radiation at cyclotron frequencies f_c. This radiation is received by other flux tubes at resonance and the modulation of f_c produces resonances as ticks of the clock. The energies involved must be above thermal energy and h_eff=h_gr hypothesis guarantees this.

Pace-maker function requires cell membrane as a generalized Josephson junction (GJJ) emitting generalized Josephson radiation with energy E_G,J, which is sum of Josephson energy E_J=ZeV and difference Δ E_c(hbar_gr) of cyclotron energies at the two sides of membrane. The TGD view about metabolic energy as manner to increase h_eff=h_gr allows to interpret irradiation by blue light as metabolic energy feed, and explains the slowing down of the circadian period as a reduction of ordinary Josephson frequency f_J= ZeV/hbar_gr. Also the loss of rhythm can be understood as a transition in which the analog of generalized Josephson junction as a gravitational pendulum makes a transition from rotational to vibrational motion. Photo-receptors such as cytochrome appear as absorbers of dark photons transformed to bio-photons and transform dark photon information to chemical information.

See the article TGD inspired model for magneto-reception and circadian rhythm or the chapter Can quantum biology really do without new physics? .

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Immortal jellyfish in zero energy ontology

Immortal jellyfish - an animal smaller than fingernail living in Mediterranian Sea - is almost immortal being able to lengthen its life cyle by reversing its aging by reverting to immature stage - polyp (see this). This represents a highly interesting time anomaly from TGD point of view.

In zero energy ontology (ZEO) based theory of consciousness the basic entity is self having causal diamond (CD) has imbedding space correlate. Zero energy states are superpositions of classical time evolutions identifiable as preferred extremals of the action principle and analogous to Bohr orbits. Quantum jumps/state function reductions (SFRs) replace zero energy state with a new one.

There are two kinds of state function reductions. Self corresponds to a sequence unitary time evolutions followed by "small" state function reductions (SSFRs) as TGD counterparts of weak measurements. Self dies in "big" state function reduction (BSFR) and re-incarnates with an opposite arrow of time. During the sequence of unitary time evolutions followed by SSFRs defining self the passive boundary of CD and the members of state pairs at it are not changed whereas the active boundary recedes from passive boundary in statistical sense and also the members of state pairs at it are affected. BSFR creates a new variant about the unchanging part of self diving kind of soul. Kind of Karma's cycle would be in question.

At this moment the most plausible view about zero energy ontology (ZEO) is that the sizes of CDs serving as correlates for selves stay below fixed upper bound during the sequences of life cycles in opposite time directions. The size scale would be reduced in BSFR and then increase as the active boundary to which sensory input is assignable recedes farther away from the fixed passive boundary. The reduction of the size implies that all reincarnations of self experience "childhood". This option allows to avoid the growth of self to entire sub-cosmology.

The dramatic prediction is that selves and corresponding CDs has more or less fixed position in imbedding space H= M^4xCP_2. Our past would be living and consciousness. In particular, our memories live and also evolve in geometric past and to remember is to communicate with these entities. M^8-H duality gives support for this picture and allows to understand the failure of precise determinism of the classical theory.

The notion of self makes sense for systems with arbitrarily large size scales and one can solve several cosmological time anomalies by assuming that even astrophysical objects correspond to selves, which repeatedly reincarnate with opposite time direction and evolve as number theoretical vision about TGD predicts.

In the case of jellyfish this picture suggests that sub-..-sub-selves of jellyfish at some level of the hierarchy - perhaps the cells of jellyfish -, have very short life-cycle and remain therefore in the immature state. To live in an eternal childhood is to die often enough!

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Three condensed matter surprises

I learned about 3 surprising findings related to condensed matter physics and defying standard quantum theory and having a natural explanation in TGD framework.

The strange behavior of light

Light does not behave quite in the manner expected (see this). What was studied was splitting of photons to entangled pairs of photons in the crystal beam entering a crystal. Quantum field theory based on the idea of completely point-like particle predicts that photon pairs should be created at single point. What was observed that members of entangled photon pairs can be also created at separate points. The distances of these points can be about 1/100 microns- which happens to the size scale of cell membrane and fundamental scale in living matter. This length scale is about 100 times the atomic length scale.

Researchers argue that this findings supports new kind of Uncertainty Principle. I am not quite easy with this proposal unless it is taken to mean that particle has geometric size.

1. In TGD Universe geometric size would be due to the fact that particles are not point-like but correspond to 3-D surfaces whose "orbits" define basic building bricks of space-time as 4-D surface in 8-D space-time H= M⁴ × CP₂. Particles can exiss superpositions of their variants with different size scales.
   
   
2. p-Adic physics for various primes p fusing together with real number based physics to what I call adelic physics would provide physical correlates of cognition and sensory experience. The number theoretic vision assigns to each particle extension of rationals characterized by so called ramified primes, which are excellent candidates for defining preferred p-adic length scales. The dimension n of extension defining a measure for algebraic complexity and serving as a kind of universal IQ has interpretation as effective Planck constant h_eff/h₀=n so that a connection with quantum physics - or rather its TGD based generalization - emerges.
   
   
3. p-adic mass calculations rely on p-adic length scale hypothesis stating that primes near powers of 2 are especially interesting physically and massive elementary particles and also hadrons correspond to this kind of primes. p-Adic mass scale would be proportional to p^1/2.
   
   

A lot of new physics is predicted.

1. TGD predicts caled variants of strong and weak interaction physics corresponding to different values of p and LHC provides handful of bumps having identification as scaled variants of ordinary hadrons and having mass which is 512 higher.
   
