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Year 2017

Potential "missing link" in chemistry that led to life on Earth discovered

In the attempts to understand pre-biology the basic challenge is to understand how the needed short RNA, DNA, and amino-acid sequences managed to form. Phosphorylation is known to be crucial for this process and means energization in standard bio-chemistry. Organic phosphate possesses somewhat mysterious high energy phosphate bond, which stores energy and makes possible metabolism: in metabolic ATP with three phosphates transforms to ADP with two phosphates by giving one phosphate with high energy phosphate bond to the acceptor molecule, which is therefore phosphorylated.

In the recent biology phosphorylation of various biomolecules such as DNA, RNA, amino-acid sequences is catalyzed by proteins known as enzymes known as phosphorylases. Kinase is one particular enzyme transferring phosphate from ATP to the acceptor molecule. Proteins consist of amino-acids and would not be present in RNA world, which serves almost as a standard model for the prebiotic period. Ribozymes are catalysts formed from RNA but they catalyze typically only the reversal of phosphorylation.

1. The problem and its possible solution

The phosphorylation of short nucleotide sequences and amino-acid sequences, and also lipids making possible formation of small cell membrane like structures is necessary for the formation of larger structures from their building bricks. As noticed, ribozymes catalyze only dephosphorylation. How RNA was phosphorylated during RNA era or were the amino-acid present all the time?

The popular article with the title Potential 'missing link' in chemistry that led to life on Earth discovered tells about a mechanism allowing phosphorylation during RNA era in absence of enzymes. The discovery is that an organic molecule known as diamidophosphate (DAP) having chemical formula PO2(NH2)2-1 could do the job in presence of water and imidazol. Imidazol has chemical formula C3N2H4 and is a molecule possessing aromatic hetero-cycle consisting of 3 C atoms and 2 N atoms.

Remark: Pyrimidine in turn is aromatic hetero-6-cycle consisting of 4 C atoms and 2 N atoms and having formula C4N2 H4. DNA has as basic building bricks phosphates PO4- having valence bonds with deoxy-ribose molecules (containing 5-rings with 4 C atoms and one O). Each sugar has valence bond with N of nucleoside C, T, A or G. C and T are pyrimidines with single aromatic 6-ring and A and G are purines obtained by fusing imidazol 5-ring and pyrimidine 6-ring to obtain purine double ring. By replacing one OH of de-oxyribose of DNA with H one obtains RNA.

DAP could solve several problems simultaneously: how the short sequences of RNA (later DNA) and amino-acids were formed, and how the predecessors of cell membranes emerged. It is not however clear to me whether this process could have been fast enough or whether the slowness only made the first step painful.

2. How the discovery could relate to TGD inspired quantum biology?

It is interesting to interpret the discovery in TGD framework. The basic question is whether the presence of dark atoms and electrons in bio-molecule distinguish between atomic physics, in-organic chemistry, and organic chemistry. Usually organic chemistry is defined to be chemistry of carbon compounds, typically hydrocarbons. Could it be that the formation of hydrocarbons involves dark variants of proton and electron identified as heff=n× h variants of ordinary proton and electron?

2.1 From atomic physics to chemistry

How could one proceed from atomic physics to atomic physics to chemistry in TGD framework. The basic question is how to understand valence bond: it is not at all clear whether mere Schrödinger equation allows to understand it. Could the emergence of dark electrons allow their delocalization and formation of valence bonds? It has been known for decades that the heating of rare-earth metals leads to a mysterious loss of some valence electrons and the explanation would be the energy provided by heating kicks them to higher energy states by making some valence electrons dark (see this). The explanation would be in terms of dark electron orbitals for valence electrons which have radii scaled up by factor n2 and are analogous to Rydberg states identified as orbitals with large value of principal quantum number and having very large radius.

The dark variants of atoms have binding energy scale reduced by factor 1/n2 so that their formation requires energy feed (perhaps radiation at required frequencies). One or more valence electrons of ordinary atom could be dark so that the size of the orbital is scaled up by factor n2. The valence bond central for chemistry in general and in particular for basic biopolymers could contain dark electrons delocalized because of larger value of n than for the non-valence electrons. Note that one could be n=n0> 1 for ordinary atoms making in principle possible atoms with n< n0 with anomalous large binding energy also for the filled shells as the findings of Randel Mills indeed suggest (see this).

Surprisingly, dark electrons would be essential in ordinary chemistry thought to reduce to standard model physics! The increase of n reduces binding energy scale and requires energy feed. This would allow to understand why anabolism - that is generation of biopolymers from their building blocks by generating valence bonds - requires energy feed and why catabolism - the splitting of biopolymers to their building blocks by splitting the valence bonds liberates energy.

