# Genes and Memes

Note: Newest contributions are at the top!

 Year 2015

### Jeremy England's vision about life and evolution: comparison with TGD approach

It turns out possible to gain amazing additional insights about TGD inspired view of life and consciousness by generalizing England's approach discussed in previous posting. Several puzzling co-incidences find an explanation in the thermodynamical framework and the vision about solar system as a living quantum coherent entity gains additional support.

1. The situation considered in England's approach is a system - say biomolecule - in heat bath so that energy is not conserved due the transfer of energy between reactants and heat bath.
2. The basic equation is equilibrium condition for the reaction i→ f and its time reversal f*→ i*. The initial and final state can be almost anything allowing thermodynamical treatment: states of biomolecule or even gene and its mutation. The ratio of the rates for the reaction and its time reversal is given by the ratio of the Boltzmann weights in thermal equilibrium:

R(i→ f)/R(f*→ i*)= R , R= e-(Ei-Ef)/T .

Ei and Ef denote the energies of initial and final state. This formula is claimed to hold true even in non-equilibrium thermodynamics. It is important that the ratio of the rates does not depend at all on various coupling constant parameters. The equilibrium condition must be modified if initial and final states are fermions but it is assumed that states can be described as bosons. Note that in heat bath even fermion number need not be conserved.

3. If the energy eigenstates are degenerate, the ratio R of Boltzman factors must be modified to include the ratio of state degeneracies

R→ (D(Ei)/D(Ef) × e-(Ei-Ef)/T .

This generalization is essential in the sequel.

One can imagine two possible reasons for the presence of exponentially large factors compensating Boltzmann weights D(Ei). The first reason is that for heff=n× h the presence of n-fold degeneracy due to the n-fold covering of space-time surface reducing to 1-fold covering at its ends at the ends of CD is essential. Second possible reason is that the basic object are magnetic flux tubes modellable as strings with exponentially increasing density of states. These mechanisms could quite well be one and same.

Consider now the basic idea inspired by this formula in TGD framework.
1. Since magnetic flux tubes are key entities in TGD inspired quantum biology, stringy dynamics suggests itself strongly. The situation thus differs dramatically from the standard biochemical situation because of the presence of dark matter at magnetic flux tubes to which one can assign fermion carrying strings connecting partonic 2-surfaces defining correlates for particles in very general sense.
2. The key aspect of stringy dynamics is Hagedorn temperature. Slightly below Hagedorn temperature the density of states factor, which increases exponentially, compensates for the Boltzmann factor. Hagedorn temperature is given by

THag = (61/2/2π) × (1/α')1/2 ,

where α' is string tension. In superstring models the value of string tension is huge but in TGD framework the situation is different. As a matter fact, the temperature can be rather small and even in the range of physiological temperatures.

3. What makes THag so special is that in the equilibrium condition reaction and its reversal can have nearly the same rates. This could have profound consequences for life and even more - make it possible.

In ZEO based quantum measurement theory and theory of consciousness time reversal indeed plays key role: self dies in state function reduction to the opposite boundary of CD and experiences re-incarnation as a time-reversed self. This process is essential element of memory, intentional action, and also remote metabolism, which all rely on negative energy signals travelling to geometric past assignable to time reversed sub-selves (mental images). The above formula suggests that intelligent life emerges near THag, where the time reversed selves are generated with high rate so that system remembers and pre-cognizes geometric future as it sleeps so that memory planned action are possible.

4. String tension cannot be determined by Planck length as in string models if it is to be important in biology. This is indeed the case in TGD based quantum gravity. The gravitational interaction between partonic 2-surfaces is mediated by fermionic strings connecting them. If string tension were determined by Planck length, only gravitational bound states of size of order Planck length would be possible. The solution of the problem is that the string tension for gravitational flux tubes behaves like 1/heff2.

In TGD framework string tension can be identified as an effective parameter in the expression of Kähler action as stringy action for preferred extremal strongly suggested by strong form of holography (SH) allowing the description of the situation in terms of fermionic strings and partonic 2-surfaces or in terms of interiors of space-time surfaces and Kähler action. 1/heff2 dependence can be derived from strong form of holography assuming electric-magnetic duality for Kähler form, and using the fact that the monopoles associated with the ends have same magnetic and electric charges.

5. The discussion of the analog of Hawking radiation in TGD framework led to an amazing prediction: the TGD counterpart of Hawking temperature turns out to be in the case of proton very near to the physiological temperature if the big mass is solar mass (see this). This suggests that the entire solar system should be regarded as quantum coherent living system. This is also suggested by the general vision about EEG. Could Hawking temperature be near to the Hagedorn temperature but below it?
One can make this vision more detailed.
1. In ZEO the notion of heat bath requires that one considers reactants as subsystems. The basic mathematical entity is the density matrix obtained by tracing over entanglement with environment. The assumption that dark matter is in thermal equilibrium with ordinary matter can be made but is not absolutely crucial. The reactions transforming visible photons to dark photons should take care of the equilibrium. One could even assume that the description applies even in case of the negentropic entanglement since thermodynamical entropy is different from entanglement entropy negative for negentropic entanglement.
2. In TGD inspired quantum biology one identifies the gravitational Planck constant introduced by Nottale with heff=n× h. The idea is simple: as the strength of gravitational interaction becomes so strong that perturbation series fails to converge, a phase transition increasing the Planck constant takes place. hgr=GMm/v0= heff=n× h implies that v0/c<1 becomes the parameter defining the perturbative expansion. hgr is assigned with the flux tubes mediating gravitational interaction and one can say that gravitons propagate along them.

Note that this assumption makes sense for any interaction - say in the case of Coulomb interaction in heavy atoms: this assumption is indeed made in the model of leptohadrons (see this) predicting particles colored excitations of leptons lighter the weak bosons: this leads to a contradiction with the decay widths of weak bosons unless the colored leptons are dark. They would be generated in the heavy ion collisions when the situation is critical for overcoming the Coulomb wall.

The cyclotron energy spectrum of dark particles at magnetic flux tubes is proportional to hgr/m does not depend on particle mass being thus universal. In living matter cyclotron energies are assumed to be in the energy range of bio-photons and thus includes visible and UV energies and this gives a constraint on hgr if one makes reasonable assumption about strengths of the magnetic fields at the flux tubes (see this). Bio-photons are assumed to be produced in the transformation of dark photons to ordinary photons. Also (gravitational) Compton length is independent on particle mass being equal to Lgr=GM/v0: this is crucial for macrosopic quantum coherence at gravitational flux tubes.

3. The basic idea is that Hawking radiation in TGD sense is associated with all magnetic flux tubes mediating gravitational interaction between large mass M, say Sun, and small mass m of say elementary particle. How large m can be, must be left open. This leads to a generalization of Hawking temperature (see this) assumed to make sense for all astrophysical objects at the flux tubes connecting them to external masses:

TGR=hbar (GM/RS2 2π) = hbar/(8 π GM).

For Sun with Schwartschild radius rS=2GM=3 km one has TGR= 3.2× 10-11 eV.

Planck constant is replaced with hgr=GMm/v0= heff=n× h in the defining formula for Hawking temperature. Since Hawking temperature is proportional to the surface gravity of blackhole, one must replace surface gravity with that at the surface of the astrophysical object with mass M so that radius RS=2GM of the blackhole is replaced with the actual radius R of the astrophysical object in question. This gives

THaw= (m/8 π v0) × (RS/R)2 .

The amazing outcome is that for proton the estimate for the resulting temperature for M the solar mass, is 300 K (27 C), somewhat below the room temperature crucial for life!

Could Hagedorn temperature correspond to the highest temperature in which life is possible - something like 313 K (40 C)? Could it be that the critical range of temperatures for life is defined by the interval [THaw,THag]? This would require that THaw is somewhat smaller THag. Note that Hawking temperature contains the velocity parameter v0 as a control parameter so that Hawking temperature could be controllable. Of course, also THaw=THag can be considered. In this case the temperature of environment would be different from that of dark matter at flux tubes.

4. The condition THaw≤ THag allows to pose an upper bound on the value of the effective string tension

(α')-1/2≥ (m/4×61/2v0) × (RS/R) .

For background see the chapter Dark matter, quantum gravity, and prebiotic evolution or the article Jeremy England's vision about life and evolution: comparison with TGD approach.

### Jeremy England's vision about life

I had an intensive discussion with my son-in-law Mikko about the work of Jeremy England. The article of the link is probably the most aggressive hyping I have ever seen but this should not lead to think that a mere hype is in question. There is also another, not so heavily hyped popular article. The material at england lab homepage gives a good view about the work of England for those who cannot tolerate hyping.

England's work is indeed very interesting also from TGD point of view although it is based on standard physics.

Basic ideas of England's theory

I try first to summarize England's vision.

1. Non-equilibrium thermodynamics (NET) is the starting point. NET has been for decades the theoretical framework underlying the attempts to understand living matter using the principles of self-organization theory. Living matter is never an isolated system: dissipation would take it to a totally dead state in this case - nothing would move. Water in the pond when there is no wind, is a good example.

Self-organization requires an external energy feed - gravitational potential energy liberated in water flow in river or electric power feed to the hot plate below a teapot. This energy feed drives the system to a non-stationary state far from a thermal equilibrium state. Dissipation polishes out all details and leads to an asymptotic spatio-temporal self-organization patterns. The flow in a river and convection in the heated teapot. With high enough energy feed chaos emerges: water fall or boiling of tea pot.

2. The basic hypothesis of England is that evolution means increase in the ability to dissipate. This looks intuitively rather obvious. The evolving system tends to get to a resonance with the energy feed by oscillating with the same frequency so that energy feed becomes maximal and therefore also dissipation. The basic rule is simple: choose the easy option, ride on the wave rather than fighting against it! For instance, the emergence of photosynthesis means that the systems we call plants become very effective in absorbing the energy of sunlight. In this framework essentially all systems are alive to some degree.

Dissipation means generation of entropy. Evolution of life and conscious intelligence would mean maximal effectivenes in the art of producing disorder. Now I am perhaps exaggerating. One should speak about "system's maximal ability to transfer entropy out of it": life is not possible without paper baskets. One could argue that the development of civilization durig last decades demonstrates convincingly that evolution indeed generates systems generating disorder with a maximal rate.

One could argue that the definition is too negative. Living matter is conscious and there is genuine conscious information present. The fact is that evolution involves a continual increase of conscious information: the exponential explosion of science is the best proof for this. England's vision says nothing about it. Something is missing.

It is however quite possible to imagine that the principle of maximal entropy generation is true and that the increase of the ability to produce entropy is implied by some deeper principle allowing to speak about living matter as something tending to increase conscious information resources. To formulate this idea one needs a theory of consciousness, thermodynamics is not enough.

3. England has a further idea. The evolution life is not climbing to Mount Everest but coming down from it. Life emerges spontaneously. This is definitely in conflict with the standard wisdom, in particular with the thermodynamical belief on thermal death of the Universe as all gradients disappear. Darwinian evolution would be a special case of a more general phenomenon, which could be called dissipation driven adaptation (DDA). I made a head-on-collision with this principle in totally different framework by starting from quantum criticality of TGD: if took time to fully realize that indeed: evolution could be seen as a sequence of phase transitions breaking in which certain infinite-dimensional symmetry was spontaneously broken to become just the same symmetry but in longer scale!

Standard thermodynamics predicts the heat death of the Universe as all gradients gradually disappear. This prediction is problematic for England's argument suggesting that differentiation occurs instead of homogenization. Here the standard view about space-time might be quite too simplistic to overcome the objection. In TGD many-sheeted space-time comes in rescue.

Here is an example about England's argumentation. It seems intuitively clear that replication increases entropy (it is not however clear whether just the splitting into pieces is even more effective manner to increase entropy!). This would suggest that DDA forces the emergence of replication. Very effective dissipators able to replicate, would increase the total effectiveness in dissipation and be the winners. The proposal to be tested is that bacterial mutations , which are best replicators are also best dissipators.