   
2. For given particle several mass scales are in principle allowed. Quite generally, particle can correspond to several p-adic primes and therefore can exist in states with different masses differing by power of 2^1/2. The existence of this kind of states in the case of neutrinos would solve some problems related to neutrinos and their masses.
   
   
3. In the case of massless particles different p-adic mass scales do not mean that masses are different (or more precisely, the masses depend on p but are extremely small and below measurement resolution so that mass differences cannot be detected). The p-adic length scale defines the geometric size of the particle as 3-surface to be distinguished from quantum size defined by Compton length. Quantum classical correspondence (QCC) strongly suggests that these two scales are same or at least closely correlated.
   
   

The hierarchy of Planck constants h_eff= n× h₀ having an interpretation in terms of dark variants of ordinary particles predicts second kind of scale hierarchy.

1. The mass of the dark variant of elementary particle would not differ from the mass of ordinary particle but Compton size for a dark particle is proportional to n - a good guess is that n=6 would correspond to ordinary particle and ordinary value h of h_eff.
   
   
2. The scales defined by dark matter hierarchy could relate to p-adic length scales. There could be kind of resonance coupling for massless particles: dark massless particle labelled by n and particle labelled by p-adic prime p could transform to each other with high rate if the p-adic and dark length scales are nearly the same. This could be very relevant for biology.
   
   

The experimental findings could be understood if photons can correspond to several p-adic length scales. The length scale 10 nm defining the upper bound for distance between members of entangled photon pair in experiments would correspond to p-adic length scale L(151), which corresponds to Gaussian Mersenne prime p= (1+i)¹⁵¹-1. A simple model for photon could be as a closed flux tube like structure of this length. Also k=157, 163, and 167 define Gaussian Mersenne primes, which is a number theoretical miracle. What is fascinating that these scales are fundamental biological length scales assignable to the basic structures of DNA.

New surprises related to super-conductors

So called Anderson's theorem applying to the conventional super-conductors (BCS) states that the addition of non-magnetic impurities does not destroy super-conductivity. It has been however found (see this) that this is not the case for iron based high Tc super-conductors. This gives a valuable hints in still-continuing to attempts to understand high Tc super-conductivity.

I have been preaching for fifteen years new kind of super-conductivity explaining high Tc superconductivity making living systems high Tc superconductors (see for instance, this and this).

1. The TGD view about magnetic fields differs from Maxwellian view. The counterparts of Maxwellian magnetic fields are flux quanta, flux tubes or sheets realized as space-time surfaces (or regions of them). Besides counterparts of ordinary magnetic fields there are also monopole flux tubes and they appear in all scales and form the basis of entire TGD view of Universe. They carry dark matter as h_eff= n× h₀ phases and for large value of h_eff> h there is quantum coherence in long scales making possible super-conductivity along dark magnetic flux tubes. This could explain also high Tc superconductivity in iron based super-conductors.
   
   
2. What was found that the addition of Cobalt atoms destroys the super-conductivity by inducing quantum phase transition. Anderson's theorem for ordinary super-conductivity however states that non-magnetic perturbations do not affect superconductivity. In TGD framework the natural interpretation would be that the quantum phase transition reduces the value of h_eff/ h₀=n and thus also the quantum coherence length meaning that flux tube length is reduces and super-conductivity is possible only in short scales. Note that dark matter is identified as phases with non-standard value of h_eff different from h.
   
   
3. Also the nature of so called energy gap assignable to super-conductors was modified as Cobalt atoms were gradually addedto destroy super-conductivity. This is not surprising if the value of h_eff was reduced. The reduction of h_eff in general decreases energies for other parameters kept constant and now it would mean reduction of energy gap and loss of superconductivity.
   
   

Conductors of electricity, which are poor conductors of heat

The so called Wiedemann-Franz Law states that good conductors of electricity are also good conductors of heat. The two conductivities are proportional to each other. The metal found 2017 however volates this law (see this) Vanadium dioxide VO₂ transforms from insulator to a conductive metal at 67 degrees Celsius. The experimenters argue that this property could make possible new technologies. For instance, conversion of wasted heat from engines could be transformed to electricity.

Electrons are found to move in coordinated, synchronous manner and this would explain the reduction of heat conductivity to 1/10 of the expected value. There is no super-conductivity however. TGD explanation would be in terms of coherence and synchrony induced from the quantum coherence of dark phases of matter having h_eff/ h₀=n residing at the magnetic body of the system controlling it.

This forced coherence would be also crucial in living matter: ordinary living matter would not be quantum coherent but the magnetic body carrying dark matter would force the coherence. In fact, all self-organization processes could involve magnetic body and dark matter.

See the article Three condensed matter surprises or the chapter Quantum criticality and dark matter .

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Time reversal of blackhole like object observed?

A very strange object behaving like time reversal of blackhole - or a candidate rather blackhole like object (BHE) has been observed (see this). The blackhole in question is super-massive and in the middle of galaxy cluster.

Usually blackhole "eats" the surrounding matter and also prevent the formation of stars since they are powerful emitters of gamma rays - this is not in accordance with the naive view about blackholes. The weird blackhole does not emit gamma rays and the environment around it cools and this makes possible star formation. Instead of eating the surrounding matter it should feed matter to surroundings making possible the star formation.