The valence bonds would be classified by the value of n and it is quite possible that in organic chemistry the values of n are larger than in in-organic chemistry. Could this mean that valence bonds H and C and N and O have higher values in bio-chemistry? Also the valence bonds between O and H in water could have larger value of n.

To sum up, the transition from atomic physics to ordinary chemistry involved generation of dark electrons associated with valence bonds. The value of n for dark electrons can vary and allow hierarchy of evolutionary steps with increasingly delocalized valence electrons.

2.2 From chemistry to bio-chemistry

What about the step leading to a genuine bio-chemistry involving genetic code? Magnetic body (MB) is the basic aspect of biochemistry according to TGD. Pollack effect leading to the formation of negatively charged regions - exclusion zones (EZs) - would involve generation of dark protons at magnetic flux tubes of MB with electrons left to the EZ - possible as ordinary particles (see this). Also Pollack effect requires feeding of energy, say as irradiation by photons.

DNA is stable against spontaneous hydration only inside cell membrane. This suggests that the EZs of Pollack containing partially dark water molecules satisfying effectively the stoichiometry H3/2O allowed to stabilize DNA. Therefore EZs are excellent candidates for the predecessors of cell.

The TGD inspired proposal is that DNA strand for which each phosphate has negative unit charge is companied by dark analog of DNA consisting of dark protons such that the states of 3-proton units are in one-one correspondence with DNA, RNA, tRNA and amino-acids and the degeneracies of the vertebrate genetic code (number of codons coding for given amino-acid) come out correctly (see this). A more general picture is that ordinary chemistry is kind of shadow for the dynamics of dark matter at magnetic flux tubes doing its best to emulate it. This would explain also why genetic code has also other variants.

It would be the emergence of dark protons with large enough value of n, which would distinguish between ordinary chemistry and bio-chemistry. Water is basic element of life and hydrogen bonding is responsible for the formation of water clusters - certainly one of the key aspects of bio-chemistry. Hydrogen bonds appear between highly electronegative atoms such as O, N, and F (electronegativity is roughly the tendency to attract electrons). What distinguishes hydrogen bond from valence bond is that it is proton rather than electron, which is delocalized. This suggests that the delocalized proton is dark proton at magnetic flux tube connecting the hydrogen bonded molecules.

2.3 The emergence of metabolism

In the proposed framework the first basic aspect of life would be the generation of dark electrons and protons using energy feed and their transfer between molecules and their generation by providing the needed energy.

  1. Metabolism (anabolism) would provide the energy needed to transform ordinary atom (that is electron bound to it) to a dark atom with large value of heff/h=n. This requires energy since the binding energy is proportional to 1/n2 and reduced in the process. This is quite generally true for all dark variants of quantum states. One can say that the increase of the complexity of the system by increasing n characterizing its "IQ" requires metabolic energy (in adelic physics "IQ" has concrete interpretation as cognitive resources). Therefore the first steps of prebiotic life was the emergence of energy feed mechanism making possible the increase of n.
  2. I have considered the possibility that the period of prebiotic life preceding the the emergence of chemical storage of energy used dark nucleosynthesis (see this) as the source of metabolic energy. The recently discovered life-like properties of a very simple system consisting of negatively charged plastic balls in the plasma of Ar+ ions allows to develop rather detailed ideas about this phase of life. (see this).
  3. A fundamental question is about the step leading to the chemical storage of metabolic energy to valence bonds with non-standard value of n. Solar radiation could have generated both negatively charged EZs identifiable as possible predecessors of cell membrane and valence bonded molecules storing metabolic energy.
2.4 About bio-catalysis

Without bio-catalysis biochemical reactions leading to the formation of biopolymers and cell membrane would be quite too slow. Here phosphorylation enters the game.

  1. The TGD based model for bio-catalysis relies on the temporary reduction of heff =n×h liberating energy kicking the reactants over potential wall. After this step the catalyst - at least in the ideal situation - receives the energy and the atom becomes dark again.
  2. Acid catalyst gives a proton and base catalyst gives an electron. Most bio-catalysts are acid catalysts The TGD based interpretation should rely on the possibility of dark valence electrons and dark protons at flux tubes. Since base catalysts are associated with non-organic chemistry, the identification of the electron given by base catalyst as dark electron looks natural. Acid catalysts would give dark proton.
Bio-catalysts are usually activated by phosphorylation and de-activated by de-phosphorylation but there are exceptions to this rule. This can be understood if the catalyst activates a molecule acting as a switch for a reaction. Catalysts related to phosphorylation are known as phosphotransferases and contain kinases transferring phosphate from ATP to the acceptor molecules.

Phosphatases remove phosphate from the target molecule: they are hydrolases and use water to remove the phosphate and to hydrate the molecule.

2.5 The difference between organic and inorganic phosphates

Phosphate appears as too variants: organic and inorganic.