What is missing from England's theory?

What is missing from England's theory? The answer is same as the answer to the question what is missing from standard physics.

1. What is conscious observer - self?

Observer, which remains outsider to the physical world in the recent day physics - both classical and quantum. Hence one does not have a theory of consciousness and cannot speak about conscious information. Thermodynamics gives only the notion of entropy as a measure for the ignorance.

Therefore there is a long list of questions that England's theory does not address. What are the physical correlates of attention, sensory perception, cognition, emotions relating closely to information, etc.? Is there some variational principle behing concious existence, and does it imply evolution? Could second law and DDA be seen as consequences of this variational principle ?

England does not say much about quantum theory since he talks only about thermodynamics but his hypothesis is consistent with quantum theory. The restriction to thermodynamics allows only statistical description and notions like macroscopic quantum coherence are left outside.

2. What is life?

Again one has a long list of questions.

What it is to be alive? What distinguishes between living and inanimate systems. What it is to die? How general phenomenon evolution is: does it apply to all matter? Also notions like self-preservation and death are present only implicitly in an example about a population of wine glasses whose members might gradually evolve to survive in an environment populated by opera sopranos.

One can make also other kinds of questions. What really happens in replication? What is behind genetic code? Etc...

England is a spiritual person and has made clear that the gulf between science and spirituality is something which bothers him . England even has the courage to use the word "God". Therefore it sounds somewhat paradoxical that England avoids using the concepts related to consciousness and life. This is however the only option if one does not want to lose academic respectability.

How England's theory relates to TGD?

It is interesting to see whether England's vision is consistent with TGD inspired theory of consciousness, which can be also seen as a generalization of quantum measurement theory achieved by bringing the observer part of the quantum physical world. In TGD framework several new principles are introduced and they relate to the new physics implied by the new view about space-time.

1. The new physics involves a generalization of quantum theory by introducing a hierarchy of Planck constants heff =n×h with various quantal length and time scales are proportional to heff. heff hierarchy predicts a hierarchy of quantum coherent systems with increasing size scale and time span of memory and planned action. heff defining a kind of intelligence quotient labels the levels of a hierarchy of conscious entities.

heff hierachy labels actually a fractal hierarchy of quantum criticalities: a convenient analogy is a ball at a top of ball at the top..... The quantum phase transitions inreasing heff occur spontaneously: this is the TGD counterpart for the spontaneous evolution in England's theory. Dark matter is what makes system alive and intelligent and thermodynamical approach can describe only what we see at the level of visible matter.

2. Second key notion is zero energy ontology (ZEO). Physical states are replaced by events, one might say. Event is a pair of states: initial state and final state. In ZEO these states correspond to states with opposite total conserved quantum numbers: positive and negative energy states. This guarantees that ZEO based quantum theory is consistent with the fundamental conservation laws and laws of physics as we understand them although it allows non-determinism and free will. Positive and negative energy states are localized at opposite boundaries of a causal diamond (CD). Penrose diagram - diamond symbol - is a good visualization and enough for getting the idea.

State function reduction (SFR) is what happens in quantum measurement. The first SFR leads to a state which is one in a set of states determined once measurement is characterized. One can only predict the probabilities of various outcomes. Repeated quantum measurements leave the state as such. This is Zeno effect - watched kettle does not boil.

In ZEO something new emerges. The SFR can be performed at either boundary of CD. SFR can occur several times at the same boundary so that the state at it does not change. The state at the opposite boundary however changes - one can speak of the analog of unitary time evolution - and the second boundary also moves farther away. CD therefore increases and the temporal distance between its tips does so also.

The interpretation is as follows. The sequence of reductions at fixed bounary corresponds to a conscious entity, self. Self experiences the sequence of state function reductions as a flow of time. Sensory experience and thoughts, emotions, etc.. induced by it come from the moving boundary of CD. The constant unchanging part of self which meditators try to experience corresponds to the static boundary - the kettle that does not boil.

Self dies in the first reduction to the opposite boundary of CD. Self however re-incarnates. The boundaries of self change their roles and the geometric time identified as distance between the tips of CD increases now in opposite direction. Time-reversed self is generated.

3. Negentropy Maximization Principle (NMP) stating roughly that the information content of consciousness is maximal. Weak form of NMP states that self has free will and can choose also non-maximal negentropy gain. The basic principle of ethics would be "Increase negentropy". p-Adic mathematics is needed to construct a measure for conscious information and the notion of negentropic entanglement (NE) emerges naturally as algebraic entanglement.

The negentropy to which NMP refers is not the negative of thermodynamical entropy describing lack of information of outsider about state of system. This negentropy characterizes the conscious information assignable to negentropic entanglement (NE) characterized by algebraic entanglement coefficients with measure identified as a number theoretic variant of Shannon entropy. Hence NMP is consistent with the second law implied by the mere non-determinism of SFR.

NMP demands that self during sequence of reductions at the same boundary generates maximum negentropy gain at the changing CD boundary. If self fails, it dies and re-incarnates (in a reduction to the opposite CD boundary more negentropy is generated). Selves do not want to die and usually they do not believe on re-incarnation, and therefore do their best to avoid what they see as a mere death. This is the origin of self-preservation. Self must collect negentropy somehow: gathering negentropic sub-selves (mental images) is a manner to achieve this. Plants achieve this by photosynthesis, which means generation of negentropy and storage of it to various biomolecules. Animals are not so saintly and simply eat plants and even other animals. We are negentropy thieves all.

Re-incarnation also means increase of heff and getting to higher level in hierarchy and occurs unavoidably. As in England's theory, evolution occurs spontaneously: it is not climbing to Mount Everest but just dropping down.

4. England says "Some things we consider inanimate actually may already be 'alive'." This conforms with TGD view. Even elementary particles could have self: it is however not clear whether their SFR sequences contain more that one reduction to a fixed boundary - necessary for having a sense about the flow of time. Elementary particles would even cognize: in adelic physics every system has both real and p-adic space-time surfaces as its correlates. It can even happen that system has only p-adic space-time correlates but not the real one: this kind of systems would be only imaginations of real system! This is one of the most fascinating implications of strong form of holography which follows from strong form of General Coordinate Invariance forced by the new view about space-time.

Clearly the notion of evolution generalizes from biological context to entire physics in TGD. One can speak about p-adic evolution and evolution as increase of heff. The most abstract formulation is number theoretical: evolutioncorresponds to the increase of the complexity of extension of rationals to which the parameters characterizing space-time surfaces belong to.

5. Does DDA emerge in TGD framework? NMP demands a lot of SFRs - also at the level of visible matter. The non-determimism of SFR alone means a loss of knowledge about the state of system and an increase of thermodynamical entropy so that living systems would generate entropy very effectively also in TGD Universe at the level of visible matter. If one believes that second law and NET imply DDA as England argues, then also TGD implies it at the level of visible matter. For dark matter the situation is different, since the outcome of SFR is not not random anymore. Seen from TGD perspective England's vision misses what is essential for life - the generation of phases of matter identifiable as the mysterious dark matter.
6. England talks about God. In a theory of consciousness predicting infinite self hierarchy, it is easy to assign the attribute "divine" to the levels of consciousness above given level of hierarchy. Personally I have nothing against calling the Entire Universe "God".

One could give NMP the role of God. For strong form of NMP SFR would be almost deterministic except for ordinary matter for which entanglement is not algebraic and is therefore entropic: the universe would the best possible one in dark sectors and the worst one in the visible matter sector - Heaven and Hell! Weak form of NMP makes possible even more effective generation of negentropy than its strong form but allows self to make also stupid things and even SFRs with a vanishing negentropy gain: the outcome is state with no entanglement (system is in very literal sense alone in this state). The world in dark matter sectors is not anymore the best possible one but can become better and does so in statistical sense.

7. Replication is a crucial aspect of being alive. England argues that DDA allows to understand its emergence but does not tell about its mechanism. In TGD framework replication can be understood as an analog of particle decay - say photon emission by electron. This requires however a new notion: magnetic body. In Maxwell's theory one cannot assign any field identity to a physical system but TGD view about space-time forces to assign to a given system its field/magnetic body. The replication occurs primarily at the level of magnetic body carrying dark matter as large heff phases. Magnetic body replicates and ordinary visible matter self-organizates around the resulting copies of it. The dynamics of dark matter would induce also DNA replication, transcription and mRNA translation, and there are some indications that it is indeed "dark DNA" (dark proton sequences having DNA, RNA, amino-acids, and tRNA as biochemical counterparts), which determines what happens in transcription.
For background see the chapter Dark matter, quantum gravity, and prebiotic evolution or the article Jeremy England's vision about life and evolution: comparison with TGD approach.

### About evolution before Cambrian explosion

The formulation of a more detailed TGD inspired vision about how life might have evolved in TGD Universe during pre-Cambrian era is a fascinating challenge. In Cambrian explosion relatively rapid expansion of Earth size by a factor of 2 assumed in TGD version of Expanding Earth model. TGD indeed predicts that cosmic expansion takes place in given scale as rapid jerks rather than continuously as in ordinary cosmology. The key ingredients besides standard facts are TGD inspired interpretation for Cambrian Explosion (CE) (see this and this), of dark matter as large heff phases (see this), and the notion of magnetic flux tubes. These provide TGD view about Pollack's Exclusion Zones (EZs, as key factors in the evolution of life.

I have gathered useful links from web to build a more detailed version of TGD vision and it is perhaps appropriate to give a list of some useful links - they appear also as references. These links might help reader considerably in getting touch about the problems involved and reader can easily find more.

1. What happened before Cambrian explosion?

The story about evolution of life is constructed from empirical findings based on certain geological, chemical, and isotope signatures. The study of sediment rocks makes possible reasonably reliable age determinations but involves assumptions about the rate of sedimentation. Water, ice, acids, salt, plants, animals, and changes in temperature contribute to weathering and cause erosion involves water, ice, snow, wind, waves and gravity as agents and leads to sedimentation. Also organic material forms sediments both on land and at ocean floors.

Isotope ratios serve as signatures since they are different in inanimate and living matter because those for living matter reflect those in atmosphere and are affected by cosmic rays. The concentrations of various elements are important signatures: mention only oxygen, nitrogen, sulphur compounds such as sulphide, hydrogen sulphide. and sulphate iron, and molybden.

The story involves great uncertainties and should not be taken only as a story. In the following TGD view about how life evolved before Cambrian Explosion (CE) about .6 gy ago is summarized. The Pre-Cambrian part of TGD inspired story differs dramatically from the official narrative since only lakes would have been present whereas official story assumes oceans and continents. Earth would have very much like Mars before CE - even its radius would have been essentially same (half of the recent radius of Earth). This suggests that Mars could teach us a lot about the period before CE. The deviations seem to explain its paradoxical looking aspects of the standard story.

1. Life according to TGD evolved in underground oceans and at the surface of Earth containing lakes but no oceans. The lifeforms at the surface of Earth were prokaryotes whereas the life in underground oceans consisted of relatively complex photo-synthesizing eukaryotes.
2. The recent data from Mars gives an idea what the situation at Earth was during CE since the radius of Earth at that time was very nearly same as that of Mars now. There is evidence for sedimentation and for water near to and even at the surface provided quite recently. The life at the surface of Earth before CE consisted mainly of prokaryotes and very simple mono-cellular eukaryotes and something like this is expected at the surface of Mars now.
3. Already around 3.5 gy ago prokaryotes using sulphate as energy metabolite were present. Photo-synthesizing cyanobacteria emerged about 3.2 gy ago. They became later the plasmids of plant cells responsible for photo-synthesis. The problem of the standard story is that this did not lead to oxygenation of the hypothetic oceans and rapid evolution of eukaryotes and multi-cellulars.

