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Year 2018

Did animal mitochondrial evolution have a long period of stagnation?

I encountered an interesting popular article telling about findings challenging Darwin's evolutionary theory. The original article of Stoeckle and Thaler is here.

The conclusion of the article is that almost all animals, 9 out of 10 animal species on Earth today, including humans, would have emerged about 100,000 200,000 years ago. According to Wikipedia all animals are assumed to have emerged about 650 million years ago from a common ancestor. Cambrian explosion began around 542 million years ago. According to Wikipedia Homo Sapiens would have emerged 300,000-800,000 years ago.

On basis of Darwin's theory based on survival of the fittest and adaptation to a new environment, one would expect that the species such as ants and humans with large populations distributed around the globe become genetically more diverse over time than the species living in the same environment. The study of so called neutral mutations not relevant for survival and assumed to occur with some constant rate however finds that this is not the case. The study of so called mitochondrial DNA barcodes across 100,000 species showed that the variation of neutral mutations became very small about 100,000-200,00 years ago. One could say that the evolution differentiating between them began (or effectively began) after this time. As if mitochondrial clocks for these species would have been reset to zero at that time as the article states it This is taken as a support for the conclusion that all animals emerged about the same time as humans.

The proposal of (at least ) the writer of popular article is that the life was almost wiped out by a great catastrophe and extraterrestrials could have helped to start the new beginning. This brings in mind Noah's Ark scenario. But can one argue that humans and the other animals emerged at that time: were they only survivors from a catastrophe. One can also argue that the rate of mitochondrial mutations increased dramatically for some reason at that time.

Could one think that great evolutionary leap initiating the differentiation of mitochondrial genomes at that time and that before it the differentiation was very slow for some reason? Why this change would have occurred simultaneously in almost all animals? Something should have happened to the mitochondria and what kind of external evolutionary pressure could have caused it?

  1. To me the idea about ETs performing large scale genetic engineering does not sound very convincing. That only a small fraction of animals survived the catastrophe sounds more plausible idea. Was it great flood? One can argue that animals living in water would have survived in this case. Could some cosmic event such as nearby supernova have produced radiation killing most animals? But is mass extinction really necessary? Could some evolutionary pressure without extinction caused the apparent resetting of mitochondrial clock?
  2. In TGD based quantum biology the great leaps could be caused by quantum criticality perhaps induced by some evolutionary pressure due to some kind of catastrophe. The value of heff=nh0 (h0 is the minimal value of Planck constant) - kind of IQ in very general sense - in some part of mitochondria could have increased and also its value would have fluctuated. Did a new longer length scale relevant to the functioning of mitochondrias emerge? Did the mitochondrial size increase? Here I meet the boundaries of my knowledge about evolutionary biology!
  3. Forget for a moment the possibility of mass extinction. Could the rate of mutations, in particular the rate of neutral mutations, have increased as a response to evolutionary pressure? Just the increased ability to change helps to survive. This rate would become high at quantum criticality due to the presence of large quantum fluctuations (variations of heff). If the mitochondria were far from quantum quantum criticality before the catastrophe, the rate of mutations would have been very slow. Animal kingdom would have lived a period of stagnation. The emerging quantum criticality - forced by a catastrophe but not involving an extinction - could have increased the rate dramatically.
See the chapter Quantum Criticality and dark matter.

The experiments of Masaru Emoto with emotional imprinting of water

Sini Kunnas sent a link to a video telling about experiments of Masaru Emoto (see this) with water, which is at criticality with respect to freezing and then frozen. Emoto reports is that words expressing emotions are transmitted to water: positive emotions tend to generate beautiful crystal structures and negative emotions ugly ones. Also music and even pictures are claimed to have similar effects. Emoto has also carried out similar experiments with rice in water. Rice subjected to words began to ferment and water subject to words expressing negative emotions began to rotten.