  1. Organic phosphates bound to biomolecules have charge -1. Some electrons of organic phosphate ion have transformed to valence electrons and are therefore dark. Also some protons - one dark proton per dark electron to not affect the observed charge in short scales - would be dark and at the magnetic body of the organic phosphate. Both dark protons and dark electrons would be present and give rise to somewhat mysterious high energy phosphate bond.
  2. Free phosphate in water environment appears in ionized variants HnPO4n-4 and is regarded as in-organic and have negative charge 4-n. In inorganic phosphate some dark protons and ordinary electrons giving rise to the negative charge have combined to hydrogen atoms. The larger the number of hydrogens is, the higher the level of inorganicity is.

    The fractions of variants of free phosphate in water depend on pH characterizing the density of protons present. Could pH in fact characterize the fraction of dark protons at magnetic flux tubes? Or could it also characterize the fraction of dark hydrogen atoms present. Similar question applies to the counterparts of pH for other biologically important ions.

2.6 About phosphorylation and the interpretation of DAP

At chemical level phosphorylation attaches phosphate ion to the hydroxyl group (R-OH) of the acceptor molecule. At deeper level phosphorylation would give dark electron to the acceptor molecule and dark proton to its MB. Phosphorylation would increase the quantum coherence length: the formation of short RNA, amino-acid sequences and of cell membrane like structures would be a basic example of this.

What about the interpretation of the role of DAP in this framework? DAP has charge -1 as also the phosphate bound to DNA and RNA have (in ATP the outermost phosphate has charge -2). DAP is very similar to the phosphate in DNA and RNA and expected to carry high energy phosphate bond. In TGD framework it would possess both dark valence electrons and dark protons at magnetic flux tubes with only one ordinary electron responsible for the charge of DAP. Due to the properties of phosphatase the phosphorylation would be very simple process at the level of dark electron and proton. Hence DAP and imidazole could make possible the phosphorylation.

2.7 About dephosphorylation and phosphoryl transfer

The scanning of web shows that some sources talk of dephosphorylation and some sources about phosphoryl transfer reactions and it remained unclear to me whether the two terms really have the same meaning. In any case, in TGD framework one can distinguish between these notion. Dephosphorylation could mean either phosphoryl transfer (transfer of phosphate between donor and acceptor molecules) or "dropping" of organic phosphate to water environment and giving it negative additional negative charge (the transfer would be now to water environment) and making it inorganic.

  1. Phosphoryl would transfer removes PO4- group and presumably also the associated dark proton from the target and transfers them to the acceptor molecule and its MB. I have proposed that reconnection of flux tubes transforms the flux tubes entering to the donor molecule to that associated with the acceptor molecule so that dark proton is automatically transferred. In ATP-ADP process the phosphate group and presumably also the dark proton and electron would be transferred to the acceptor molecule from ATP. ADP is dephosphorylated and acceptor phosphorylated.
  2. In "dropping" the outcome would be in-organic phosphate denoted by Pi, which is a mixture of HPO4-2 and H2PO4-1. One interpretation is that 1 or 2 dark protons from magnetic flux tubes have transformed to ordinary protons and combined with electrons to form hydrogen atoms. This operation would reduce the number of dark particle and thus the "evolutionary level" of the system.
Dephosphorylation is known to lead to a decomposition of the donor molecule to smaller structures, indicating the reduction of heff/h and thus of quantum coherence length. In RNA world dephosphorylation would be catalyzed by ribozymes and in some important cases also in the recent biology. Dephosphorylation would reduce quantum coherence length and lead to the decomposition of structures to smaller ones: mRNA splicing is one example of this. Catabolism of nutrients and the decay process of dead organic matter provide further basic examples.

Catabolism of nutrients and the decay process of dead organic matter suggest what happens. In the first preliminary step of catabolism catalysts are involved. At the second step of catabolism inorganic phosphate is formed, which suggests that the number of dark protons is reduced in the process. This conforms with the reduction of the value of heff/h=n.

See the chapter Dark matter, quantum gravity, and prebiotic evolution or the article Potential "missing link" in chemistry that led to life on Earth discovered.

From RNA world to RNA-tRNA world to RNA-DNA-tRNA world to DNA-RNA-protein world: how it went?

I told already earlier about how the transition from RNA world to RNA-tRNA world to DNA-RNA-protein world might have taken place in TGD Universe. Last night I realized a more detailed mechanism for the last step of the transition relying on the TGD based general model model of bio-catalysis based on heff=n×h phases of ordinary matter at dark magnetic flux tubes. It also became clear that DNA-RNA-tRNA world very probably preceded the transition to the last world in the sequence. Therefore I glue below the appropriately modified earlier posting.