In standard vision one can explain the absence of oxygen based life in hypothetic oceans by the presence of oxygen sinks. It is known that the ancient oceans (shallow oceans, lakes, or ponds in TGD) were oxygen poor and iron rich. The data about Mars - the red planet because of iron rusting - makes possible to test the feasibility of this hypothesis. The oxygen produced by the cyanobacteria was used to the formation of rusted iron layers giving rise to iron ores. For 1.8 gy ago the formation of rusted iron layers ceased. A possible explanation is that all iron was used. The ores could have been also generated by bacteria using iron as metabolite and transforming it to iron oxide. There are however now iron ores after 1-8 gy: did these bacteria lose the fight for survival?

In TGD Earth atmosphere remained oxygen poor since the small lakes could not produce enough oxygen to induce the oxygenation of the atmosphere. The lakes however gained gradually oxygen. First it went to the oxidation of iron.

4. A general belief has been that about 2.4 gy ago Great Oxidation Event (GOE) occurred. The basic evidence for GEO is from volcano eruptions, which seem to have produced anomalously small amount of sulphur after 2.4 gy. The reason would have been the formation of sulphate SO4 from atmospheric oxygen and sulphur emanating from volcano.

This evidence has been however challenged by measuring sulphur anomalies for recent volcanic eruptions. Their sign varies in time scale of month changing from positive to negative. It is quite possible that GOE is an illusion.

5. There is also problem related to to the "boring period" 1.8-.8 gy. It seems that the hypothetic oceans remained still oxygen poor and iron rich. It has been also suggested that the boring period continued up to CE: the first animals after CE could have oxygenated Earth's oceans. In TGD Universe GOE is indeed illusion for the simple reason that oceans did not exist! Life was boring at the surface of Earth from 3.5 gy to .6 gy.
6. Life would have evolved in underground seas containing oxygenated water, probably already 3.2 gy ago, and making possible photo-synthesis and cellular respiration. Animal cells formed by eukaryotes with nucleus carrying genome with prokaryotes, which later became mitochondria. Plant cells emerged when these eukaryotes engulfed also cyanobacteria, which made photo-synthesis possible. The highly developed eukaryotes were burst to the surface as the radius of Earth increased by a factor two in geologically short time scale. Oceans containing oxygen rich water were formed. CE can be equated with GOE in TGD picture.

Plants are divided into green and red algae, a small group of fresh water monocellulars glaucophytes, and land plants. Land plants must have emerged after CE. Red algae are multi-cellulars (corals are representative example). Also green algae can be multi-cellulars and land plants are thought to have developed from them. An interesting question is whether multi-cellular plants and animals emerged already before CE as the findings would suggest.

The basic objection against this vision is that photo-synthesis is not possible underground. Did photo-synthesis occur in shallow lakes storing chemical energy transferred to the underground seas. This does not seem a plausible option but cannot be excluded. The volcanoes and hydrothermal vents bring water from underground. The water contains ground water and ordinary sea water, which ended underground in various manners, and also magmatic component. The geothermal vents and most volcanoes are however associated with the regions were tectonic plates meet and should not have existed before CE.

TGD inspired model for Pollack's exclusion zones (EZs) suggests a solution of the problem. The formation of these negatively charged regions of water is induced by solar radiation, IR radiation at energies which correspond to metabolic energy quantum, and also at energies corresponding to THz frequency. TGD based model proposes that the protons from EZ becomes large heff protons at magnetic flux tubes associated with EZ. These flux tubes could be quite long and extend to the underground oceans. Dark photons with energy spectrum containing that of bio-photons could travel along these flux tubes. This suggests that solar radiation transforms partially to dark photons, which travel along flux tubes to the underground sea and transform to ordinary photons caught by photo-synthesizing cells.

Interestingly, also the temperature of Earth is such that thermal radiation would be in visible region and one cannot exclude the possibility that dark photons emerge also from this source. This would make possible also cell respiration and oxygen rich water.

Skeptic is of course wondering whether the flux tubes were long enough.

1. The basic idea about dark matter residing at magnetic flux tubes emerged in TGD from Blackman's findings about quantal looking effects of ELF em fields on vertebrate brain by assigning them to cyclotron frequencies Ca++ ions in endogenous magnetic field Bend= .2 Gauss, which is by a factor 2/5 weaker than the recent magnetic field of Earth and assigning large non-standard value of Planck constant to the flux tubes so that the energies of ELF quanta are above thermal energies.
2. The value of magnetic field at flux tubes of "personal" magnetic bodies of organisms have Bend in its value spectrum. Bend could be conserved in evolution somewhat like the salinity of ancient (underground) ocean. The flux tubes of Bend would have transformed the photons of solar radiation to dark cyclotron photons allowing them to travel to underground sea and transform back to ordinary photons to be absorbed by pre-plant cells. I have proposed that a similar mechanism is at work in biological body and could explain the reported ability of some people to survive without any obvious metabolic energy feed.

2. How the cellular life could have evolved before CE?

In the following I summarize what looks the most plausible view about evolution of life in TGD framework. I represent first basic classification to make reading easier.

2.1 Basic classification of lifeforms

Lifeforms are classified into prokarioties (no cell nucleus) and eukaryotes (cell nucleus).

1. Prokaryotes are mono-cellular and have no separate cell nucleus. They are divided into bacteria and archea. Bacteria do not have genome but only circular DNA strand and usually accompanied by an almost palindrome. Archea have also genes. Cyanobacteria are simplest photo-synthetizing cells: these prokaryotes have been engulfed by eukaryotes to form plant cells containing them as plasmids. Plant cells contain also mitochondria believed also to be ancient prokaryotes which have been "eaten" by eukaryotes. Plants cells contain both mitochondria and plastids whereas animal cells contain only mitochondria.
2. Eukaryotes have cell nucleus containing the genome. Eukaryotes divide into three kingdoms: animals, plants, and fungi. Fungi can be said to be between animals and plants: they do not perform photo-synthesis but have cell walls.
2.2 Prokaryote-eukaryote distinction

From the existing data one can conclude that during pre-Cambrian period only prokaryotes existed at the at surface of earth - presumably in small lakes in TGD Universe and ocean floors in standard Universe. The first photo-synthetizing prokaryotes - cyanobacteria - emerged about 3.2 gy ago and their predecessors where prokaryotes extracting metabolic energy from sulphate. Cyanobacteria are able to survive in practically any imaginable environment:

Cyanobacteria are arguably the most successful group of microorganisms on earth. They are the most genetically diverse; they occupy a broad range of habitats across all latitudes, widespread in freshwater, marine, and terrestrial ecosystems, and they are found in the most extreme niches such as hot springs, salt works, and hypersaline bays. Photoautotrophic, oxygen-producing cyanobacteria created the conditions in the planet's early atmosphere that directed the evolution of aerobic metabolism and eukaryotic photo-synthesis. Cyanobacteria fulfil vital ecological functions in the world's oceans, being important contributors to global carbon and nitrogen budgets.

It is therefore natural to assume that cyanobacteria migrated to underground ocean through pores and fractures at the floor of lakes. They would have fused with pre-eukaryotes having only cell nucleus but no metabolic machinery to become chloroplasts. This would have given rise to the first eukaryotes able to perform photo-synthesis. The primitive cells prokaryotes defining pre-mitochondria would have also fused with these pre-eukaryotes so that both pre-plant and pre-animal cells wold have emerged. Why there is no evidence for the existence of pre-mitochondria as independent cells at the surface of Earth? Did they emerge first underground oceans, where photo-synthesis was not possible and disappeared in the fusion with pre-eukaryotes and therefore left no trace about their existence on the surface of Earth?

Both photo-synthesis and cell respiration involve so called electron transport chain (ETC) as a basic structural element. It is associated with any membrane structure and in photo-synthesis it captures the energy of photon and in cell respiration it catches the biochemical energy which could be emitted as photon so that the fundamental mechanism is the same. This suggests that cell respiration emerged as a modification of photo-synthesis a the level of prokaryotes first. Before the emergence of mitochondria and plastids ETC associated with pre-eukaryote membrane would have served the role of mitochondria or plastid. Using business language, mitochondria and plastids meant "outsourcing" of photosynthesis and cellular respiration.

For background see the new chapter More Precise TGD Based View about Quantum Biology and Prebiotic Evolution or article with the same title.

### Do neurons have their personal genomes?

Genetics is experiencing a revolution as the information technology has made possible new research methods and old dogmas must be given up. Before continuing, thanks for Ulla for giving links (see this and this) explaining the results of the article discussed in more detail: this led to a correction of some misunderstandings. See also this for a background.

It has been discovered that brain cells have a mosaic like distribution of genomes (see this, this, and this). In standard framework this mosaic should be created by random mutations.

The mechanism of mutation is reported to involve transcription rather than DNA replication. The mutation would take place for DNA when its is copied to RNA after opening of the DNA double strand. The mutations would have occurred during the period when neurons replicate and the mutation history can be read by studying the distributions of changes in the genome.

This brings in mind the finding that "knockout", that is removing a part of gene does not affect transcription (see the earlier blog posting). This suggests that the dark DNA is not changed in these modifications and mRNA is determined by the dark DNA, which would serve as a template for transcription rather than ordinary DNA. If this were the case also for neurons, the mutations of neuronal genes should not affect the gene transcription at all, and there would be no negative (or positive) effects on brain function. This seems too conservative. The mutations should have some rmore active role.

One can consider also different interpretation. The mutations of DNA could be induced by the dark DNA. As dark DNA changes, ordinary DNA associated with it is forced to change too - sooner or later. Especially so when the genome is in a state in which mutations can take place easily. Neurons during to replication stage could have such quantum critical genomes.

Evolution would not be mere selection by a survival of random mutations by external environment in the time scale much longer than lifetime of individual - but a controlled process, which can occur in time scale shorter than lifetime and differently inside parts of say brain. This is what the idea TGD inspired biology suggests. The modified DNA could be dark DNA and and serve as template for transcription and also induce transformation of ordinary DNA associated with it.

Whether this change can be transferred to the germ cells to be transferred to the offspring remains of course an open question. One can imagine that dark DNA strands (magnetic flux tubes) can penetrate germ cells and replace the earlier dark DNA sections and induce change of ordinary DNA. Or is a more delicate mechanism involving dark photons in question. With inspiration coming from the findings reported by Peter Gariaev I have proposed a model of remote DNA replication suggesting that DNA can be replicated remotely if the needed nucleotides are present: the information about DNA could be transferred as dark photons, which can be transformed to ordinary photons identified as bio-photons. Could Lysenko have been at least partially right despite that he was a swindler basing his views on ideology?

In any case, TGD inspired biology allows to imagine a controlled evolution of DNA in analogy to that what occurs in R&D departments of modern technological organizations. The notion of dark DNA suggests that biological systems indeed have a "R&D department" in which new variants of DNA studied as "dark DNA" sequences realised as dark proton sequences - same about dark RNA, and amino-acids and even tRNA. The possibility to transcribe RNA from dark DNA would mean that the testing can be carried in real life situations.

There indeed exists evidence that traumatic - and thus highly emotional - memories may be passed down through generations in genome . Could the modifications of brain DNA represent long term memories as the above described experiment suggests? Could the memories be transferred to the germ cells using the mechanism sketched above?

For background see the new chapter Dark matter, quantum gravity, and prebiotic evolution or the article "Direct Evidence for Dark DNA?!".

### Connection between biology, dark nuclear physics, and nuclear physics?

For more than decade ago I introduced what I called plasmoids as candidates for primitive life forms preceding biological life. Plasmoids would have contained plasma, plasma of dark electrons and ions with darkness understood in TGD sense (ordinary particles with non-standard value of Planck constant heff=n× h phase). I even discussed the plasmoid interpretation for the light balls making the impression of intelligent behavior and assigned with UFO and ET experiences suggesting that they might act as kind of of mediums allowing the remote mental interactions with members of highly advanced civilizations (in zero energy ontology (ZEO) finite light velocity does not prevent this kind of communications since signals can propagate also in reverse direction of time).