Remark: Fermentation is a metabolic process consuming sugar in absence of oxygen. Metabolism is a basic signature of life so that at least in this aspect the water+rice system would become alive. The words expressing positive emotions or even music would serve as a signal "waking up" the system.

One could define genuine skeptic as a person who challenges existing beliefs and pseudo-skeptic (PS in the sequel) as a person challenging - usually denying - everything challenging the mainstream beliefs. The reception of the claims of Emoto is a representative example about the extremely hostile reactions of PSs as aggressive watchdogs of materialistic science towards anything that challenges their belief system. The psychology behind this attitude is same as behind religious and political fanatism.

I must emphasize that I see myself as a thinker and regard myself as a skeptic in the old-fashioned sense of the word challenging the prevailing world view rather than phenomena challenging the prevailing world view. I do not want to be classified as believer or non-believer. The fact is that if TGD inspired theory of consciousness and quantum biology describes reality, a revolution in the world view is unavoidable. Therefore it is natural to consider the working hypothesis that the effects are real and see what the TGD based explanation for them could be.

The Wikipedia article about Masaru Emoto (see this) provides a good summary of the experiments of Emoto and provides a lot of links so that I will give here only a brief sketch. According to the article Emoto believed that water was a "blueprint for our reality" and that emotional "energies" and "vibrations" could change the physical structure of water. The water crystallization experiments of Emoto consisted of exposing water in glasses to different words, pictures or music, and then freezing and examining the aesthetic properties of the resulting crystals with microscopic photography. Emoto made the claim that water exposed to positive speech and thoughts would result in visually "pleasing" crystals being formed when that water was frozen, and that negative intention would yield "ugly" crystal formations.

In 2008, Emoto and collaborators published and article titled "Double-Blind Test of the Effects of Distant Intention on Water Crystal Formation" about his about experiments with water in the Journal of Scientific Exploration, a peer reviewed scientific journal of the Society for Scientific Explorations (see this). The work was performed by Masaru Emoto and Takashige Kizu of Emoto’s own IHM General Institute, along with Dean Radin and Nancy Lund of the Institute of Noetic Sciences, which is on Stephen Barrett's Quackwatch (see this) blacklist of questionable organizations. PSs are the modern jesuits and for jesuits the end justifies the means.

Emoto has also carried experiments with rice samples in water. There are 3 samples. First sample "hears" words with positive emotional meaning, second sample words with negative emotional meaning, and the third sample serving as a control sample. Emoto reports (see this) that the rice subjected to words with positive emotional content began to ferment whereas water subject to words expressing negative emotions began to rotten. The control sample also began to rotten but not so fast.

In the article The experiments of Masaru Emoto with emotional imprinting of water I will consider the working hypothesis that the effects are real, and develop an explanation based on TGD inspired quantum biology. The basic ingredients of the model are following: magnetic body (MB) carrying dark matter as heff/h=n phases of ordinary matter; communications between MB and biological body (BB) using dark photons able to transform to ordinary photons identifiable as bio-photons; the special properties of water explained in TGD framework by assuming dark component of water implying that criticality for freezing involves also quantum criticality, and the realization of genetic code and counterparts of the basic bio-molecules as dark proton sequences and as 3-chords consisting of light or sound providing a universal language allowing universal manner to express emotions in terms of bio-harmony realized as music of light or sound. The entanglement of water sample and the subject person (with MBs included) realized as flux tube connections would give rise to a larger conscious entity expressing emotions via language realized in terms of basic biomolecules in a universal manner by utilizing genetic code realized in terms of both dark proton sequences and music of light of light and sound.

See the chapter Dark Nuclear Physics and Condensed Matter or the article The experiments of Masaru Emoto with emotional imprinting of water.

How molecules in cells "find" one another and organize into structures?

The title of the popular article How molecules in cells 'find' one another and organize into structures expresses an old problem of biology. Now the group led by Amy S. Gladfelter has made experimental progress in this problem. The work has been published in Science (see this).