The most obvious TGD identification of the mystery object relies on zero energy ontology allowing both arrow of time. The arrow of time chances in ordinary state function reduction - the "big" one as opposed to "small" one corresponding to weak measurement. This predicts time reversed blackhole like objects (BHEs) analogous to white holes: white hole like objects (WHEs).

WHEs could appear in the very early states of the galactic evolution. They could feed the magnetic energy of monopole flux tubes to environment transformed to ordinary matter in turn forming galaxies. As a matter of fact, monopole flux tubes portions emanating it much lines of magnetic field would be formed and their local thickening and formation of tangles would give rise to stars.

If the time reversal idea is taken very seriously WHEs should suck gamma rays from environment inducing cooling making the star formation easier. This would be dissipation in non-standard direction of time identifiable as the basic metabolic mechanism associated with all kinds of self-organization process: quantum coherence at the level of magnetic body would be essential and induce long range coherence of ordinary matter as forced coherence.

WHE could be also created in BSFR for a BHE.

See the article Cosmic string model for the formation of galaxies and stars or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Did cosmology have Dark Ages at all?

A potential time anomaly of the recent cosmology relates to the "Dark Ages" of the Universe. Between the decoupling of CMB radiation from matter and the formation of stars there should have been a "Dark Ages" during which there was only neutral hydrogen. Star formation generated radiation at energies high enough to ionize hydrogen and the ionized interstellar gas started to produce radiation.

The 21 cm line of neutral hydrogen serves as a signature of neutral hydrogen. This line is redshifted and from the lower bound for the redshift one can deduce the time when "Dark Ages" ended. The popular article tells (see this) that the recent study using Murchison Widefield Array (MWA) radio telescope by Jonathan Pober and collaborators gave an unexpected result. Only a new lower upper bound for this redshift emerged: the upper bound corresponds to about 2 meters (see this). The conclusion of the experiments is optimistic: soon the upper bound for the redshift should be brought to light.

In TGD based view about cosmology and astrophysics (this) one one can formulate two questions.

1. One can ask whether there were any "Dark Ages" at all!
   
   
2. An alternative question is wheter the "Dark Ages" at distant past are prevailing anymore! This would be like asking whether the Hitler of thirties is the Hitler we know anymore. The point is that in TGD framework one must distinguish between subjective time and geometric time and this leads to some rather dramatic modifications of the prevailing view about time. The following arguments encourage a positive answer to the first question and negative answer to the second question.
   
   

The following arguments encourage positive answer to the first question and negative answer to the second question.

The answer to the first question relies of TGD based view about nuclear physics solving anomalies of standard nuclear physics and leading to a new view about stellar evolution.

1. In TGD framework the formation of stars could have preceded by a pre-stellar period during which dark fusion giving rise to dark proton sequences - dark nuclei - at monopole flux tubes happened: this is Pollack effect in biology. This would have been "cold fusion" period in the stellar evolution and would have occurred spontaneously at low temperatures. It would have already produced abundances, which are not far from modern ones and one of the recent surprises is that the abundances at very early period are already near to modern ones.
   
   
2. The model predicts also the possibility of neutral states for which electrons are at flux tubes parallel to dark proton flux tubes and have the same scaled up size (due to non-standard value of h_eff=nh₀, which is smaller by factor about 1/2000) as dark protons. In solar interior dark protons would have Compton size of electron so that h_eff for them would be about 2000 times higher H=M⁴× CP₂ than h. Also smaller and larger value of h_eff are possible. For blackholes the protons at flux tubes would be ordinary: h_eff=h.
   
   
3. The transformation of dark nuclei having much smaller binding energy would have liberated nuclear binding energy and the resulting photons having energy up to gamma ray energies would have ionized the neutral hydrogen.
   
   

Zero energy ontology (ZEO) leads to a negative answer to the question whether Dark Ages still prevail in distant past.

1. In ZEO Universe consists at the level of imbedding space H=M⁴ × CP₂ of a fractal hierarchy of CD= cd× CP₂, where cd is causal diamond of M⁴. CDs have interpretation as a hierarchy of sub-cosmologies. Each CD defines a correlate for a conscious entity and increases in size in each "small" state function reduction (SSFR) defining a counterpart of weak measurement. The flow of experienced time corresponds to the increase of distance between tips of CD. Second boundary of CD is however fixed - passive - as also members of state pairs at it defining zero energy states. The active boundary recedes farther away from the passive one. This gives rise to the arrow of time for given life of CD.
   
   
2. In a "big" (ordinary) state function reduction (BSFR) the roles of boundaries of CD change. Active becomes passive and vice versa. The arrow of time changes. Self dies and reincarnates with opposite arrow of time. The simplest possibility is that the size of CD can decrease in BSFR meaning that the formerly passive boundary becomes much nearer to active. In this case CD begins to grow from a small size: self has "childhood". In this case it can happen that self never reaches a size larger than some upper bound and lives again and its life. Each life is more evolved since the extension of rationals involved with space-time surface increases in statistical sense in BSFR. This is nothing but Karma's cycle but in all scales.
   
   
3. At the level of stars this would mean that star could undergo evolution as Karma's cycle also in cosmological remote past as an object located at fixed point of H. The abundances would be more or less the same as for modern stars. This would explain the mystery of stars older than the Universe and solve also other time anomalies of the standard cosmology. This explanation is consistent with the first one and actually the first one is needed to explain abundances of nuclei heavier than Fe and the light nuclei Li, B, Be much higher than predicted by standard model.
   