I encountered a highly interesting work related to the emergence of RNA world: warmly recommended. For a popular article see this.

First some basic terms for the possible reader of the article. There are three key enzymes involved in the process which is believed to lead to a formation of longer RNA sequences able to replicate.

  1. Ribozyme is a piece of RNA acting as catalyst. In RNA world RNA had to serve also as a catalyst. In DNA world proteins took this task but their production requires DNA and transcription-translation machinery.
  2. RNA ligase promotes a fusion of RNA fragments to a longer one in presence of ATP transforming to AMP and diphospate and giving metabolic energy presumably going to the fusion. In TGD fUniverse this would involve generation of an atom (presumably hydrogen) with non-standard value of heff=n×h having smaller binding energy scales so that ATP is needed. These dark bonds would be involved with all bio-catalytic processes.
  3. RNA polymerase promotes a polymerization of RNA from building bricks. It looks to me like a special kind of ligase adding only single nucleotide to an existing sequence. In TGD Universe heff=n×h atoms would be involved as also magnetic flux tubes carrying dark analog of DNA with codons replaced with dark proton triplets.
  4. RNA recombinase promotes RNA strands to exchange pieces of same length. Topologically this corresponds to two reconnections occurring at points defining the ends of piece. In TGD Universe these reconnections would occur for magnetic flux tubes containing dark variant of DNA and induce the chemical processes at the level of chemistry.

Self ligation should take place. RNA strands would serve as ligases for the generation of longer RNA strands. The smallest RNA sequences exhibiting self-ligation activity was found to be 40-nucleotide RNA and shorter than expected. It had lowest efficiency but highest functional flexibility to ligate substrates to itself. R18 - established RNA polymerase model - had highest efficiency and highest selectivity.

What I can say about the results is that they give support for the notion of RNA world.

The work is related to the vision about RNA world proposed to precede DNA-RNA-protein world. Why I found it so interesting is that it relates to on particular TGD inspired glimpse to what happened in primordial biology.

In TGD Universe it is natural to imagine 3 worlds. RNA world, RNA-tRNA world, and DNA-RNA-protein world. For an early rather detailed version of the idea about transition from RNA world to DNA-RNA-proteins world but not realizing the tRNA-RNA world as intermediate step see this.

  1. RNA world would contain only RNA. Protein enzymes would not be present in RNA world and RNA itself should catalyze the processes needed to for polymerization, replication, and recombination of RNA. Ribozymes are the RNA counterparts of enzymes. In the beginning RNA would itself act as ribozymes catalyzing these processes.
  2. One can also try to imagine RNA-tRNA world. The predecessors of tRNA molecules containing just single amino-acid could have catalyzed the fusion of RNA nucleotide to a growing RNA sequence in accordance with the genetic code. Amino-acid sequences would not have been present at this stage since there would be no machinery for their polymerisation.
  3. One can consider a transition from this world to DNA-RNA-tRNA world. This would storage of genetic information to DNA from which it would have been transcribed by using polymerase consisting of RNA. This phase would have required the presence of cell membrane like structure since DNA is stabilized inside membranes or at them. Transition to this world should have involved reverse transcription catalized by RNA based reverse-transcriptase. Being a big evolutionary step, this transition should involve a phase transition increasing the value of heff=n × h.
  4. My earlier proposal has been that a transition from RNA world to DNA-RNA-protein world took place. The transition could have also taken place from DNA-RNA-tRNA world to world containing also amino-acid sequences and have led to rapid evolution of catalysis based on amino-acid sequences.

    The amino-acid sequences originating from tRNA originally catalyzing RNA replication stole the place of RNA sequences as the end products from RNA replication. The ribosome started to function as a translator of RNA sequences to amino-acid sequences rather than replication of them to RNAs! The roles of protein and RNA changed! Instead of RNA in tRNA the amino-acid in tRNA joined to the sequence! The existing machinery started to produce amino-acid sequences!

    Presumably the modification of ribosome or tRNA involved addition of protein parts to ribosome, which led to a quantum critical situation in which the roles of proteins and RNA polymers could change temporarily. When protein production became possible even temporarily, the produced proteins began to modify ribosome further to become even more favorable for the production of proteins.

    But how to produce the RNA sequences? The RNA replication machinery was stolen in the revolution. DNA had to do that via transcription to mRNA! DNA had to emerge before the revolution or at the same time and make possible the production of RNA via transcription of DNA to mRNA. The most natural options corresponds to "before", that is DNA-RNA-tRNA world. DNA could have emerged during RNA-tRNA era together with reverse transcription of RNA to DNA with RNA sequences defining ribozymes acting as reverse transcriptase. This would have become possible after the emergence of predecessor of cell membrane. After that step DNA sequences and amino-acid sequences would have been able to make the revolution together so that RNA as the master of the world was forced to become a mere servant!