It is reported that RNA molecules recognize each other to condense into the same droplet due to the specific 3D shapes that the molecules assume. Molecules with complementary base pairing can find each other and only similar RNAs condense on same droplet. This brings in mind DNA replication, transcription and translation. Furthermore, the same proteins that form liquid droplets in healthy cells, solidify in diseases like neurodegenerative disorders.

Some kind of phase transition is involved with the process but what brings the molecules together remains still a mystery. The TGD based solution of this mystery is one of the first applications of the notion of many-sheeted space-time in biology, and relies on the notion of magnetic flux tubes connecting molecules to form networks.

Consider first TGD based model about condensed and living matter. As a matter fact, the core of this model applies in all scales. What is new is there are not only particles but also bonds connecting them. In TGD they are flux tubes which can carry dark particles with nonstandard value heff/h=n of Planck constant. In ER-EPR approach in fashion they would be wormholes connecting distance space-time regions. In this case the problem is instability: wormholes pinch and split. In TGD monopole magnetic flux takes care of the stability topologically.

The flux tube networks occur in all scales but especially important are biological length scales.

  1. In chemistry the flux tubes are associated with valence bonds and hydrogen bonds (see this). In biology genetic code would be realized as dark nuclei formed by sequences of dark protons at magnetic flux tubes. Also RNA, amino-acids, and even tRNA could have dark counterparts of this kind (see this). Dark variants of biomolecules would serve as templates for their ordinary variants also at the level of dynamics. Biochemistry would be shadow dynamics dictated to high degree by the dark matter at flux tubes.
  2. Dark valence bonds can have quite long length and the outcome is entangled tensor net (see this). These neuronal nets serve as correlates for cognitive mental images in brain (see this) emotional mental images in body (see this). Dark photons propagating along flux tubes (more precisely topological light rays parallel to them) would be the fundamental communication mechanism (see this). Transmitters and nerve pulses would only change the connectedness properties of these nets.
The topological dynamics of flux tubes has two basic mechanisms (I have discussed this dynamics from the point of view of AI here).
  1. Reconnection of flux tubes serves is the first basic mechanism in the dynamics of flux tube networks and would give among other things rise to neural nets. The connection between neurons would correspond basically to flux tube pair which can split by reconnection. Also two flux tube pairs can reconnect forming Y shaped structures. Flux tube pairs could be quite generally associated with long dark hydrogen bonds scaled up by heff/h=n from their ordinary lengths. Flux tube pairs would carry besides dark protons also supra phases formed by the lone electron pairs associated quite generally with hydrogen bonding atoms. Also dark ions could appear at flux tubes.

    Biomolecules would have flux loops continually scanning the environment and reconnecting if they meet another flux loop. This however requires that magnetic field strengths are same at the two loops so that a resonance is achieved at level of dark photon communications. This makes possible recognition by cyclotron frequency spectrum serving as signature of the magnetic body of the molecule.

    Water memory (see this) would rely on this recognition mechanism based on cyclotron frequencies and also immune system would use it at basic level (here one cannot avoid saying something about homeopathy although I know that this spoils the day of the skeptic: the same mechanism would be involved also with it). For instance, dark DNA strand accompanying ordinary DNA and dark RNA molecules find each other by this mechanism (see this). Same applies to other reactions such as replication and translation .