   

See the article Cosmic string model for the formation of galaxies and stars or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Snow flakes and macrocopic quantum criticality

Thanks for Nikolina Benedikovic for a link representing images of snowflakes. This led to a very interesting discussion generating new details to the view about self-organization in TGD Universe. Also phase transitions liberating heat as a new manner to generate dark matter in TGD sense in phase transition liberating heat energy suggests themselves and could provide a manner to generate artificial life in quantum sense.

The link told about snowflakes having incredibly precise symmetry. Their formation is still poorly understood and their precise symmetries remain a mystery. One would expect something like this in atomic length scales, where one has quantum coherence but certainly not in macroscopic scales. This inspires heretic questions. Could it be that the snowflakes reflect quantum coherence in their own size scale? Snowflakes are not macroscopically quantum coherent. What could be the quantum coherent system involved?

I can reveal my cards. This was mere rhetoric. I have made these questions 15 years ago but in different context. The outcome of these questions is TGD view about living matter and matter in general based now of adelic physics providing number theoretic vision about TGD (see for instance this and this) .

Magnetic body containing dark matter as h_eff=nh₀ phases (h/h₀=6 is a good guess) and inducing self-organization of ordinary matter with quantum coherence of dark matter inducing the ordinary long range coherence of ordinary matter. The relevance for quantum biology would be that the highly problematic quantum coherence of ordinary bio-matter would not be needed.

Could this explain snowflakes as impossibly perfect designs as self-organization patters forced in ordinary matter by quantum coherent magnetic body of water? I remember that some-one has said that snowflakes are like zoom-ups of atomic systems reflecting basic molecular symmetries. They could be indeed analogous to zoom-ups of atomic systems with zooming factor given by n. Quite concretely, the lengths of hydrogen bonds would be scaled up by n.

Concerning concrete model for snowflakes there is clear hint. The self-organization would increase the values of h_eff and this requires energy feed. Where does it come from?

Freezing of water liberates energy: this could serve as source of metabolic energy. More generally phase transitions liberating heat energy could generate h_eff> h phases and generate highly ordered structures. Here might a possible method to create dark matter in TGD sense.

Findings of Emoto

An interesting application is to the findings of Masaru Emoto (see this) that emotional expressions of humans seem to affect water at criticality for freezing. Angry voices are claimed to create ugly patterns and friendly voices beautiful ones. The metabolic energy needed to induce phase transition transforming ordinary matter to dark matter as exotic phase of water would come from the latent heat liberated in freezing. By macroscopic quantum coherence of MB the resulting dark parts of water's MB would be sensitive to human emotional expressions.

Could living systems utilize quantum critical phase transition liberating energy?

Wes Johnson commented about the ability of living systems to use heat as metabolic energy. Could phase transitions liberating heat produce this energy and lead to a generation of large h_eff phases?

1. In TGD Universe the efficiency of living matter to use heat as metabolic energy would a characteristic of not only life but all self-organizing systems. The distinction between living and in-animate would be only quantitative. The evolutionary aspect of self-organization would be generation of coherence in longer scales and would be induced by generation of large h_eff phases at magnetic body becoming thus quantum coherent in long scales. Energy feed would generate these phases and at criticality for a phase transition liberating heat energy (enthalpy) this is easy.
   
   
2. Living systems are conscious in a narrow temperature range. Perhaps this relates to the criticality for phase transition liberating energy in turn generating especially important h_eff phases. Water has special anomalies around the physiological temperature and looks like a two-phase system (at least). This kind of a phase transition of water could be fundamental for living matter.
   

   This could have a direct connection with the Pollack effect (see this) creating charge separation: in TGD part of protons would become dark protons at magnetic flux tubes - dark nuclei providing a fundamental representation for genetic code.
   
   

3. Carbohydrates are carriers of metabolic energy. Could this mean that they have molecular bonds (valence bonds) with non-standard value of Planck constant h_eff and that their energy is liberated when these bonds disappear in the splitting of these bonds or even in the reduction of h_eff, which would be basic element of bio-catalysis. I have indeed proposed a model for valence bonds in terms of dark flux tubes with h_eff> h (see this). The values of n involved would be relatively small and would correspond to the many-sheetedness for the space-time surface as covering of M⁴ ×CP₂ coordinates would be n-valued. n would increase towards right end of the rows of the periodic end and this would explain the different roles of the molecules at opposite ends of the rows in biology.
   
   
   

Two aspects of self-organization

Note that these phase transitions producing phases with a non-standard value of h_eff represent evolution as a statistical increase of the dimension of extension of rationals and relying on "big" (ordinary) state function reductions (BSFRs). This active, evolutionary aspect could be seen as quantal aspect of self-organization.

There is also classical, passive, aspect assignable to the evolution of subsystem by "small" state function reductions (SSFRs) serving as counterparts of weak measurements. In TGD inspired theory of consciousness, motory-sensory duality corresponds to these two aspects. Motor actions correspond to BSFRs and sensory experience to SSFRs.

1. ZEO predicts that time reversal occurs in ordinary state function reductions (BSFRs) and that these reductions occur in all scales and look like ordinary classical evolutions leading to the final state smoothly and deterministically: this was discovered by Minev et all in atomic systems (see this). This would remove the conflict between classicality and no-determinism at the level of conscious experience. Quantum systems would do their best to look like classical.
   
   
2. Self-organization as generation of structures at space-time level (passive aspect) can be understood in terms of zero energy ontology (ZEO) alone (see this). Self-organization (its sensory aspect) and metabolism (use of energy) could be seen as a dissipation in opposite direction of time: no separate models or mechanisms would be needed. Gradients would increase, structure would be generated. Basic biological processes at bio-molecular level would be controlled by magnetic bodies in time reversed states. The only challenge is to understand how living matter generates the sources of metabolic energy - how living system stores energy.
   
