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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.
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.
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.
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.
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.
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.
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).
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.
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.
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?!".
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.
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.
C. Possible technological implications
It is easy to imagine far reaching technological implications of bio-fusion if it really occurs.
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.
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.
For background see the chapter Expanding Earth Model and Pre-Cambrian Evolution of Continents, Climate, and Life
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).
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.
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.
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
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.
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.
On basis of these observations one can try to imagine how the ribosome or its predecessor "pre-ribosome" might have replicated.
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).
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.
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.
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.
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?.
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.
It is best to start by introducing some background.
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.
What about Podkletnov effect?
Also Pokdletknov effect is associated with a rotating superconductor and one can ask whether the above ideas apply also to it.
See the chapter Quantum gravity, dark matter, and prebiotic evolution or the article Could Podkletnov effect be understood using heff= heff hypothesis?.