  2. Shortening of the flux tubes heff/h reducing phase transition is second basic mechanism explaining how biomolecules can find each other in dense molecular soup. It is essential that the magnetic fields at flux tubes are nearly the same for the reconnection to form. A more refined model for the shortening involves two steps: reconnection of flux tubes leading to a formation of flux tube pair between molecules and shortening by heff/h reducing phase transition.
Also ordinary condensed matter phase transitions involve change of the topology of flux tube networks and the model for it allows to put the findings described in the article in TGD perspective.
  1. I just wrote an article (see this) about a solution of two old problems of hydrothermodynamics: the behavior of liquid-gas system in the critical region not consistent with the predictions of statistical mechanics (known already at times of Maxwell!) and the behavior of water above freezing point and in freezing. Dark flux tubes carrying dark protons and possibly electronic Cooper pairs made from so called lone electron pairs characterizing atoms forming hydrogen bonds.
  2. The phase transition from gas to liquid occurs when the number of flux tubes per molecule is high enough. At criticality both phases are in mechanical equilibrium - same pressure. Most interestingly, in solidification the large heff flux tubes transform to ordinary ones and liberate energy: this explains anomalously high latent heats of water and ammonia. The loss of large heff flux tubes however reduces "IQ" of the system.
The phase transitions changing the connectedness of the flux tube networks are fundamental in TGD inspired quantum biology.
  1. Sol-gel transition would correspond to this kind of biological phase transitions. Protein folding (see this) - kind of freezing of protein making it biologically inactive - and unfolding would be second basic example of this transition. The freezing would involve formation of flux tube bonds between points of linear protein and assignable to hydrogen bonds. External perturbations induce melting of the proteins and they become biologically active as the value of heff/h=n characterizing their maximal possible entanglement negentropy content (molecular IQ) increases. External perturbation feeds in energy acting as metabolic energy. I have called this period molecular summer.
  2. Solidification of proteins reducing is reported to be associated with diseases such neurodegenerative disorders. In TGD picture this would reduce the molecular IQ since the ability of system to generate negentropy would be reduced when heff for the flux tubes decreases to its ordinary value. What brings molecules together is not understood and TGD provides the explanation as heff reducing phase transition for flux tube pairs.

See the chapter Quantum Criticality and Dark Matter.

Maxwell's lever rule and expansion of water in freezing: two poorly understood phenomena

The view about condensed matter as a network with nodes identifiable as molecules and bonds as flux tubes is one of the basic predictions of TGD and obviously means a radical modification of the existing picture. In the sequel two old anomalies of standard physics are explained in this conceptual framework. The first anomaly was known already at the time of Maxwell. In critical region for gas liquid-phase transition van der Waals equation of state fails. Empirically the pressure in critical region depends only on temperature and is independent on molecular volume whereas van der Waals predicting cusp catastrophe type behavior predicts this dependence. This problem is quite general and plagues all analytical models based on statistical mechanics.

Maxwell's area rule and lever rule is the proposed modification of van der Waals in critical region. There are two phases corresponding to liquid and gas in the same pressure and the proportions of the phases vary so that the volume varies.

The lever rule used for metal allows allows to explain the mixture but requires that there are two "elements" involved. What the second "element" is in the case of liquid-gas system is poorly understood. TGD suggests the identification of the second "element" as magnetic flux tubes connecting the molecules. Their number per molecule varies and above critical number a phase transition to liquid phase would take place.

Second old problem relates to the numerous anomalies of water (see the web pages of Martin Chaplin). I have discussed these anomalies from TGD viewpoint in (see this). The most well-known anomalies relate to the behavior near freezing point. Below 4 degrees Celsius water expands rather than contracts as temperature is lowered. Also in the freezing an expansion takes place.

A general TGD based explanation for the anomalies of water would be the presence of also dark phases with non-standard value of Planck constant heff/h=n (see this). Combining this idea with the above proposal this would mean that flux tubes associated with hydrogen bonds can have also non-standard value of Planck constant in which case the flux tube length scales like n. The reduction of n would shorten long flexible flux tubes to short and rigid ones. This reduce the motility of molecules and also force them nearer to each other. This would create empty volume and lead to an increase of volume per molecule as temperature is lowered.

Quite generally, the energy for particles with non-standard value of Planck constant is higher than for ordinary ones (see this). In freezing all dark flux tubes would transform to ordinary ones and the surplus energy would be liberated so that the latent heat should be anomalously high for all molecules forming hydrogen bonds. Indeed, for both water and NH3 having hydrogen bonds the latent heat is anomalously high. Hydrogen bonding is possible if molecules have atoms with lone electron pairs (electrons are not assignable to valence bonds). Lone electron pairs could form Cooper pairs at flux tube pairs assignable to hydrogen bonds and carrying the dark proton. Therefore also high Tc superconductivity could be possible.