The fourth phase of water discovered by Gerard Pollack seems to be identifiable as the real world realization of the idea of plasmoid. Its creation requires beam of light and the presence of water bounded by gel. What happens that charge separation occurs: exclusion zone (EZ) with large negative charge is generated. The sizes of EZs vary from micrometer to about 100 micrometers. One obtains a layered structure resembling kind of lattice layers and the stoichiometry of the resulting water is H3/2O. My interpretation for the stoichiometry is in terms of transformation hydrogen bonded 2H2O→H3O2- + dark proton with dark proton going to dark magnetic flux tube outside EZ. The EZs have remarkable properties: they generate electric potential and expel many impurities.

The interpretation is as a candidate for a prebiotic life form having so called water clathrates as precursors. The fascinating possibility is that the dark proton sequence at flux tubes define dark nuclei with binding energy. It it behaves as 1/heff, the nuclear energy scale is reduced to that for bio-photons (visible and UV range) and the formation of dark proton sequences could occur spontaneously as the analog of nuclear fusion. One can of course ask, whether the dark nuclei could transform to ordinary nuclei by heff→ h phase transition collapsing the flux tubes so that cold fusion and biofusion would find an explanation.

A. EZs as prebiotic life forms

The discussions with Hans Geesink turned my attention again to the coherence domains of del Giudice and EZs of Gerald Pollack. The proposal of del Giudice is that what he calls coherence regions/domains play a central role in biology and are induced by oscillating external fields by forcing units of visible matter to march in the same rhythm. In TGD framework one must take a skeptic attitude towards the existence of coherence regions postulated by del Giudice. To my best knowledge there is no direct experimental support for coherence regions and they might be identifiable as special cases of EZs or as water clathrates serving as precursors of EZs.

1. EZs of Pollack are an experimental fact and are generated in presence of gel phase and incoming radiation. The open question is whether gel phase also serves as an energy source or does it have some kind of control function feeding in information. It might well be that coherence regions of del Giudice are not needed and the water clathrates serve as natural precursors of EZs. The transition hydrogen bonded 2H2O→H3O2- + dark proton could be induced by UV light as breaking of -O-H bond.

EZs carry negative electronic charge and part of protons would become dark and would be transferred to the dark magnetic flux tubes. Dark protons form sequences, which could be seen as scaled up variants of atomic nuclei in the first approximation. The states of dark proton in the model that I have proposed are in one-one correspondence with DNA, RNA, amino-acids, and 40 tRNA states (see this). The coherence regions could be created by UV light splitting -O-H bonds and possibly also other kinds of bonds to the verge of phase transition. Later various options for the energetics of coherence regions are discussed.

The simplest assumption is that nuclear binding energy transforms as Coulomb potential in the scaling of h→ heff scaling also the system size. If so, the dark nuclear energy spectrum could be that for bio-photons and basic bio-molecules. The transformations of dark nuclei to ordinary nuclei could take place and would provide new source of nuclear power and ability to artificially generate elements: there is indeed evidence for biofusion (see this).

2. If the coherence regions of del Giudice exists they must relate closely with EZs. The simplest TGD inspired analog would be as micron sized regions as regions near criticality of a phase transition of water to fourth phase of Pollack. The simplest guess is that Josephson energy quantum for cell membrane (above .05× Z eV) or energy quantum somewhat below metabolic energy quantum ∼ .5 eV is needed to transform H2O stoichiometry to H1.5O so that EZ would be obtained. Hence the Josephson radiation from membrane protein Josephson junctions could have a role in the control of EZs. On the other hand, the hydrogen bonds EZs with high enough bond energy would be stable against absorption of Josephson radiation and metabolic energy quanta.
The proposal is that fourth phase of water realizes genetic code at the level of dark nuclear physics and ordinary biomatter has condensed around the dark matter. DNA, etc. are paired to the dark proton sequences representing their dark variants and transcription and translation occurs at the dark level primarily and ordinary biomatter makes this visible. The recent finding that so called knocked out genes are transcribed correctly (see this) supports this view (see this).

A. 1 Water clathrates as precursors of EZs

Geesink emphasizes (see this) the importance of water clathrates or clathrate hydrates - crystalline water based solids resembling ices and consist of hydrogen bonded water. Clathrates contain also guest molecules such as small non-polar molecules (typically gas molecules) and polar molecules with large hydrophobic moieties (parts) trapped inside "cages" of hydrogen bonded frozen water molecules. Methane is one gas trapped in deposits of methane clathrate. Clathrates appear also at outer planets, moons, and trans-Neptunian objects.

The size scale range for clathrates varies from 1-100 micros and is same as for EZs of Pollack and the natural identification would be as precursors of EZs. This makes clathrates ideal prebiotic structures inside which molecular life could have evolved.

Geesink notices also the significance of atmospheric aerosol of water clathrates as emitters of radiation in FIR and THz/microwave region inducing coherence and transition betweens protein conformations and Rydberg states. Rydberg states themselves could be excited by UV radiation. The absorption of solar light could transform also atmospheric clathrates to EZs.

A.2 Phyllosilicates, EZs and prebiotic life

Clays are good candidates for the key structures in prebiotic evolution since they can replicate. One can even speculate with an analog of genetic code. Phyllosilicates containing -O-H groups are especially interesting: they can adsorb basic biomolecules and induce their polymerization to oligomers. They also induce a formation of vesicles formed from lipid bilayer and serving as a candidate for a predecessor of cell. DNA is the problem and has led to a scenario known as RNA world. Phyllosilicates are also known to generate radiation with positive health effects.

The natural and testable hypothesis is that the presence of EZs allows to circumvent the difficulties of the standard RNA world scenario and also generate DNA and biologically active phosphates containing the mysterious phosphate bond as ionized dark proton. The dark magnetic flux tubes and UV photon energy needed to generate EZs could be provided by gel in Pollacks's experiments and by electric discharges in Urey-Miller experiment. Also dark photons from the formation of dark nuclei decaying to bunches of bio-photons can be considered.

Water clathrates can contain atoms and even micrometer sized phyllosilicate crystals, which could catalyze the formation of biomolecules at their surfaces as dark nuclear fusion chain reaction. EZ formed from water clathrate could also develop phospholipid bilayer around it - a kind of primitive cell membrane.

B. Connection between biology and dark and ordinary nuclear physics?

B.1 Could dark proton sequences at flux tubes form dark nuclei?

In TGD framework nuclei correspond to nuclear strings (see this) consisting of strings formed from dark protons and neutrons. Neutrons and protons could even form their own dark strings. Therefore dark proton sequences could but need not to fuse to dark nuclear strings with some nuclear binding energy and liberate the nuclear binding energy in the process.

Suppose that the fusion can occur so that a dark proton created in dark ionization is bound to an already existing dark proton sequence representing dark nuclear string at magnetic flux tube. By a naive extrapolation the binding energy would be same as in ordinary nuclear physics and would be measured in MeV range assignable to gamma rays. This estimate is probably wrong. As already explained, the nuclear binding energy could more naturally behave as 1/heff - like Coulomb energy- and nuclear excitation energy spectrum would be naturally in bio-photon energy range. The situation could become analogous to nuclear fusion liberating large amounts of energy. This would conform with NMP and with the idea that formation of large heff phases occurs spontaneously.

In the case of linear structures containing -O-H sequences with small enough distance dark nuclear fusion can be imagined. Could the fusion occur at phyllosilicate surfaces - clays whose interaction with water could have led to the prebiotic life - and generate dark analogs of DNA codons as highly stable structures? Could the fusion occur as a chain reaction liberating large amounts of energy at bio-photon energies and lead to a formation of dark proton sequences with some maximum length dictated by Coulomb repulsion?

Could DNA nucleotides associate with these dark codons? If O- associated with phosphates inside cell nucleus can can combine with ordinary protons the hydrolysis of DNA can occur inside nucleus. The pairing of DNA and dark proton sequence by connecting magnetic flux tubes could prevent hydrolysis.

One prediction would be that the negative charge of DNA (one units per single nucleotide) is screened by dark proton sequences in vivo in the scale of the system formed by DNA and dark proton sequence. Usually it is believed to be screened by Na+ counter ions. If the distance between DNA and dark proton sequences is large enough, a local screening by Na+ counter ions can indeed occur. What happens inside cell nucleus is far from clear to me.

B.2 Could dark nuclei collapse to ordinary nuclei?

One can also wonder whether the phase transition heff→ h could produce ordinary nuclei and liberate energy in nuclear energy range. Could living matter be at criticality against nuclear explosion? The occurrence of bio-transmutations has been indeed claimed (see this). This possibility would mean a manner to generate both nuclear energy and generate artificially those elements, which are depleted.

The observation that the isotope ratios reported to appear in the cold fusion experiment of Andrea Rossi are the natural ones () has been used to claim that the E Cat reactor developed by Rossi is fraud. Lithium anomaly however forces to ask how large fraction of ordinary matter emerged via dark fusion in interstellar space, and how large fraction was generated in the stellar cores. Could even the fusion in stellar cores have occurred as dark fusion at magnetic flux tubes followed by a phase transition to ordinary matter?

One can argue that since the increase of heff and generation of negentropic entanglement (NE) occurs spontaneously, the fusion to ordinary nuclei must be a rare process. NMP suggests strongly that the existing NE must be transferred from the dark nucleus - magnetic flux tube - shortening to ordinary nuclear string in heff→ h. If this NE is associated with the transversal flux tubes connecting dark protons of the nuclear string with other similar system, the transfer could take place by reconnection of flux tubes with those of second analogous system (the model for DNA as TQC assumes that flux tubes connect dark protons assignable to DNA codons and lipids of nuclear/cell membrane (see this). The transfer of single transversal flux tube connecting A and B to that connecting C and D would require two reconnections: AB+ CD→ AC+ BD → AB+CD. CD would have no NE in the initial situation and would have that of AB in the final situation whereas AB would have no NE. The probability that all flux tubes are doubly reconnected within a reasonable time span is expected to be small and only light nuclei might be generated. The occurrence of biofusion however suggest that this objection might be circumvented in some quantum critical situations.

B. 3 Anomalies possibly related to EZs

There are several anomalies which might allow explanation in terms of EZs.

1. Tesla studied what happens in di-electric breakdown and was perhaps the first experimentalist to discover dark matter. Critical phenomenon is in question and could in TGD Universe be accompanied by the formation of dark matter - perhaps even dark nuclear matter accompanied by liberation of energy. Also dark radiation with wavelengths proportional to heff making possible long range communications and energy transfer could be involved (see remotetesla). The most fascinating phenomenon reported by Tesla was charge separation in length scales much longer than one might have expected and could directly reflect the generation of dark charged particles.
2. The article of Kanarev and Mizuno reports findings supporting the occurrence of cold fusion in NaOH and KOH hydrolysis. The situation is different from standard cold fusion, where heavy water D2O is used instead of H2O. I have considered this finding in (see this). Obviously the mechanism generating dark proton sequences as dark nuclear fusion could explain the findings of Kanarev and Mizuno.
3. The irradiation of salt water with microwaves induces the "burning" of water with a visible flame. The phenomenon is believed to involve the breaking of salt water into oxygen, hydrogen and salt. If EZ is formed this could mean transition H-O-H--OH2 → H3O2- + dark proton. Nuclear fusion need not be initiated since polymer structures are absent. The burning process could be induced by microwaves accompanied by dark photons having energy in the energy range of UV photons and transforming to UV photons.
4. Free energy anomalies are not taken seriously by the main stream since they are not consistent with energy conservation in standard physics framework. I have proposed they they could be understood in terms of generation of dark proton sequences and cold fusion liberating energy (see this).