   

See the article Some comments related to Zero Energy Ontology (ZEO)).

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Evidence for the anisotropy of the acceleration of cosmic expansion

Evidence for the anisotropy of the acceleration of cosmic expansion has been reported (see this). Thanks to Wes Johnson for the link. Anisotropy of cosmic acceleration would fit with the hierarchy of scaled dependent cosmological constants predicting a fractal hierarchy of cosmologies within cosmologies down to particle physics length scales and even below.

The phase transitions reducing the value of Λ for given causal diamond would induce accelerated inflation like period as the magnetic energy of flux tubes decays to ordinary particles. This would give a fractal hierachy of accelerations in various scales.

See the article Cosmic string model for the formation of galaxies and stars or the chapter of "Physics in many-sheeted space-time" with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Darvinian or neutral theory evolution or something else?

The stimulus to the posting came from an article telling that the neutral theory of evolution has been challenged by evidence for DNA selection (see this). I must admit that I had no idea what neutral theory of evolution means. I had thought that Darwinian view based on random mutations and selection of the most adaptive ones is the dominating view. The debate has been about whether Darwinian or neutral theory of evolution is correct or is some new vision needed.

Darwinian and neutral theories of evolution

1. Adaptive evolution is the Darwinian view. Random mutations are generated and organisms with the most adaptive genome survive. One can of course argue that also recombination occurring during mitosis creating germ cells creates new genetic combinations and must be important for the evolution. Selection can be either negative (purifying) and eliminate the non-adaptive ones or positive favoring the reproduction of the adaptive ones.
   

   One can argue that notions like "fight for survival" and selection do not fit with the idea about organisms as basically inanimate matter having no goals. Also second law poses problems: no evolution should take place, just the opposite.
   Metabolic energy induces self-organization but by second law all gradients about which metabolic energy feed is an example, disappear.
   
   

2. Neutral evolution theory was proposed by Morita 50 years ago and gained a lot of support because of its simplicity. Point mutations for the codons of DNA would create alleles. Already in Darwinian evolution one knows that large fraction of mutations are neutral having not positive or negative effect of survival. Morita claims that all mutations are of this kind. There would be no "fight for survival" or selection.
   

   The so called genetic drift, which is completely random process is possible in small populations and can lead to counterpart of selection: it can happen that only single allele remains and is counterpart for the winner in selection. This is purely random and combinatorial effect and in physics one would not call it drift.
   

   The first objection is that if one has several isolated small populations, the outcomes are completely random so that in this sense there is no genetic drift. Furthermore, there is no reason why further mutations would not bring the disappeared alleles back. Second objection is that there would not be no genuine evolution - how one can speak about theory of evolution?
   

   Now the feed of experimental and empirical data is huge as compared to what it was 5 decades ago and it is now known that the neutral theory fails: for instance, varying patterns of evolution among species with different population sizes cannot be understood. It is also clear that selection and adaptions really occur so that Darwin was right.
   
   

3. The shortcomings of the neutral theory led Ohta to propose nearly neutral theory of evolution. Mutations can be slightly deleterious. For large populations this leads to a purging of slightly deleterious mutations. For small populations deleterious mutations are effectively neutral and lead to the genetic drift.
   

   There is however a further problem: why the rate of evolution varies as observed between different lineages of organisms.
   
   

4. One reason for fashionability was that the model was very simple and allowed to compute and predict. Only the size of the population and rate for the mutations is enough to predict the future in small populations. The predictions have been poor but this has not bothered the proponents of the neutral evolution theory.
   

   As an outsider I see this as a typical example of a fashionable idea: these have plagued theoretical particle physics for four decades now and led to a practically complete stagnation of the field via hegemony formation. Simple arguments show that the idea cannot be correct but have no effect.
   
   

Article explains several related notions.

1. It has been possible to determine the mutation rates at the level of individual sites of genome since 2005. Only subset of mutations of say cancer cells are functionally important to cancer and they can be identified. This leads to a selection intensity as basic notion. This notion is expected to be very valuable for the attempts to find targeted cure of cancer.
   
   
2. Neutral theory of evolution assumes that only point mutations matter. Theory was therefore completely local at the level of genome - and certainly simple! Innocent outsider knowing a little bit about biology wonders why the recombination of maternal and paternal chromosomes in meiosis creating the chromosomes associated with germ cells are not regarded as important. This mechanism is non-local at the level of genome and would naturally lead to a selection at the level of individuals of the species. It has been indeed learned that the genetic variation and the rate of recombination in meiosis correlate in given region of genome. This sounds almost obvious to the innocent novice but had to be discovered experimentally.
   

   One can however still try to keep the neutral theory of evolution by assuming that recombination is completely random process and there is no selection and adaption - contrary to the experimental facts and the basic idea behind the notion of evolution. Recombination would bring only an additional complication.
   

   Besides the direct purifying selection and neutral drift there would be recombination creating differences in the levels of variation across the genomic landscape. This leads to the notion of genetic hitchiking. When beneficial alleles are closely linked to neighboring neutral mutations, selection acts as a unit on them. One speaks about linked selection. Frequencies of neutral alleles are determined by more than genetic drift but one can speak of neutrality still. Linkage of hitchiker to allele - beneficial or not - is however random. Does genuine evolution takes place at all?
   