See the chapter Quantum Criticality and Dark Matter of "Hyper-finite factors, p-adic length scale hypothesis, and dark matter hierarchy" or the article Maxwell's lever rule and expansion of water in freezing: two poorly understood phenomena.

Superfluids dissipate!

People in Aalto University - located in Finland by the way - are doing excellent work: there is full reason to be proud! I learned from the most recent experimental discovery by people working in Aalto University from Karl Stonjek. The title of the popular article is Friction found where there should be none—in superfluids near absolute zero.

In rotating superfluid one has vortices and they should not dissipate. The researchers of Aalto University however observed dissipation: the finding by J. Mäkinen et al is published in Phys Rev B. Dissipation means that they lose energy to environment. How could one explain this?

What comes in mind for an inhabitant of TGD Universe, is the hierarchy of Planck constants heff =n×h labelling a hierarchy of dark matters as phases of ordinary matter. The reduction of Planck constant heff liberates energy in a phase transition like manner giving rise to dissipation. This kind of burst like liberation of energy is mentioned in the popular article ("glitches" in neutron stars). I have already earlier proposed an explanation of fountain effect of superfluidity in which superfluid flow seems to defy gravity. The explanation is in terms of large value of heff implying delocalization of superfluid particles in long length scale (see this).

Remark: Quite generally, binding energies are reduced as function of heff/h= n. One has 1/n2 proportionality for atomic binding energies so that atomic energies defined as rest energy minus binding energy indeed increase with n. Interestingly, dimension 3 of space is unique in this respect. Harmonic oscillator energy and cyclotron energies are in turn proportional to n. The value of n for molecular valence bonds depends on n and the binding energies of valence bonds decrease as the valence of the atom with larger valence increases. One can say that the valence bonds involving atom at the right end of the row of the periodic table carry metabolic energy. This is indeed the case as one finds by looking the chemistry of nutrient molecules.

The burst of energy would correspond to a reduction of n at the flux tubes associated with the superfluid. Could the vortices decompose to smaller vortices with a smaller radius, maybe proportional to n? I have proposed similar mechanism of dissipation in ordinary fluids for more than two decades ago. Could also ordinary fluids involve hierarchy of Planck constants and could they dissipate in the same manner?

In biology liberation of metabolic energy - say in motor action - would take place in this kind of "glitch". It would reduce heff resources and thus the ability to generate negentropy: this leads to smaller negentropy resources and one gets tired and thinking becomes fuzzy.

See the chapter Quantum criticality and dark matter.

Condensed matter simulation of 4-D quantum Hall effect from TGD point of view

There is an interesting experimental work related to the condensed matter simulation of physics in space-times with D=4 spatial dimensions meaning that one would have D=1+4=5-dimensional space-time (see this and this). What is simulated is 4-D quantum Hall effect (QHE). In M-theory D= 1+4-dimensional branes would have 4 spatial dimensions and also 4-D QH would be possible so that the simulation allows to study this speculative higher-D physics but of course does not prove that 4 spatial dimensions are there.

In this article I try to understand the simulation, discuss the question whether 4 spatial dimensions and even 4+1 dimensions are possible in TGD framework in some sense, and also consider the general idea of the simulation higher-D physics using 4-D physics. This possibility is suggested by the fact that it is possible to imagine higher-dimensional spaces and physics: maybe this ability requires simulation of high-D physics using 4-D physics.

See the chapter Quantum Hall effect and Hierarchy of Planck Constants or the article Condensed matter simulation of 4-D quantum Hall effect from TGD point of view.

Exciton-polariton Bose-Einstein condensate at room temperature and heff hierarchy

Ulla gave in my blog a link to a very interesting work about Bose-Einstein condensation of quasi-particles known as exciton-polaritons. The popular article tells about a research article published in Nature by IBM scientists.