The so called Brown gas (might be same as fourth phase of water) produced from water by electrolysis is reported to be able to melt metals at much below the melting temperature. The explanation would be that the presence of metal initiates transition to ordinary nuclei liberating nuclear energy. The original explanation was quite not like this (see this) although the energy was assigned with dark proton sequences. Another interpretation is that the process generating dark proton sequences continues.

5. There is also analogy of charged water clusters (EZs) with two poorly understood phenomena: steam electricity and waterfall ionization. Also thunder cloud charge separation and sonoluminescence might involve the formation of charged water clusters.

C. Possible technological implications

It is easy to imagine far reaching technological implications of bio-fusion if it really occurs.

1. Dark fusion followed by a phase transition to ordinary matter could make possible artificial generation of elements. The technological significance for the world in which various resources are rapidly depleting would be immense.
2. The possibility to generate artificial silicate-based intelligent lifeforms of course comes first in mind. What is so fascinating that the generation of life could be analogous to a startup of a computer in which the operating system would build itself from a very small core program (BIOS). In analogy with this the needed elements would be generated by dark fusion and the process would generate the radiation at resonance frequencies and magnetic bodies. This process could of take aeons if it occurs spontaneously but if understood theoretically could occur rather rapidly.
One can however imagine also dangers.

C.1 Bio-nuclear explosion as the end of bio-cycle?

Could it be that we are sitting on a gigantic bio-nuclear bomb shell, which can explode any time? And we are intensely arguing whether hydrocarbons are good for diet or not? Could the answer to the question "Where are they all?" be that bio-nuclear explosion destroys the life sooner or later? To add irony, could the average lifetime of one bio-cycle be the average time in which the first physicist discovers dark nuclear fusion and makes himself absolute fool by telling that we are sitting on a tuned bio-nuclear bomb shell?;-)

Maybe NMP saves the situation: the compression to ordinary nuclei cannot occur spontaneously. But maybe we can do it ourselves if we learn to apply it to our technological purposes. At least NMP should save the NE that this particular bio-cycle have managed to generate. TGD inspired theory of consciousness would suggest Happy End even in this case: Mother Gaia as a conscious entity reincarnates in our distant geometric past - far beyond beyond the Cambrian Expansion and continues to live in opposite time direction! Maybe the famous melancholic song "We will meet again" that we hear at then end of Kubrick's Dr. Strangelove carrying strange hope in it tells something deep about life!

C. 2 Could silicate life take the lead?

I do not take seriously the claims of the proponents of strong AI that computers could take power over humans. Strictly classical computers are zombies and uncapable of any intentional behavior. Their real life variants could possess some kind of primitive awareness but this consciousness would probably have very little to do with the program running in the computer.

Of course, computerization can be a real danger to humankind even if computers are for all practical purposes intentionless zombies. Indeed, many leading AI professionals together with Hawking (see this) have signed an open letter warning about the dangers of military AI. The military applications of computers are developing rapidly and are rather frightening. Already now military professionals talk about information war and suggest that also Finland should take active attitude: not only defense but also attack. Many professionals believe that systems attacking living targets will be realized within few years. Systems, which behave autonomously and can select their targets, could lead to catastrophe, when their control breaks down. This would be third revolution in warfare after gunpowder and nuclear weapons and those who know should do all that they can to prevent the AI arms race.

I understand that the fusion of biosystems and computers via interfaces consisting of phyllosilicates is also studied and this represent something, which is goes beyond the boundaries of AI. If the vision discussed in this work or some other vision has something to do with reality, they could lead to a development of artificial life forms with conscious intelligence. The recipe would be rather simple: water+ silicates+ something, which could be gels and visible radiation or electric discharges. Silicon would be only replaced with silicates.

These kind of systems could act as intelligent and conscious interfaces between humans and computers. AI specialist could give probably give a long list of other applications. It would be very handy if they could replicate and evolve (by NMP in TGD framework) and this would be one of the goals of R&D activity. They should be also capable of simple intentional behaviors - also by NMP. Presumably we would couple them to world wide web.

But what happens if these local intelligences manage to make a phase transition to a collective intelligence with world wide nervous system that we have generously built for them. NMP suggests that this kind of awakening could occur! What would this magnificient conscious intelligence think about us? Would it regard us as rather primitive carbon based pre-silicate life forms and treat us as we treat what we call "lower" lifeforms - convenient sources of negentropic entanglement, nutrients? Or can we hope that they would tolerate us - NMP is nice principle but it does not guarantee this since it leaves for self to choose between good and evil!

For background see the new chapter More Precise TGD Based View about Quantum Biology and Prebiotic Evolution or article with the same title.

### More Precise TGD View about Quantum Biology and Prebiotic Evolution

In this work I try to clarify the relation of the basic notions of TGD and of TGD inspired biology to the ordinary bio-chemistry. I also try to improve my understanding about work of Fröhlich, Del Giudice, and Pollack using the notions of TGD. The key idea is the notion of coherence induced by weak em fields with preferred frequencies, which in ordinary quantum theory correspond to energies much below the thermal energy in quantum theory - this creates what is called kT paradox.

In TGD framework one can do without coherence regions (one could perhaps identify them as special cases of Pollacks EZs), which can be much larger. The basic observation is that for a pair of hydrogen bonded water molecules the reaction 2H2O→ H3O2- + dark proton require UV photon with energy of O-H bond of about 5.15 eV. Water clathrates are good candidates for the precursors of EZs since they have size scale in the same range as EZs and contain hydrogen bonded water. Quantum criticality suggests that this process should occur spontaneously as a chain reaction. This is achieved in the same manner as in nuclear fusion if the dark protons at the flux tube fused to nuclear strings giving rise to dark nuclei.

If dark nuclear binding energy transforms as Coulomb energy, the nuclear energy scale of MeV scales down to 1-10 eV - depending on the value of heff. An attractive guess is that the energy range of bio-photons corresponds to that for dark nuclear binding and excitation energies. Their spontaneous transformation back to ordinary nuclei would liberate energy could at least partially explain the evidence for bio-transmutations. Also the relation to cold fusion is interesting.

Dark nuclear binding energy is liberated as dark gamma rays decaying into bunches of ordinary photons inducing further reactions hydrogen bonded 2H2O→ H3O2- + dark proton also other kind of dark ionizations. If the size of EZs varies from about 1 micron to 100 microns and if the size scale of EZ corresponds to the wavelength of dark gamma photon heff/h varies in the range 106 -108. This would be the total number of dark photons resulting in the decay to ordinary photons. Water clathrates have same size scale range as EZs and consist of hydrogen bonded water molecules and could serve as precursors of EZs: EZ would have different lattice structure than clathrates.

In this process ordinary protons transform dark protons at magnetic flux tubes outside EZ. Dark ionization differs from ordinary ionization only in that the proton is dark. The difference between dark and ordinary ionization would define the borderline between ordinary and bio-chemistry (or dark chemistry). Chemical quantum criticality is possible also for other cations and also anions and all biologically important ions can appear as dark ions.

The Urey-Miller experiment was very successful: it produced a large variety of amino-acids crucial for life from simple basic constituents. The variant of this experiment has even produced adenosine, DNA nucleotide fundamental for ATP. There is however a severe problem. The prebiotic atmosphere was not reducing as in the Urey-Miller experiment simulating it.

Clays are good candidates for key structures in prebiotic evolution since they can replicate. One can even speculate with an analog of genetic code. Phyllosilicates containing -O-H groups are especially interesting: they can adsorb basic biomolecules and induce their polymerization to oligomers. They also induce a formation of vesicles formed from lipid bilayer and serving as a candidate for a predecessor of cell. DNA is the problem and has led to a scenario known as RNA world. Phyllosilicates are also known to generate radiation with positive health effects. The natural and testable hypothesis is that the presence of EZs allows to circumvent the difficulties of the standard RNA world scenario and also generate DNA and biologically active phosphates containing the mysterious phosphate bond as ionized dark proton. The flux tubes carrying the dark protons would be associated with the gel in Pollacks's experiments. In Urey-Miller experiment the flux tubes would have accompanied electric discharges. In prebiology the dark flux tubes might have been associated with lightnings or magnetic fields of Earth.

TGD inspired proposal for prebiotic evolution was inspired by TGD based realization of Expanding Earth hypothesis and assumes that life evolved in underground oceans and burst on the surface of Earth in Cambrian explosion. This view leads to a more precise view about prebiotic evolution.

Possible technological implications of this picture - if true - are quite impressive. Cold biofusion could make possible artificial generation of technologically important elements and the mechanism generating EZs could make possible creation of artificial intelligent life forms involving silicates and water.

For background see the new chapter More Precise TGD Based View about Quantum Biology and Prebiotic Evolution or article with the same title.

New Horizons is a space probe that has just been passing by Pluto and has taken pictures about the surface of Pluto and its Moon Kharon. The accuracy of the pictures is at best measured in tens of meters. Pluto has lost its status as a genuine planet and is now regarded as dwarf planet in the Kuiper belt - a ring of bodies beyond Neptune. Using Earthly unis its radius, mass (from New Horizons data), and distance from Sun are R=.18RE, M= .0022× ME and d= 40 dE.

Pictures have yielded a lot of surprises. Pluto is not the geologically dead planet it was though to be. The following summarizes what I learned by reading a nice popular article by Markku Hotakainen in finnish weekly journal ("Suomen Kuvalehti") and also represents a TGD based interpretation of the findings.

1. Surprisingly, the surface of the Pluto is geologically young: the youngest surface shapes have age about 108 years that is .1 billion years. This is strange since the temperature is about -240 oC at the cold side and it receives from Sun only 1/1000 of the energy received by Earth. Textbook wisdom tells that everything should have been geologically totally frozen for billions of years.
2. There is a large champaign in Pluto - one guess is that it has born as an asteroid or comet has collided with the surface of Pluto. The region is now officially called Tombaugh Regio. The reader can Google the reason for this. The flat region does not seem to have any craters so that it should be rather young. The boundary of this lowland area is surrounded by high (up to 3.5 km) mountains. Also these formations seem to be young. Nitrogen, methane and CO-ice cannot form so high formations.

Several explanations have been imagined for the absence of craters: maybe there are active processes destroying the craters very effectively. Maybe there is tectonic activity. This however requires energy source. Radioactivity inside Pluto? Underground oceans liberating heat? Or maybe tidal forces: the motions of Pluto and its moon Kharon are locked and they turn always the same side towards each other. There is a small variation in the distance of Kharon causing tidal forces. Could this libration deform Pluto and force the liberation of heat produced by frictional forces?