    The really science fictive option would be the identification of the reverse transcription as time reversal of transcription. In zero energy ontology (ZEO) this option can be considered at least at the level of dark DNA and RNA providing the template of dynamics for ordinary matter.

How the copying of RNA strand to its conjugate strand catalysed by amino-acid of tRNA could have transformed to translation of RNA to amino-acid sequence? Something certainly changed.
  1. The change must have occurred most naturally to tRNA or - less plausibly - to the predecessor of the ribosome machinery. The change in the chemical structure of tRNA is not a plausible option. Something more than chemistry is required and in TGD Universe dark matter localized at magnetic flux tubes is the natural candidate.
  2. Evolution corresponds in TGD Universe gradual increase of heff=n × h. A dramatic evolutionary step indeed took place. The increase of the value of heff for some structural element of tRNA could have occurred so that the catalysis for amino-acid sequence instead of that for RNA sequence started to occur.

  3. The general model for bio-catalysis in TGD Universe involves a contraction of magnetic flux tubes by a reduction of heff and bringing together the reacting molecules associated with flux tubes: this explains the magic looking ability of biomolecules to find each other in the dense molecular soup. The reduction of heff for some dark atom(s) of some reacting molecules(s) to a smaller value liberates temporarily energy allowing to kick the reactants over a potential wall so that the reaction can occur (atomic binding energies scale as 1/heff2). After than the liberated energy is absorbed and ordinary atom transforms back to dark atom.

    In the recent case heff associated with a dark atom (or atoms) of tRNA could have increased so that the binding energy liberated would have increased and allowed to overcome a higher potential wall than before. If the potential wall needed to overcome in the fusion of additional amino-acid to a growing protein is higher than that in the fusion of additional RNA to a growing RNA sequence, this model could work.

  4. The activation energy for the addition of amino-acid should be larger than that for RNA nucleotide. A calculated estimate for the activation energy for the addition of amino-acid is 63.2 eV. An estimate for the activation energy for the addition of RNA nucleotide at the temperature range 37-13 C is in the range 35.6 -70.2 eV . An estimate for the activation energy for the addition of DNA nucleotide is 58.7 eV. The value in the case RNA would be considerably smaller than that in the case of amino-acids at physiological temperature. For DNA and amino-acid the activation energy would be somewhat smaller than for amino-acid. This is consistent with the proposed scenario. I am not able to decide how reliable these estimates are.
The natural first guess is that the dark atoms are hydrogen atoms. It is however not at all clear whether "ordinary" hydrogen atoms correspond to n=heff/h=n=1.
  1. Randell Mills has proposed his notion of hydrino atom to explain anomalous energy production and EUV radiation in 10-20 nm range taking place in certain electrolytic system and having no chemical explanation. The proposal of Mills is that hydrogen atom can make in presence of a catalyst a transition to a lower energy state with a reduced size. I have already earlier considered some TGD inspired models for hydrino. The resemblance with the claimed cold fusion suggests that the energy production involved in the two cases might involve the same mechanism.

    I have considered two models for the findings (see this). The first model is a variant of cold fusion model that might explain the energy production and the observed radiation at EUV energy range. Second model is a variant of hydrino atom assuming that ordinary hydrogen atom corresponds to heff/h=nH>1 and that catalyst containing hydrogen atoms with lower value of nh<nH could induce a phase transition transforming hydrogen atoms to hydrinos with binding energy spectrum scaled up by scaling factor (nH/nh)2 and radii scaled down by (nh/nH)2. The findings of Mills favour the value nH=6.

  2. Suppose the transition corresponds to a transition analogous to photon emission so that it occurs between Δ J=1 transitions of hydrogen atom. There are two simple options: either the direction of electron spin change but orbital angular momentum remains unaffected or the angular momentum of electron changes by Δ L=1 but spin direction does not change.

    The simplest assumption is that the principal quantum numbers in the initial and final state are ni=1 and nf≥ ni. Assume first that initial state with (nHi,ni=1) having Li=0 and final state with (nHf,nf≥ ni).

  3. The energy difference between the initial state with (nHi,ni=1) and final state with (nHf, nf). The initial binding energy is the ordinary binding of thought-to-be hydrogen atom in the ground state: Ei= Ef(nHf/nHi)2 ≈ 13.6 eV. Here Ef denotes the final ground state binding energy. The final state binding energy is Efnf= Ef/nf2.

    The liberated energy defining the order of magnitude for the activation energy (thermodynamical quantity) is given by

    Δ E=Efnf-Ei= Efnf2- Ef(nHfnHi)2= Ei[(nHinHf)2 nf-2-1].

    The condition Δ E > 0 gives

    nHi/nHf >nf .