Bose-Einstein condensation happens for exciton-polaritons at room temperature, this temperature is four orders of magnitude higher than the corresponding temperature for crystals. This puts bells ringing. Could heff/h=n be involved?

One learns from Wikipedia that exciton-polaritons are electron hole pairs- photons kick electron to higher energy state and exciton is created.These quasiparticles would form a Bose-Einstein condensate with large number of particles in ground state. The critical temperature corresponds to the divergence of Boltzmann factor given by Bose-Einstein statistics.

  1. The energy of excitons must be of order thermal energy at room temperature: IR photons are in question. Membrane potential happens to corresponds to this energy. That the material is organic, might be of relevance. Living matter involves various Bose-Einstein condensate and one can consider also excitons.

    As noticed the critical temperature is surprisingly high. For crystal BECs it is of order .01 K. Now by a factor 30,000 times higher!

  2. Does the large value of heff =n×h visible make the critical temperature so high?

    Here I must look at Wikipedia for BEC of quasiparticles. Unfortunately the formula for n1/3 is copied from source and contains several errors. Dimensions are completely wrong.

    It should read n1/3= (ℏ)-1 (meffkTcr)x, x= 1/2.

    [not x=-1/2 and 1/ℏ rather than ℏ as in Wikipedia formula. This is usual: it would important to have Wikipedia contributors who understand at least something about what they are copying from various sources].

  3. The correct formula for critical temperature Tcr reads as

    Tcr= (dn/dV)y2/meff , y=2/3.

    [Tcr replaces Tc and y=2/3 replaces y=2 in Wikipedia formula. Note that in Wikipedia formula dn/dV is denoted by n reserved now for heff=n×h].

  4. In TGD one can generalize by replacing ℏ with ℏeff=n ×ℏ so that one has

    Tcr→ n2Tcr .

    Critical temperature would behave like n2 and the high critical temperature (room temperature) could be understood. In crystals the critical temperature is very low but in organic matter a large value of n≈ 100 could change the situation. n≈ 100 would scale up the atomic scale of 1 Angstrom as a coherence length of valence electron orbitals to cell membrane thickness about 10 nm. There would be one dark electron-hole pair per volume taken by dark valence electron: this would look reasonable.

One must consider also the conservative option n=1. Tcr is also proportional to (dn/dV)2, where dn/dV is the density of excitons and to the inverse of the effective mass meff. meff must be of order electron mass so that the density dn/dV or n is the critical parameter. In standard physics so high a critical temperature would require either large density dn/dV about factor 106 higher than in crystals.

Is this possible?

  1. Fermi energy E is given by almost identical formula but with factor 1/2 appearing on the right hand side. Using the density dne/dV for electrons instead of dn/dV gives an upper bound for Tcr ≤ 2EF. EF varies in the range 2-10 eV. The actual values of Tcr in crystals is of order 10-6 eV so that the density of quasi particles must be very small for crystals: dncryst/dV≈ 10-9dne/dV .
  2. For crystal the size scale Lcryst of the volume taken by quasiparticle would be 10-3 times larger than that taken by electron, which varies in the range 101/3-102/3 Angstroms giving the range (220-460) nm for Lcryst.
  3. On the other hand, the thickness of the plastic layer is Llayer= 35 nm, roughly 10 times smaller than Lcryst. One can argue that Lplast ≈ Llayer is a natural order of magnitude for Lcryst for quasiparticle in plastic layer. If so, the density of quasiparticles is roughly 103 times higher than for crystals. The (dn/dV)2-proportionality of Tcr would give the factor Tcr,plast≈ 106 Tcr,cryst so that there would be no need for non-standard value of heff!

    But is the assumption Lplast ≈ Llayer really justified in standard physics framework? Why this would be the case? What would make the dirty plastic different from super pure crystal?

The question which option is correct remains open: conservative would of course argue that the now-new-physics option is correct and might be right.

For background see the chapter Criticality and dark matter.

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