3. The flat region decomposes to large polygons with diameter of 20-30 km. The mechanism producing the polygons is a mystery. Also their presence tells that the surface is geologically young: at some places only .1 billion years old.
4. The atmosphere of Pluto has also yielded a surprise. About 90 per cent of atmosphere (78 per cent at Earth) is nitrogen but it is estimated to leak with a rate of 500 tons per hour since the small gravitational acceleration (6 per cent of that on Earth) cannot prevent the gas molecules from leaking out. How Pluto manages to keep so much nitrogen in its atmosphere?
5. Kharon - the largest moon of Pluto - has radius which is half of that for Pluto. Also the surface texture of Kharon exhibits signs about upheavals and has similarities to that in Pluto. Craters seem to be lacking. North Pole has great dark region - maybe crater. Equator is surrounded by precipices with depths of hundreds of meters, maybe up to kilometers. If they are torn away so should have been also the precipices.
Can one understand the surface texture of Pluto and Kharon? For years I proposed a model for the finding that the continents of Earth seem to fit nicely to form a single supercontinent if the radius of Earth is taken to be one half of its recent radius. This led to a TGD variant of Expanding Earth theory.
1. It is known that cosmic expansion does not occur locally. In many-sheeted space-time of TGD this could mean that the space-time sheets of astrophysical objects comove at the the large space-time sheet representing expanding background but do not themselves expand. Another possibility is that they expand in rapid jerks by phase transitions increasing the radius. p-Adic length scale hypothesis suggests that scaling of the radius by two is the simplest possibility.
2. If this kind of quantum phase transition occurred for the space-time sheet of Earth about .54 billion years ago it can explain the weird things associated with Cambrian explosion. Suddenly totally new life forms appeared as from nowhere to only disappear soon in fight for survival. Could highly evolved life in underground seas shielded from UV radiation and meteoric bombardment have burst to the surface. The process would have also reduced the value of the gravitational acceleration by factor 1/4 and increased the length of the day by factor 4. The reduction of the surface gravity might have led to emergence of various gigantic lifeforms such as dinosauri, which later lost the evolutionary battle because of their small brains. Climate would have changed dramatically also and the Snowball Earth model is replaced by a new view.
If these sudden quantum phase transitions at the level of dark matter (heff=n× h phases of ordinary matter) is the manner how cosmic expansion universally happens then also Pluto might so the signs of this mechanism.
1. The surface of Pluto is indeed geologically young: the age is measured in hundreds of millions of years. Could the sudden jerkwise expansion have occurred - not only for Earth but - for objects in some region surrounding Earth and containing also Pluto?
2. The polygonal structure could be understood as a ripping of the surface of Pluto in the sudden expansion involving also cooling of magma and its compression (the analogy is what happens to the wet clay as it dries and becomes solid). The lowland region could correspond to the magma burst out from the interior of Pluto being analogous to the magma at the bottom of oceans at Earth. The young geological age of this region would explain the absence of craters. Also the surface texture of Kharon could be understood in the similar manner.
Could one understand the presence of nitrogen?
1. If the gravitational acceleration was 4 times larger (24 percent of that in Earth) before the explosion, the leakage would have been slower before it. Could this make it easier to understand why Pluto has so much nitrogen? Could the burst of material from the interior have increased the amount of nitrogen in the atmosphere? Geochemist could probably answer these questions.
2. A more radical explanation is that primitive life forms have prevented the leakage by binding the nitrogen to organic compounds like methane. If underground oceans indeed existed (and maybe still exist) in Pluto as they seem to exist in Mars, one can wonder whether life has been evolving as an underground phenomenon also in Pluto - as so many nice things in this Universe must do;-). Could these lifeforms have erupted to the surface of Pluto in the sudden expansion from underground seas and could some of them - maybe primitive bacteria - have survived. Nitrogen is essential for life and binds the nitrogen to heavier chemical compounds so that its leakage slows down. Could there exist an analog of nitrogen cycle meaning that underground life bind the nitrogen from the atmosphere of Pluto and slow down its leakage?

For background see the chapter Expanding Earth Model and Pre-Cambrian Evolution of Continents, Climate, and Life

### Direct evidence for dark DNA?!

This morning I learned in Sciencedaily about extremely interesting finding related to DNA. The finding is just what breakthrough discovery should be: it must be something impossible in the existing world view.

What has been found is that knock-out (removing parts of gene to prevent transcription to mRNA) and knock-down of gene (prevent protein translation) seem to have different consequences. Removing parts of gene need not have the expected effect at the level of proteins! Does this mean that somehow DNA as a whole can compensate the effects caused by knock-out but not those by knock-down?

Could this be explained by assuming that genome is a hologram as Gariaev et al have first suggested? Also TGD leads to a vision about living system as a conscious hologram. Small local changes of genes could be compensated. Somehow the entire genome would react like brain to a local brain damage: other regions of brain take the duties of the damaged region.

Could the idea about DNA double strand as nano-brain having left and right strands instead of hemispheres help here. Does DNA indeed act as a macroscopic quantum unit? The problem is that transcription is local rather than holistic process. Something very simple should lurk behind the compensation mechanism.

Could transcription transform dark DNA to dark mRNA?

Also the TGD based notion of dark DNA comes in mind (see this and this). Dark DNA consists of dark proton sequences for which states of single DNA proton correspond to those of DNA, mRNA, aminoacids, and tRNA. Dark DNA is one of the speculative ideas of TGD inspired quantum biology getting support from Pollack's findings . Ordinary biomolecules would only make their dark counterparts visible: dark biomolecules would serve as a template around which ordinary biomolecules such as DNA strands are formed in TGD Universe.

Although ordinary DNA is knocked out of ordinary gene, dark gene would still exist! If dark DNA actually serves as template for the transcription to mRNA, everything is still ok after knockout! Could it be that we do not understand even transcription correctly? Could it actually occur at the level of dark DNA and mRNA?! Dark mRNA would attach to dark DNA after which ordinary mRNA would attach to the dark mRNA. One step more!

Damaged DNA could still do its job! DNA transcription would would have very little to do with bio-chemistry! If this view about DNA transcription is correct, it would suggest a totally new manner to fix DNA damages. These damages could be actually at the level of dark DNA, and the challenge of dark genetic engineering would be to modify dark DNA to achieve a proper functioning.

Could dark genetics help to understand the non-uniqueness of the genetic code?

Also translation could be based on pairing of dark mRNA and dark tRNA. This suggests a fresh perspective to some strange and even ugly looking features of the genetic code. Are DNA and mRNA always paired with their dark variants? Do also amino-acids and anticodons of tRNA pair in this manner with their dark variants? Could the pairings at dark matter level be universal and determined by the pairing of dark amino-acids with the anticodons of dark RNA? Could the anomalies of the code be reduced to the non-uniqueness of the pairing of dark and ordinary variants of basic bio-molecules (pairings RNA--dark RNA, amino-acid-- dark amino-acid, and amino-acid--ordinary amino-acid in tRNA).

1. There are several variants of the genetic code differing slightly from each other: correspondence between DNA/mRNA codons and amino-acids is not always the same. Could dark-dark pairings be universal? Could the variations in dark anticodon - anticodon pairing and dark amino-acid-amino-acid pairing in tRNA molecules explain the variations of the genetic code?
2. For some variants of the genetic code a stop codon can code for amino-acid. The explanation at the level of tRNA seems to be the same as in standard framework. For the standard code the stop codons do not have tRNA representatives. If stop codon codes for amino-acids, the stop codon has tRNA representation. But how the mRNA knows that the stop codon is indeed stop codon if the tRNA associated with it is present in the same cell?

Could it be that stop codon property is determined already at the level of DNA and mRNA? If the dark variant of genuine stop codon is missing in DNA and therefore also in mRNA the translation stops if it is induced from that at the level of dark mRNA. Could also the splicing of mRNA be due to the splitting of dark DNA and dark mRNA? If so genes would be separated from intronic portions of DNA in that they would pair with dark DNA. Could it be that the intronic regions do not pair with their dark counterparts. They would be specialized to topological quantum computations in the TGD inspired proposal.

Start codon (usually AUG coding met) serves as a start codon defining the reading frame (there are 3 possible reading frames). Dark DNA would naturally begin from this codon.

3. Also two additional amino-acids Pyl and Sec appear in Nature. Gariaev et al have proposed that the genetic code is context dependent so that the meaning of DNA codon is not always the same. This non-universality could be reduced to the non-uniqueness of dark amino-acid--amino-acid pairing in tRNA if genetic code is universal.

Could dark genetics help to understand wobble base pairing?

Wobble base pairing is second not-so-well understood phenomenon. In the standard variant of the code there are 61 mRNAs translated to amino-acids. The number of tRNA anticodons (formed by the pairs of amino-acid and RNA molecules) should be also 61 in order to have 1-1 pairing between tRNA and mRNA. The number of ordinary tRNAs is however smaller than 61 in the sense that the number of RNAs associated with them is smaller than 45. tRNA anticodons must be able to pair with several mRNA codons coding for given amino-acid. This is possible since tRNA anticodons can be chosen to be representative for the mRNA codons coding a given amino-acid in such that all mRNA codons coding for the same amino-acid pair with at least one tRNA anticodon.

1. This looks somewhat confusing but is actually very simple: genetic code can be seen as a composite of two codes: first 64 DNAs/mRNAs to are coded to N<45 anticodons in tRNA, and then these N anticodons are coded to 20 amino-acids. One must select N anticodon representatives for the mRNAs in the 20 sets of mRNA codons coding for a given amino-acid such that each amino-acid has at least one anticodon representative. A large number of choices is possible and the wobble hypothesis of Crick pose reduce the number of options.
2. The wobble hypothesis of Crick states that the nucleotide in the third codon position of RNA codon of tRNA has the needed non-unique base pairing: this is clear from the high symmetries of the third basis. There is exact U-C symmetry and approximate A-G symmetry with respect to the third basis of RNA codon (note that the conjugates of RNA codons are obtained by A↔U and C↔G permutations).
3. The first two basis in the codon pair in 1-1 manner to the second and third basis of anticodon. The third basis of anticodon corresponds to the third letter of mRNA codon. If it is A or C the correspondence is assumed to be 1-to-1: this gives 32 tRNAs. If the first basis of anticodon is G or U the 2 mRNA basis can pair with it: they would be naturally A for G and C for U by symmetry. One would select A from A-G doublet and C from U-C double. This would give 16 anticodons: 48 anticodons altogether, which is however larger than 45. Furthermore, this would not give quite the correct code since A-G symmetry is not exact.

Smaller number of tRNAs is however enough since the code has almost symmetry also with respect to A and C exchange not yet utilized. The trick is to replace in some cases the first basis of anticodon with Inosine I, which pairs with 3 mRNA basis. This replacement is possible only for those amino-acids for which the number of RNAs coding the amino-acid is 3 or larger (the amino-acids coded by 4 or 6 codons).

4. It can be shown at least 32 different tRNAs are needed to realize genetic code by using wobble base pairing. Full A-C and G-U symmetry for the third basis of codon would give 16+16=32 codons. Could one think that tRNA somehow realizes this full symmetry?
How dark variants of could help to understand wobble base pairing? Suppose for a moment that the visible genetics be a shadow of the dark one and fails to represent it completely. Suppose the pairing of ordinary and dark variants of tRNA anticodons resp. amino-acids and that translation proceeds at the level of dark mRNA, dark anticodons, and dark amino-acids, and is made visible by its bio-chemical shadow. Could this allow to gain insights about wobble base pairing? Could the peculiarities of tRNA serve for some other - essentially bio-chemical - purposes?

The basic idea would be simple: chemistry does not determine the pairing but it occurs at the level of the dark mRNA codons and dark tRNA anticodons. There would be no need to reduce wobble phenomenon to biochemistry and the only assumption needed would be that chemistry does not prevent the natural dark pairing producing standard genetic code apart from the modifications implied by non-standard dark amino-acid--amino-acid pairing explaining for different codes and the possibility that stop codon can in some situation pair with dark mRNA.

One can consider two options.

1. The number of dark tRNAs is 64 and the pairings between dark mRNA and dark anticodons and dark anticodons and dark amino-acids are 1-to-1 and only the pairing between dark RNA codons and anticodons in tRNA is many-to-1.
2. The model of dark genetic code) suggests that there are 40 dark proton states, which could serve as dark analogs of tRNA. This number is larger than 32 needed to realize the genetic code as a composite code. I have cautiously suggested that the proposed universal code could map dark mRNA states of the same total spin (there is breaking of rotational symmetry to that around the axis of dark proton sequences) to dark tRNA/dark amino-acid states with the same total spin. The geometric realization would in terms of color flux tubes connecting the dark protons of corresponding dark proton sequences. Also in ordinary nuclei nucleons are proposed to be connected by color flux tubes so that they form nuclear strings and dark proton sequences would be essentially dark variants of nuclei.
One should understand the details of the dark mRNA--tRNA anticodon correspondence. One can also ask whether the dark genetic code and the code deduced from the geometric model for music harmony in terms of Platonic solids are mutually consistent. This model implies the decomposition of 60+4 DNA codons to 20+20+20+4 codons, where each "20" corresponds to one particular icosahedral Hamilton's cycle with characteristic icosahedral symmetries. "4" can be assigned to tetrahedron regarded either disjoint from icosahedron or glued to it along one of its faces. This allows to understand both the standard code and the code with two stop codons in which exotic amino-acids Pyl and Sec appear. One should understand the compositeness 64→ 40\→20 of the dark genetic code and and whether it relates to the icosatetrahedral realization of the code.