   

3. Most of the DNA is not expressed as proteins. It would not be surprising if this part of DNA could have important indirect role in gene expression or perhaps be expressed in some other manner - say electromagnetically. How important role this part of DNA has in evolution? There are also transposons inducing non-point like mutations of this part of DNA: what is their role. There also proposals that viruses, usually though to be a mere nuisance, could play decisive role in evolution by modifying the DNA of host cells.
   
   
4. It is now known that up to 80-85 per cent of human genome is probably affected by background selection. Moreover, height, skin color blood pressure are polygenic properties in the sense that hundreds or thousands of genes are acting in concert to determine these properties. This strongly suggests that point-like mutations cannot be responsible for evolution and not even recombinations are enough if random. A control of evolution in longer scales seems to be required. This of course relates to the basic problem of molecular biology: what gives rise to the coherence of living matter. Mere bio-chemistry cannot explain this. Something else perhaps controlling the bio-chemistry is needed.
   
   

TGD based view about evolution

One can start by criticizing the standard view.

1. Is the standard view (to the existent that such exists) about evolution consistent with second law? One can even ask whether standard view about thermodynamics assuming a fixed arrow of time is correct.
   
   
2. If mutations and more general changes of genome occur by pure change, can they really lead to a genuine evolution. The notions of selection and survival of fittest are notion, which do not conform with the view about evolution as mere standard physics. A probable motivation for neutral evolution theory has been the attempt to get rid of these notions: physicalism taken to extreme.
   
   
3. The reduction of life to bio-chemistry does not allow to understand the coherence of organisms.
   
   
4. One can also criticizing the reduction of life to mere genetics.
   
   
   1. Genetic dogma does not tell much about morphogenesis.
      
   2. Is genetic determinism a realistic assumption? Clones of bacterium are know know to have personalities behaving differently under given conditions (see this).
      
   3. Most of the genome of the higher organisms consists of DNA not transcribed to RNA still interpreted as junk by some biologists. What about introns? Could there exists other forms of gene expression - say electromagnetic.
      
      

TGD based view about evolution can be seen as a response to these criticisms but actually developed from a proposal for a unification for fundamental interactions and from the generalization of quantum measurement theory leading to a theory of consciousness and generalization of quantum theory itself.

1. TGD leads to a new view about space-time and classical fields. In particular, many-sheeted space-time and magnetic body bring in new element changing dramatically the views about biology.
   

   The notion of Maxwellian fields is modified. Unlike in Maxwellian theory any system has field identity, field body, in particular magnetic body (MB) carrying dark matter n TGD sense and in well-define sense at higher evolutionary level as compared to ordinary bio-matter. This expands the standard pairing organism-environment to a triple MB-organism-environment.
   

   MB can be seen as the controlling intentional agent and its evolution would induce also the evolution of the ordinary bio-matter. MB carries dark matter as h_eff/h₀=n phases giving rise to macroscopic quantum coherence at level of MB. MB forces the ordinary bio-matter to behave coherently (not quantum coherently).
   

   TGD leads also to a realization of genetic code at the level of dark analog of DNA represented as dark proton sequences (see this) - dark nuclei, which are now essential element of TGD based view about nuclear physics (see this). Dark photons are essential for the communications between MB and ordinary bio-matter. Also dark photons would realize genetic code with codon represented as 3-chord consisting of 3 dark photons.
   

   Genetic modification would take place at the level of magnetic flux tubes containing dark analog of DNA and induce changes of the ordinary genome, which would do its best to mimic dark genome. In particular, the recombination occurring during the meiosis would be induced by the reconnection of the flux tubes of dark genome.
   
   

2. Number theoretical vision about evolution deriving from the proposal that p-adic physics for various primes combining to what I call adelic physics is second needed element (see this). Any system can be characterized by a extension of rationals defining its algebraic complexity. The dimension of extension identifiable in terms of the effective Planck constant h_eff/h₀=n defines evolutionary level as a kind of IQ. What is remarkable that n increases in statistical sense since the number extensions with n larger than that for given extension is infinitely larger than that of lower-dimensional extensions. Intelligent ones have larger scale of quantum coherence and thus coherence of bio-matter and survive. Evolution is directed process forced by number theory alone.
   

   Quantum jumps in the sense of ZEO tending to increase n occurring naturally in mitosis generating germ cells lead also to a more intelligent genomes. Point mutations could be seen something occurring at the level of ordinary matter rather than being induced by dark matter.
   
   

3. Zero energy ontology (ZEO) is behind the generalization of quantum measurement theory solving the basic problem of standard quantum measurement theory. There are two kinds of state function reductions: "small" state function reductions (SSFRs) as analogs of weak measurements and giving rise to the the life cycle of conscious entity self having so called causal diamond (CD) as a correlate. Under SSFRs the passive boundary of CD is unaffected as also members of state pairs at it: this gives rise to the "soul" of unchanging part of self. "Big" state function reductions (BSFRs) correspond to ordinary state function reductions. They change the arrow of time and one can say that self dies and re-incarnates with a reversed arrow of time. This applies in all scales since consciousness and cognition predicted to be universal. In BSFRs the value of h_eff increases in statistical sense and this gives rise to evolution also at the level of genome. The reversal of the arrow of time allows to see self-organization and metabolism as dissipation in non-standard time direction so that generalization of thermodynamics to allow both arrows of time allows to understand both self-organization and evolution.
   