    For nHi/nHf=nf one has Δ E=0. For instance, this occurs for (nHi,nHf)∈ {(2,1),(6,3),(6,2)}. Δ E>0 condition gives nHi > 2.

  4. Consider first ni=nf=1 for which the spin direction of electron changes if the transition is analogous to photon emission. By putting nf=1 in above equation one obtains a formula for the transition energy in this case. For instance, (nNi,ni)=(6,1)→ (nHf,nf) =(3,1) would correspond to Δ E=40.8 eV perhaps assignable to RNA polymerization and the transition (nHi,ni)=(7,1)→ (nHf,nf)=(3,1) to Δ E= 60.4 eV perhaps assignable to amino-acid polymerization and DNA polymerization. Note that nH=6 is supported by the findings of Mills.
  5. The table below gives the liberated energies Δ E for transitions with (ni,nf)=(1,2) in some cases. The liberated energy in transition (nHi,ni=1)→ (nHf,nf=2) in some cases.

    (nHi,ni) (nHf,nf) Δ E/eV
    (3,1) (1,2) 17.0
    (4,1) (1,2) 40.8
    (4,1) (2,2) 0.0
    (5,1) (1,2) 71.4
    (5,1) (2,2) 7.7
    (6,1) (1,2) 109.0
    (6,1) (3,2) 17.0

    The transitions (4,1)→ (1,2) resp. (5,1)→ (1,2) might give rise to the activation energies associated with RNA resp. amino-acid polymerization.

  6. If ordinary hydrogen atom and atoms in general correspond to heff/h=n=1, the liberated energies would be below the ground state energy E0=13.6 eV of hydrogen atom and considerably below the above estimates. For heavier atoms the binding energy scale would be Z2-fold and already for carbon with Z=6 by a factor 36 higher. It is difficult to obtain Δ E in the scale suggested by the estimates for the activation energies.
One could try to test whether tRNA could be modified to a state in which RNA is translates to RNA sequences rather than proteins. This would require a reduction of heff=n× h for the dark atom in question.

See the chapter Evolution in Many-Sheeted Space-Time or the article From RNA world to RNA-tRNA world to RNA-DNA-tRNA world to DNA-RNA-protein world: how it went?

Retrocausality and TGD

The comments below were inspired by a popular article ("Physicists provide support for retrocausal quantum theory, in which the future influences the past" in Phys.org telling about the preprint ("Is a time symmetric interpretation of quantum theory possible without retrocausality?" of Leifer and Pusey related to the notion of retrocausality (I am grateful to Maria Vihervaara for the link).

Retrocausality means the possibility of causal influences propagating in non-standard time direction. Retrocausality has been also proposed by Cramer as a possible manner to obtain deterministic quantum mechanics and allowing to interpret wave functions as real objects. Bell theorem and Kochen-Specker theorem however pose difficult challenges for this program and the condition that the theory is classical in strong sense (all observables have well-defined values) seems impossible.

The work is interesting from TGD view point for several reasons.

  1. TGD leads to a new view about reality solving the basic problem of quantum measurement theory. In ZEO quantum states are replaced by zero energy states which are analogous to pairs of initial and final states in ordinary ontology and can be regarded as superpositions of classical deterministic time evolutions. The sequence of state function reductions means sequence of re-creations of the superpositions of classical realities. The TGD based view about scattering amplitudes has a rather concrete connection with the view of Cramer as I interpret it. There is however no attempt to reduce quantum theory to a purely classical theory. The notion of "world of classical worlds" consisting of classical realities identified as space-time surfaces replaces space-time as a fixed observer independent reality in TGD.
  2. Retrocausality is basic aspect of TGD. Zero Energy Ontology (ZEO) predicts that both arrows of time are possible. In this sense TGD is time symmetric. On the other hand, the twistor lift of TGD predicts a violation of time reflection T and this might imply that second arrow of causality dominates in some sense. The ZEO based view about state function reduction essential for TGD inspired theory of consciousness and implying generalized Zeno effect giving rise to conscious entities -"selves" - is also essential. One might say that when conscious entity dies it re-incarnates as time-reversed self.
  3. The possibility of superposing states with opposite causal arrows (see this) is a fascinating idea and its plausibility is discussed already earlier in TGD framework (see this).
In the article Retrocausality and TGD I will discuss the articles from TGD point of view criticizing the hidden assumptions about the nature of time leading to the well-known problems of quantum measurement theory and consider also the concrete implications for theories of consciousness. Also the empirical evidence for retrocausality is discussed briefly. Contrary to the article the discussion is non-technical: I do not believe that the introduction of technicalities helps to understand the deep conceptual problems involved and possible solutions to them.

See the article Retrocausality and TGD or the chapter Topological quantum computation in TGD Universe.