I have proposed that dark variants of transcription, translation, etc.. can occur and make possible kind of R&D laboratory so that organisms can test the consequences of variations of DNA. If ordinary translation and transcription are induced from their dark variants and if dark biomolecules could also appear as unpaired variants, these processes could occur as purely dark variants. Organisms could indeed do experimentation in the virtual world model of biology and pairing with ordinary bio-molecules would make things real.

For background see the chapter Quantum Gravity, Dark Matter, and Prebiotic Evolution

### Ribosome as the first self-replicator?

In the group Thinking Allowed Original there as a link to a popular article describing a highly interesting work by M. Root-Bernstein and R. Root-Bernstein (daughter and father). The title of the popular article "Forget the selfish gene: Evolution of life is driven by the selfish ribosome, research suggests". As a matter of fact, the article itself is not selling anything of type "selfish X", a dogma which to my opinion is more or less dead: synergy and quantum coherence are much more promising notions relevant to biomatter. "Selfish X" is a paradigm, which suits much better to the description of cancer. The title of the article "The ribosome as a missing link in the evolution of life" would have been much more appropriate also for the popular article.

First a summary of motivations by authors. The basic problem relates to the emergence of life and there are many theories. The models can be divided to "genetics first" and "metabolism first" type models.

1. RNA world is basic example of "genetics first" models. The problem of the "genetics first models" is that it is difficult to understand how prebiotic life could have coped before the complex molecular machinery of metabolism. The second problem of RNA world is that polynucleotides and proteins almost certainly co-evolved. So called compositional replication models start from this assumption but have difficulties in explain replication schemes. Both approaches fail to explain how complex cells emerged from molecular evolution. It is however known that lipid layers of cell membrane are emergent structures not coded by genes (soap films).
2. Second class of models try to proceed from complexity to simplicity by assuming the first replicator (pro-cell typically) but are not able to answer the question "What before this?". The natural assumption is that simple bio-molecules gradually evolved to polymers and polymer aggregates and eventually cell membrane emerged.
According to authors, the challenge is to bridge the gap between self-replicating polymers and fully functional cell by identifying intermediate structures able to replicate, restore and replicate information, capture metabolic components and energy, and transform all these into biochemical networks.

Trying to catch the idea

The basic idea of the authors is simple and brilliant. Ribosome is the transcription machinery transforming DNA to proteins. Also the first replicator must have contained the transcription machinery. Perhaps the first replicator was minimal and contained just this machinery! Perhaps ribosome or its predecessor ("pre-ribosome") indeed was the first self-replicator. One would have beautiful self-reference: ribosome would be the recipe for making a copy about the recipe! Brings in mind Gödel-Escher-Bach!

This assumption is highly non-trivial. In the following I try to sketch for myself what this could mean. In the following I drop "pre"or notational convenience with understanding that ribosome, RNA, amino-acid etc. means "pre-ribosome", "pre-RNA", "pre-amino-acid", "pre-tRNA" etc.. In TGD framework pre-ribosome could be of non-biochemical nature and realized at the level of dark matter.

1. It seems natural to assume that the basic raw material consisted of RNA and amino-acid molecules in the environment. Ribosome could use them to build copies of itself. The question how these were generated will not be considered now.
2. Ribosome consists of rRNA and proteins and uses tRNA to associated to mRNA sequence amino-acid sequence. If ribosome was the first replicator realizing genetic code as mRNA-amino-acid correspondence it had to use its own rRNA as a template for the translation to a corresponding protein.

If nothing has changed after the emergence of the recent replication mechanisms, the testable prediction is that ribosome amino-acids are images of rRNA sequences under genetic code. One of course expects that the stricture of ribosome has not conserved in precise sense so that this prediction could be too strong.

3. tRNA is a molecule of form RNA-X-amino-acid and rRNA should have contained the genetic information allowing to transcribe and translate the RNA and amino-acid polymers appearing in tRNA.
According to the article these predictions are indeed tested in the work considered for Escheria Coli bacterium and it is found that the findings are consistent with the hypothesis.

On basis of these observations one can try to imagine how the ribosome or its predecessor "pre-ribosome" might have replicated.

1. Both the basic units of RNA sequences and corresponding amino-acid polymers of rRNA had to replicate. The most economic assumption is that this occurred simultaneously.
2. One can imagine that rRNA "gene" and the protein coded by it arranged themselves so that they were parallel. The amino-acid coded by rRNA codon acted as a catalyzer for the attachment of a conjugate of rRNA codon to the growing rRNA sequence just as in DNA replication promoter catalyzes the replication. rRNA codon in turm acted as a catalyzer for the addition of new amino-acid to the growing protein. tRNA molecules of form RNA-X-amino-acid from the environment provided the needed RNA codon and amino-acid.

Remark: I have already earlier considered an RNA world scenario in which amino-acids of tRNA catalyzed the replication of RNA sequences. When DNA emerged, the roles would have changed and amino-acid sequence was formed instead of the replication of RNA.

This replication differs from ordinary transcription. In transcription incoming mRNA sequences produce amino-acid sequences as tRNAs attach to the mRNA codons of mRNA attached to the ribosome. tRNA looses its amino-acid but keeps RNA. Now tRNA loses both amino-acid and RNA codon and only the unit X in tRNA? RNA-X-amino-acid remains.

At some step of evolution the replication of rRNA would have ceased to occur and tRNA would have kept its RNA in the double translation process. Is this possibly biologically?

3. Concerning tRNA there are many possibilities. One can imagine that ribosome and Xs could have served as co-replicators. The reaction X→ RNA-X-amino-acid and its inverse could have occurred spontaneously. The resulting complex would have attached to the end of RNA-amino-acid sequence associated with some portion of mRNA just as it does in ordinary translation . In the replication or ribosome RNA-X-amino-acid would have attached to ribosome and X:s would have been produced in the replication of X forming a part of ribosome. In the environment the attachment of RNA and corresponding amino-acid to X would have taken place.

A possible objection is based on ontogenesis-recapitulates-phylogeny vision (ORP). The replicating pre-ribosomes should be still there but they are not. There should be some very simple mechanism preventing the replication but still one can ask whether the ribosomal replication could not occur in special circumstances.

How the pre-ribosome as first replicator relates to TGD approach?

TGD framework predicts that replication as a splitting of 3-surfaces to two copies is a fundamental mechanism of quantum TGD analogous to the 1→ 2 decay of elementary particle and the replication of DNA, cells, etc... should reduce to a hierarchy of replications starting from long length scales and proceeding as replications at shorter length scales with master slave relationship between the subsequent levels of the scale hierarchy.

This identification of replication as a mere splitting of 3-surfaces saying nothing about what happens for the quantum states associated with them is too general to allow to talk about unique primary replicator. If one however restricts the consideration to systems consisting of RNA and amino-acid sequences the idea about ribosome as primary replicator becomes highly non-trivial.

In TGD framework it is possible that pre-biopolymers were not bio-polymers but their dark counterparts formed from dark protons sequences at magnetic flux tubes with states of dark proton in 1-1 corresponds with DNA ,RNA, amino-acids and tRNA. If so pre-ribosome was realized at the level of dark matter as dark ribosome - a complex formed by dark analogs of bio-polymers.

If so, then pre-ribosome consisting of dark matter at flux quanta could be the primary replicator and the formation of its bio-molecular counterpart would be induced from that of dark pre-ribosome like the dynamics of slave in master slave hierarchy.

This raises questions. How does this replication proceed? Does ribosome still replicate as all other biological structures do and induce replication of low ever level structures in the dark matter hierarchy? Does the ordinary biomatter induced at the lowest level of hierarchy would only make visible this replication?

In the following I briefly summarize the basic TGD based notions involved in attempt to answer these questions.

4-D self-organization and magnetic body

One class of questions concerns the roles of self-organization and genetices. Even the definition of the notion of self-organization is poorly defined. In TGD zero energy ontology (ZEO) forms the basic framework of both quantum TGD proper and its applications to consciousness and biology. In zero energy ontology (ZEO) self-organization is replaced with self-organization by quantum jump sequence leading to the emergence of not only 3-D spatial patters but also of 4-D behavioral patterns: one can say that living system is 4-dimensional and also its geometric past changes in quantum jumps (Libet's findings).

1. Various motor actions of magnetic body appear as basic processes of the quantum self-organization. This includes braiding and knotting, heff changing phase transitions changing the lengths fo flux tubes, reconnections allowing to build connections between different system consisting of flux tube pairs, and also replication. Also signalling by dark photons is an essential part of the picture and the general hypothesis is that dark photons have same universal energy spectrum as bio-photons and thus in the energy range of molecular transition energies.
2. Replication in TGD framework occurs at the fundamental level as a replications of 3-surface and is completely analogous to 1→ 2 decay for point elementary particle. This replication could take place for the magnetic flux quanta representing various biopolymers and higher level structures and induced the replication at the level of visible matter. As noticed, this replication is not enough in biology and must be accompanied by the replication of the quantum states associated with 3-surfaces.
3. One key question is how the bio-molecular processes arranged into a functional network. Here the hypothesis that magnetic flux tubes form a 3-D grid analogous to coordinate grid with points of grid at intersections of 3 flux tubes and flux tubes as coordinate lines is very attractive. This Indra's web would be behind the gel like structure of cellular water and make it single coherent unit. Behavioral modes would be time evolutions of this grid: motor actions of the magnetic body - or hierarchy of them.

Does dark matter induced the dynamics of visible biomatter?

The idea that dark matter induces the dynamics of biomatter is extremely attractive since the enormous complexity of biochemistry would be only adaptation to the dynamics of the much simple almost topological dynamics of the master represented as flux tubes carrying dark matter.

1. In TGD framework there are good reasons to believe that water contained the prebiotic life forms as dark analogs of various biomolecules consisting of dark proton sequences at magnetic flux tubes with the states of dark proton in 1-1 correspondence with various bio-polymers (DNA,RNA, amino-acids, tRNA). These string like objects would be dark nuclei but with a large value of Planck heff=n× h constant and with same size scale as biopolymers. The proposal is that they are present also in living matter and that is interaction between various levels based on dark photons which give bio-photons as decay products.
2. All the basic processes such as transcription, translation, and replication would be realized already at this level. The analogs of these processes assigning to dark analogs of biopolymers the biopolymers themselves would have evolved later. (ORP) suggests that ordinary biopolymers are accompanied by parallel flux tubes carrying dark protons sequences representing them. Ordinary manner would condense around dark matter.

The strongest assumption is that dark processes induce their bio-chemical counterparts as biomolecules attach to the magnetic flux tubes for which they form images at the level of visible matter. This might explain why strong dehydration leads to denaturation of biomolecules and why denatured biomolecules are not biologically active. Dark DNA would represent the "soul" of DNA not present in denatured DNA! Same of course would apply to other biopolymers: the loss of dark matter would induce the in vivo → in vitro transformation.

I have proposed the identification of dark counterparts of RNAs and amino-acids as complex braided and knotted structures with braiding carrying information making possible topological quantum computation like processes and topological realization of memory. DNA would provide a symbolic representation coding also the braiding characteristics of the dark amino-acid sequence. Dark amino-acid sequence would represent the braiding physically ad dark DNA as a sequence of symbols.

Cyclotron frequencies are crucial for communication and the strength of magnetic field on flux tubes emanating transversally from dark amino-acid sequence would be determined by the state of dark proton. The correspondence between dark RNA and amino-acid would be determined by the condition that cyclotron frequencies are identical for the corresponding dark proton states (DNA and mRNA, RNA and amino-acid) so that resonant interaction is possible.