   

Evolution at DNA level

A possible application would be TGD based model for meiosis and fertilization. The starting point is that recombinations occurring in meiosis represent a fundamental step in evolution preserving the species and point mutations are mostly noise having also negative effects. There are also modification which produce a new species. Consider first recombinations.

1. In meiosis BSFR for the dark proton sequences defining dark DNA could induce reconnections of parallel maternal and paternal dark proton flux tubes inducing recombination at the level of the ordinary genome.
   
   
2. The resulting germ chromosomes - or rather their dark variants realized in terms of dark proton sequences would have arrow of time opposite that of chromosomes. They would be in a dormant state analogous to sleep.
   
   
3. Fertilization involves the pairing of paternal and maternal germ chromosomes and looks almost like time reversal of meiosis. In the proposed picture it would indeed change the arrow of time for the germ chromosomes - wake up them. The sequence meiosis replication-meiosisI-division - meiosisII would correspond to 4 BSFRs leading to germ cells having dark genome as as time reversal of ordinary genome.
   

   Remark: One can ask whether also the passive strand of ordinary DNA has arrow of time opposite to that of the active strand.
   
   

Recombinations do not change the genome dramatically and can be said to be species preserving. Big leaps in evolution change genome more drastically - say by adding new genes - to yield what might be regarded as a new species. They represent a challenge also for the TGD based view.

The big changes should occur at the level of the magnetic body inducing in turn modifications at the level of ordinary genome. The addition of a portion of DNA double strand of same length to the end of DNA double strand could be a species changing modification. This would not change the earlier genome and could add a new gene for instance. How this change could occur?

1. In TGD dark genome acts as master controlling the ordinary genome playing the role of slave. Dark genes correspond to dark proton sequences with possibly subset of protons behaving like neutrons due to the presence of negatively charged bonds between two neighboring protons of the sequence. Large modification would add to this sequence new dark protons: dark counterpart of nuclear fusion would take place.
   

   In water Pollack effect would correspond to this process this process and would give rise to charge separation creating negatively charged regions called exclusion zones (EZs) by Pollack. There is no reason why this process could not occur also inside cells containing pairs maternal and paternal chromosomes.
   
   

2. At the level of dark magnetic body the modification of dark double strand could be realized if it corresponds to a closed monopole flux loop having double helical structure: the conjugate strand would carry the return flux. The addition of a piece of DNA would be induced by a reconnection gluing shorter helical flux loop to the end of the helical loop. The chemical counterpart of dark DNA would be formed by the pairing of dark codons with the ordinary codons - kind of transcription process.
   
   
3. The modifications of paternal and maternal dark genomes are expected to occur independently and typically lead to different lengths of paternal and maternal DNAs. Hence the condition that the paternal and maternal modifications of germ cells are identical (same length) is too strong.
   

   Can the maternal and paternal DNA double strands have different lengths? This seems to be possible. The reconnection process in meiosis does not require same lengths for maternal and paternal genomes. In fertilization the chromosomes of paternal and maternal gametes form pairs and also this allows different lengths. Therefore the big leaps in the evolution could correspond to additions of new pieces to maternal an/or paternal dark genome.
   
   

This picture is of course over-simplified. Also addition of DNA portions in the middle of genome - say adding a new gene or par of gene - should be possible at the level of dark matter. Also this process should occur by reconnection process at the level of dark matter. Also now it seems that the process can occur independently for maternal and paternal chromosomes.

See the article Darwinian or neutral theory of evolution or something else?, the longer article Getting philosophic: some comments about the problems of physics, neuroscience, and biology, or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Multilocal viruses

I learned about very interesting piece of strangeness in biology known already for half a century (see this): there are viruses which can split into segments going into different host cells, replicate and produce proteins there, and self-assemble to original virus after this.

Virus (see this) consist of DNA or RNA, protein coat, and in some cases outside envelope consisting of lipids and analogous to cell membrane. Typically viruses consist of DNA or RNA decomposing to short segments coding for single protein. The reason for this is that RNA replication is prone to errors and for short segments these errors are not so fatal. Also DNA can be segmented but the segments are longer. RNA can be have positive sense in which it can be directly translated to protein or negative sense in which case replication producing positive sense RNA is needed made possible by an enzyme contained by the virus.

The usual thinking about viruses is that virus finds its way to cell and then uses the genetic machinery of the cell to replicate its DNA and RNA and produce also proteins. This does not not occur in the case of multipartite viruses infecting plants. The virus can split into segments infecting host cells separately. The segments of RNA and proteins contained by the virus are thus shared by different cells are replicated and coded to proteins. The outcome of the process is then brought together in some cell which need not contain gene segments in it and self-assembly to full virus can occur. Also fractured viruses can flourish and can infect some other plant.

It has been found that the full complement of most viral segments is missing from most plant cells. Protein required for viral replication present in cells that did not have genome for producing it so that the produced proteins can be transferred from the cell where they are produced to neighboring cells: it is though that so called plasmodesmata connecting cells to a network make this possible.

In standard view assuming that the viral segments are completely independent systems multi-partitioning has high risks. In this view theoretically not more than 4 segments are possible. For instance, 8 has been observed in the examples discussed. Even flu virus decomposes into 8 DNA segments with the cell inside which it replicates. Multi-partitioning produces also problems for spreading. In the case of FBNSV viruses mentioned in the article on the insect - aphid- eating FBNSV spreads the virus to plants. How can it get all 8 parts of virus simultaneously? This is very difficult to understand if the segments are really independent.

This suggests that the view about these viruses somehow wrong. Multi-partitioning happens and standard view does not allow it.