Two steps towards understanding of the origins of life

Two highly interesting findings providing insights about the origins of life have emerged and it is interesting to see how they fit to the TGD inspired vision.

The group led by Thomas Carell has made an important step in the understanding the origins of life (see this). They have identified a mechanism leading to the generation of purines A and G which besides pyrimidines A,T (U) are the basic building bricks of DNA and RNA. The crucial step is to make the solution involved slightly acidic by adding protons. For year later I learned that a variant of Urey-Miller experiment with simulation of shock waves perhaps generated by extraterrestrial impacts using laser pulses generates formamide and this in turn leads to the generation of all 4 RNA bases (see the popular article and article).

These findings represent a fascinating challenge for TGD inspired quantum biology. The proposal is that formamide is the unique amide, which can form stable bound states with dark protons and crucial for the development of life as dark matter-visible matter symbiosis. Pollack effect would generate electron rich exclusions zones and dark protons at magnetic flux tubes. Dark protons would bind stably with unique amine leaving its chemical properties intact. This would lead to the generation of purines and the 4 RNA bases. This would be starting point of life as symbiosis of ordinary matter and dark matter as large heff/h=n phases of ordinary matter generated at quantum criticality induced by say extraterrestrial impacts. The TGD based model for cold fusion and the recent results about superdense phase of hydrogen identifiable in TGD framework as dark proton sequences giving rise to dark nuclear strings provides support for this picture.

There is however a problem: a reductive environment (with ability to donate electrons) is needed in these experiments: it seems that early atmosphere was not reductive. In TGD framework one can imagine two - not mutually exclusive - solutions of the problem. Either life evolved in underground oceans, where oxygen concentration was small or Pollack effect gave rise to negatively charged and thus reductive exclusion zones (EZs) as protons were transferred to dark protons at magnetic flux tubes. The function of UV radiation, catalytic action, and of shock waves would be generation of quantum criticality inducing the creation of EZs making possible dark heff/h=n phases.

For details and background see the article Two steps towards understanding of the origins of life or the chapter Evolution in Many-Sheeted Space-Time.

Is conscious experience without definite causal order possible?

The exciting question is what the superposition of causal orders could mean from the point of view of conscious experience. What seems obvious is that in the superposition of selves with opposite arrows of clock-time there should be no experience about the flow of time in definite direction. Dissipation is associated with the thermodynamical arrow of time. Therefore also the sensory experience about dissipation expected to have unpleasant emotional color should be absent. This brings in mind the reports of meditators about experiences of timelessness. These states are also characterized by words like "bliss" and "enlightenment".

Why I find this aspects so interesting is due to my personal experience for about 32 years ago. I of course know that this kind of personal reminiscences in an article intended to be scientific, is like writing one's own academic death sentence. But I also know I long ago done this so that I have nothing to lose! The priests of the materialistic church will never bother to take seriously anything that I have written so that it does not really matter! This experience - I dared to talk about enlightenment experience - changed my personal life profoundly, and led to the decision to continue work with TGD instead of doing full-day job to make money and keeping TGD as a kind of hobby. The experience also forced to realize that our normal conscious experience is only a dim shadow of what it can be and stimulated the passion to understand consciousness.

In this experience my body went to a kind of light flowing state: liquid is what comes in mind. All unpleasant sensations in body characterizing the everyday life (at least mine!) suddenly disappeared as this phase transition propagated through my body. As a physicist I characterized this as absence of dissipation, and I talked to myself about a state of whole-body consciousness.

There was also the experience about moving in space in cosmic scales and the experience about the presence of realities very different the familiar one. Somehow I saw these different worlds from above, in bird's eye of view. I also experienced what I would call time travel and re-incarnation in some other world.

Decades later I would ask whether my sensory consciousness could have been replaced with that only about my magnetic body only. In the beginning of the experience there was indeed a concrete feeling that my body size had increased with some factor. I even had the feeling the factor was about 137 (inverse of the fine structure constant) but this interpretation was probably forced by my attempt to associate the experience with something familiar to physicist! Although I did all the time my best to understand what I was experiencing, I did not direct my attention to my time experience, and cannot say whether I experienced the presence or absence of time or time flow.

Towards the end of the experience I was clinically unconscious for about day or so. I was however conscious. For instance, I experienced quite concretely how the arrow of time flow started to fluctuate forth and back. I somehow knew that permanent change would mean death and I was fighting to preserve the usual arrow of time. My childhood friend, who certainly did not know much about physics, told about about alternation of the arrow of time during a state that was classified by psychiatrists as an acute psychosis.