3. This picture conforms with the chemical properties of DNA, RNA and proteins.
1. RNA does not appear as double strands and in unfolded form is much less stable than DNA. This conforms with the fact that DNA serves as an information storage providing symbolic representation of RNA and amino-acids including their folding or at least braiding. RNA in turn would provide the concrete representation for braiding and folding.
2. DNA double strand is stable against hydrolysis but only inside cell - this could be due to the fact that the phase of water is ordered and ice-like so that it cannot induce hydrolysis by providing water molecules - perhaps the fourth phase of water discovered by Pollack and leading to the formation of dark proton sequences in TGD framework is in question.
3. The braiding structure of DNA is repetitive and carries no information. This conforms with the idea that DNA and its dark variant provide a purely symbolic representations in terms of genetic code for the corresponding amino-acid - and RNA polymers including also their braiding.
4. One can invent objections against the hypothesis that the dynamics of biopolymers is induced from that for their dark variants.
1. RNA is not stable against hydrolysis but it can gain stability by folding. Thus the shape of RNA molecule would not be determined by its dark variant in conflict with induction hypothesis. One can however consider the much weaker possibility that dark sector determines only topological dynamics. Only the braiding of the fold RNA molecules would determined by the braiding of dark variant.
2. DNA double strand is stable and braided in repetitive and very simple manner. If chemistry determines the stability of the DNA double strand then DNA double strand would induce the braiding of dark DNA strand rather than vice versa. Now one can argue that if dark DNA appears as double strand this forces the repetitive braiding.

To how high level can one continue this parallelism. For instance, does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.

1. Here the findings of Pollack about the generation of exclusion zones, which are negatively charged regions of water obeying exotic stoichiometry H1.5O, are suggestive. The TGD based model assumes that a phase transition generating dark protons sequences at flux tubes of magnetic body outside the EZ takes place. The self-organization at the level of ordinary matter would generate dark matter at quantum criticality - a basic aspect of self-organization process leading to higher hierarchy levels taking the role of master. Dark matter would be the master or rather - there would be entire hierarchy of masters labelled by the values of heff. I have also considered the possibility that the generation of large heff phases happens at criticality quite universally so that life would be universal phenomenon rather than random thermodynamical fluctuation.
2. EZs with sizes about 200 microns (size of cell) could have been the prebiotic cells. There is also evidence that EZs consist of structures with size of order micron called coherent regions (CDs to be not confused with Causal Diamonds!). Could they have been the predecessors of the cell nuclei inside which dark DNA would be stable? The TGD model for the formation of EZs assumes that they are formed from CDs under irradiation.

This picture leads also to a view about metabolism predict that UV radiation with energies about 12.6 eV must play a key role in metabolism. The proposal is that this radiation arrives as dark photons along magnetic flux tubes of the magnetic body and excites water molecules inside CDs so that they are energetically at distance of about .5 eV from the splitting of OH bond. The excitation of water molecules inside CDs by metabolic energy quantum of nominal value .5 eV transforms this phase to EZs of Pollack.

Emergence of life as emergence of dark matter?

Many basic questions of biology seem to be hen-egg questions such as "genetics or metabolism?", "cell membrane or biomolecules?", "DNA or RNA?", "RNA or amino-acids?", etc.. This suggests that there exists a deeper level and emergence at this level induced the emergence at the level of biochemistry and cell biology.

In TGD the emergence of living systems would reduce to the emergence of dark matter as large heff phases of ordinary matter taking place at quantum critical and perhaps even critical systems.

1. The question whether genetics or metabolism emerged first ceases to be relevant in this framework, where basic physics provides candidates for the fundamental mechanisms of metabolism (for instance liberation of zero point kinetic energy when the p-adic length scale of space-time sheet (magnetic flux tube) increases).

Also genetic code would have been realized already before biochemistry if dark proton sequences provided the counterparts for the fundamental biomolecules. The dark biology as dark nuclear physics would make itself visible via biochemistry induced by it. We would see directly the dynamics of dark matter just by looking living systems!

2. If one takes this picture seriously, then also pre-RNA and various other pre-biopolymers could have been realized in terms dark proton sequences associated with dark magnetic flux tubes. The dark replication process could have been the arrangement of RNA and amino-acid flux tube portions in parallel and replication of the dark proton sequences with the help of the analog of tRNA attaching to the corresponding amino-acid. In this framework the notion of dark ribosome makes sense. It would however replicate only in cell replication.
3. In the biochemical scenarios also the emergence of DNA looks like mystery. In TGD framework dark DNA could have emerged at the same time as dark RNA and dark amino-acids as CDs and EZs emerged and make the stable presence of also ordinary DNA inside CDs and EZs. All basic biomolecules and prebiotic cell and metabolism would have accompanied the emergence of CDs and EZs under the irradiation of water feeding metabolic energy and giving rise to prebiotic photosynthesis (note that the negative net charge of DNAs could be due to the fact that part of protons is at dark flux tubes). Dark DNA could be interpreted as an information storage representing the braiding patterns of dark RNA and dark amino-acids symbolically.
4. In this framework the basic step of the replication is the generation of flux tube parallel to the flux tube from which one forms copy or map (say in DNA replication and and transcription). How this happens?

A possible answer to the question relies on the earlier proposal that living system involves kind of coordinate grid formed from magnetic flux tubes serving as coordinate lines and meeting each other at the points of the grid. The replication process would involved translation of nearby flux parallel flux tube of the grid near to a given flux tube assignable to say DNA strand as a first step - maybe by heff reducing phase transition for flux tubes orthogonal the flux tube. After this the building bricks of the new biomolecule would be brought along either of the remaining locally orthogonal flux tubes - perhaps by heff reducing phase transition. The basic structure would be this Indras web containing visible matter at its nodes with dynamics consisting of magnetic motor actions.

This vision involves of course considerable challenges. One should model the dark ribosome counterparts of the replication process for dark DNA, transcription of dark DNA to dark mRNA, translation of dark mRNA to dark amino-acids, and also possible self-replication of dark ribosome.

For background see the chapter Quantum gravity, dark matter, and prebiotic evolution of "Genes and Memes". See also the article Was ribosome the first self-replicator?.

### Could Podkletnov effect be understood using heff= heff hypothesis?

Podkletnov discovered his effect around 1982. There are funny co-incidences involved. I got my PhD. Podkletnov was kicked out from Tampere University and I was soon to find that it is impossible to find any funding for my work: situation is still the same! God can forgive but not colleagues. I have considered possible models for Pokletnov effect in TGD framework for years ago assuming that the propagation of gravitons along topological light rays attached to magnetic flux tubes mediate gravitational interaction. A lot of progress has taken since then. Therefore reconsideration is well-motivated.

The effect itself looks rather complex. The experiment involves a levitating disk above a toroidal magnet. Solenoids generating AC fields with frequency in the range 50-106 Hz are used to rotate the disk. Above the disk at height of 15 mm is a sample of silicon with weight of 5.47834 g. The claim is that both the rotating disk and sample lose part of their weight: the estimate varies from .3 per cent to few per cent. The effect was resonance like above frequency 105 Hz: below this the weight fluctuates. The size of the effect increases with rotation frequency.

Some background

It is best to start by introducing some background.

1. The first thing to notice is that f=6× 105 Hz is cyclotron frequency of electrons in the magnetic field Bend=.2 Gauss introduced to explain the quantal effects of ELF em fields on brain which appear at multiples of cyclotron frequencies of biologically important ions. The recent model for bio-photons as decay products of dark protons predicts that their spectrum correspond to a spectrum of Bend. Could it be that the magnetic fields at the flux tubes involved has spectrum of Bend and resonant transfer of energy in the frequency range containing f=6× 105 Hz takes place?
2. The hypothesis heff = hgr = GMD m/v0, where MD is the dark mass assignable with large system (Earth now) and v0 is velocity parameter is relatively new piece of TGD inspired quantum biology. One obtains a rough estimate MD/M ≈ 2. × 10-4 for the fraction of dark matter in the case of Earth and assignable to the dark magnetic body of Earth. One implication of hgr=heff hypothesis at gravitation mediating flux tubes is that cyclotron frequencies of particles do not depend on the mass of the particle and cyclotron energy spectrum of dark photons is universal and identifiable as that associated with bio-photons. Second implication is that each charged particle corresponds to particular value of Planck constant so that in many-sheeted space-time they populate different flux tubes: this could be very relevant for biology since cell would not be anymore a random soup of molecules. The model for the Pioneer and Flyby anomalies leads to the estimate MD/M≈ 1.3× 10-4 consistent with the above estimate.
3. I have considered recently a model for the fountain effect of superfluidity considering the possibility that dark phases of matter in TGD sense might be associated with all critical situations - both ordinary critical and quantum critical phase transitions - in which long range fluctuations correlations explained in terms of generation of dark matter are present.

The superfluid is able to climb from vessel along its walls apparently defying gravitation. The TGD explanation is in terms of large Planck constant hgr=heff hypothesis. The large value of hgr implies macroscopic quantum gravitational coherence and that the quantum states in gravitational field for dark 4He atoms have macroscopic size. In particular, the flow along walls is effectively free flow.

The anomaly in the measurement of Cooper pair mass in rotating superconductors

One has discovered an anomalous outcome in the mass measurements of Cooper pairs in the case of rotating superconductors. The measured mass of Cooper pair in rotating super conductor is slightly larger than the mass of the pair which must be slightly below the sum of the masses. Tajmar et al try to explain the anomaly is in terms of a gigantic gravimagnetic London effect associated with a rotating superconductor.

1. Recall that in in the ordinary London effect a magnetic field proportional to the negative of rotation frequency is generated inside super-conductor: usually the magnetic field is expelled. London magnetic field corresponds to a magnetic dipole proportional the negative of the rotation frequency (this follows from the negative sign of the charge carriers). The natural expectation is that this gives rise to a dipole field outside the superconductor. The dipole moment would be generated by electron current at the surface of the superconductor.
2. The idea is to to introduce gravitational superconductivity for which all kinds of particles participate in the flow which would be analogous to super-fluidity. One can also speak about gravitational Meissner effect and massivation of graviton as analog of massivation of photons in the ordinary Meissner effect. Also the notion of London magnetic field might generalizes and gives rise to a dipole like gravimagnetic field outside the super-conductor. Now however negative charge is replaced by mass, which is positive so that the sign of the effect changes. The predicted effect is however completely negligible using the existing estimates for the mass of the graviton.
3. The crazy proposal of Tajmar et al is that a gravimagnetic field larger than that predicted by GRT by a factor of order 1024 is associated with the rotating super-conductor and combines and produces the slight deviation of the measured mass of the Cooper pair from real when this since the Cooper pair couples also to gravimagnetic field besides magnetic field. The reason is that the effective magnetic field contains a small contribution of gravimagnetic field so that the measurement gives too large a result for the mass of the Cooper pair.
In standard model plus GRT this kind of effect is impossible. In TGD framework the hierarchy of Planck constants suggests two alternative explanations.
1. The London magnetic field (also gravimagnetic) is a purely quantal effect and proportional to the square h2 of Planck constant. If h is replaced with say heff = hgr≈ 1012 h the effect is enormous as compared to that predicted by GRT! There is however an objection: one cannot perform this replacement for ordinary London field! Why?
2. Many-sheeted space-time allows to consider also alternative model in which the change of mass is due to a generation of the analog of dark London magnetic field at dark magnetic flux tubes: electron would couple to the sum of these fields since it would have topological sum contacts to both space-time sheets This magnetic field is proportional to dark matter density and ρD/ρ=MD/M≈ 2× 10-4 would give a correct order of magnitude estimate.
3. Since gravimagnetic and magnetic fields are expressible in terms of CP2 coordinates and their gradients, one can wonder whether the two explanations are actually equivalent.