One can start by asking why the multi-partitioning implying modular reproduction (something analogous to that in industry!)? One good reason is that host cell might not be able to recognize the segments. Also transcription of too large number of RNAs might be too much for the host and kill it. It seems that viruses act as populations.

TGD based model is based on familiar basic notions.

1. The basic mystery of the biology is coherence of organisms. Bio-chemistry alone cannot explain it. In TGD quantum coherence of dark matter identified as h_eff=nh₀ phases of ordinary matter at magnetic flux tubes of the magnetic body (MB) of the system is quantum coherent in long scales and this quantum coherence forces the coherence of ordinary living matter.
   
   
2. The flux tubes of MB connect cells to larger networks (tensor networks). In particular the segments of virus can be connected to a network in this manner. The segments would be effectively free but their behavior would be correlated.
   Virus would be multi-local entity at the level of ordinary matter but single connected structure at the level of MB.
   
   
3. The TGD based model for bio-catalysis and replication and the model for monopole flux tubes suggests that
   the the phase transition increasing h_eff/h₀ =n increases the length of the flux tube. This process requires metabolic energy since quite generally the energy of system increases with n serving as a kind of IQ of the system measuring its algebraic complexity and identifiable as the dimension of extension of rationals assignable to the system. Multi-partitioning requires metabolic energy presumably given by a host cell. The components of multi-partitioned virus are virtually independent but flux tube connections are not lost. There are very many possible multi-partitionings and the individual host cell can contain several segments.
   
   
4. If the decay of virus to multi-partition corresponds to ordinary state function reduction ("big" state function reduction (BSFR) in zero energy ontology (ZEO) the arrow of time changes at the level of MB of virus (dark matter). h_eff/h₀=n increases in statistical sense in BSFR so that the multi-partitioned state should have higher IQ and is thus favored by quantum TGD. One might perhaps say that when virus is not active it does not need too much IQ: IQ requires metabolic energy feed and low IQ is the most economical choice in the dormant space. When virus infects the host it become active and and increase of n makes it multi-local at the level of ordinary matter.
   

   If this view is correct the self-assembly of the virus would lead back to dormant state with opposite arrow of time. That dormant state of virus would correspond to opposite arrow of time for "virus self" would conform with the general view that observer with opposite arrow of time than conscious entity experiences it as sleeping. One must be of course however very cautious with interpretations.
   
   

5. This dormant states would not be specific to viruses. Also folded protein would be dormant. External perturbation would feed metabolic energy feed waking up the dormant protein and protein would un-fold and become active and intelligent.
   

   Same applies to multi-locality. Also bacterial colony could be seen as single organism multi-local only at the level of ordinary bio-matter. When bacterial colony suffers starvation the bacteria form a single tightly connected structure also at the level of ordinary bio-matter. In the absence of metabolic energy feed the values of n associated with the flux tubes would be reduced and they would shorten causing the phenomenon.
   

   For cellular organisms the multi-locality at the level of ordinary bio-matter be realized for cell but the distances of cells would be fixed. Also at the level of DNA, RNA, tRNA and amino-acids multi-locality would be realized but the distances would not be fixed. In bio-catalysis the reactants are brought together and here h_eff reducing phase transition would take place providing also the energy needed to overcome the potential wall making the reaction extremely slow otherwise. In TGD based model for replication, transcription, and translation this flexible multi-locality is indeed assumed (see this).
   
   

6. How sexual reproduction (see this) emerged is one of the mysteries of biology. The formation of tightly bound multi-local states of mono-cellulars would have increased the probability for lateral gene transfer between neighboring cells, and also the replacement of mere replication with a two-step process consisting of replication followed by meiosis and fertilization as its inverse. The reconnection of flux tubes assignable to DNA is a prerequisite of this process in TGD framework so that the formation of states analogous multi-cellulars would have made this process plausible.
   
   

It has been found (see this), thanks for Nikolina Bendedikovic for a link) that multicellulars have monocellular colonies as predecessors in the sense that the bacteria (monocellulars) form temporarily tight structures resembling multicellular embryos. The transition from loose multi-locality to a more tight one suggets itself. When metabolic energy feed is low bacteria form tightly bound non-multilocal structures analogous to multi-cellulars. The flux tubes are shorten and metabolic energy is liberated, and also the need form metabolic energy is lower when flux tubes have lower values of h_eff. Multi-cellulars would be permanently in this configuration and their intelligence coded by distribution of h_eff:s would be realized differently.

Multi-cellulars would have been formed when these multi-cellular like bacterial colonies became permanent and began to evolve from embryos to more developed forms (see this and this). Hitherto I have assumed that multi-cellulars were formed already before the Cambrian explosion assumed to be induced by a relatively rapid phase transition increasing reducing the local cosmological constant by factor 1/2, and increasing the radius of Earth by a factor 2. This transition would have brought multi-cellulars to the surface from underground oceans giving also rise to the ordinary oceans. I have compared underground oceans to a womb of magnetic Mother Gaia. Ontogeny recapitulates phylogeny principle suggests that the life of the multicellular embryo in womb corresponds to the period of multicellular life in underground oceans.

Second possibility is that the multi-cellulars emerged from underground mono-cellulars during this transition or immediately after it. Could the emergence of bacterial colonies to the surface perhaps providing less metabolic energy feed forced them to form tightly bound colonies forcing the evolution of multi-cellulars?

See the article Multilocal viruses or the chapter Dark matter, quantum gravity, and prebiotic evolution.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.