See the chapter Topological Quantum Computation in TGD Universe and the article Quantum computations without definite causal structure: TGD view

Quantum computations without definite causal structure: TGD view

I encountered a link to a interesting popular article "Causal Witness" Provides First Experimental Evidence Of Indefinite Causal Order (see this). The article tells about an article Experimental verification of an indefinite causal order by Rubio et al (see this). In the following are my first impressions. Probably I mest update impressions. The findings are however so fascinating that I cannot resists the temptation to post them in blog.

1. Indefinite causal order

The abstract of the article Rubio et al might give some idea about what is involved.

Investigating the role of causal order in quantum mechanics has recently revealed that the causal relations of events may not be a priori well-defined in quantum theory. Although this has triggered a growing interest on the theoretical side, creating processes without a causal order is an experimental task. We report the first decisive demonstration of a process with an indefinite causal order. To do this, we quantify how incompatible our setup is with a definite causal order by measuring a "causal witness">. This mathematical object incorporates a series of measurements that are designed to yield a certain outcome only if the process under examination is not consistent with any well-defined causal order. In our experiment, we perform a measurement in a superposition of causal orders—without destroying the coherence—to acquire information both inside and outside of a causally non-ordered process. Using this information, we experimentally determine a causal witness, demonstrating by almost 7 SDs that the experimentally implemented process does not have a definite causal order.

Unfortunately, I do not have prerequisites to say anything interesting about the delicacies of the experiment itself. Since causal order is fixed by that associated with space-time in standard physics, the implications of the experiment could be world view changing.

The key quantum information theoretic notions are causal order, causal separability, quantum wittness, quantum process called SWITCH changing causal order, and superposition of causal orders.

  1. The notion of causal order is discussed in the article "Quantum correlations with no causal order" by Oreshkov et al (see this). One has two events A and B. If they are causally separable, one can tell which causes which. In Minkowski space causally separable events would connected by a time-like curve. If not, one cannot speak about causal order. One can tell whether A precedes B or vice versa. For light-like distances, the situation is not so clear.

    Relaxing the standard assumption about fixed arrow of time one can at quantum level consider also a situation in which one has quantum superposition of different causal orders. One has causal non-separability.

  2. The notion of causal wittness (see this) provides a method allowing to deduce experimentally whether the process is causally separable or not. The notion is similar to that of entanglement wittness (see this) allowing to deduce whether the two systems are entangled. Essentially one has observable whose expectation is negative for states with indefinite causal order and positive for those with definite causal order. Causal wittness is not universal but must be constructed for each causally indefinite state separately. The construction of causal wittness expectation value of operator is far from trivial and requires deeper understanding of operator theory. The abstract definition goes as follows:

    Causal wittness represents a set of quantum operations, such as unitaries, channels, state preparations, and measurements, whose expectation value is non-negative as long as all the operations are performed in a definite causal order, i.e., as long as only causally separable resources are used. The observation of a negative expectation value is thus sufficient to conclude that the operations were not performed in a definite order.

    Causal witness can be constructed efficiently and the construction is discussed here).

  3. SWITCH is a further basic notion. One has two events A and B, which can be connected by a time-like curve. One can tell whether A precedes B or vice versa. SWITCH is a quantum operation switching the causal order. The obvious manner to do this would permute A and B and would require "time travel" not allowed in standard physics. Obviously, SWITCH cannot be realized as operation respecting fixed causal order.
  4. If superpositions of causal orders are possible, one can have a situation in which causal order is indefinite. Also this is something which does not conform the ordinary view about physics in fixed space-time but is allowed by postulates for quantum computation and SWITCH represents an example of quantum computation impossible with a fixed causal order.
Needless to say, the notions of causal order and superposition of causal orders are revolutionary ideas and the article claims that they have been experimentally verified. Therefore there are excellent motivations to find whether they could be be understood in TGD framework.

In TGD Zero Energy Ontology (ZEO) replaces ordinary ontology and the arrow of time is not fixed, and it is interesting to see whether superposition of different causal orders related by time inversion T for causal diamond (CD) and SWITCH could be realized in ZEO. The twistor lift of TGD leads to the proposal that CD is accompanied by a Minkowskian generalization of self-dual Kähler form J(CD). Although the moduli space of CDs allows to avoid breaking of Poincare invariance, self-duality of J(CD) leads to violation of T implying that different causal orders correspond to disjoint sectors of "world of classical worlds". This makes possible also superposition of different causal orders and SWITCH would map these sectors to each other.

2. ZEO and discrete symmetries for twistor lift of TGD

Some background about TGD is necessary in order to to proceed.

  1. Zero Energy Ontology (ZEO) is the cornerstone of TGD and TGD inspired theory of consciousness. Zero energy states appear as two variants and correspond to different WCW spinor fields (WCW for "world of classical worlds"). I have proposed that they correspond also to WCW spinor fields localized to different sectors of WCW but this might be un-necessarily strong assumption.

    Zero energy states for given basis have been subject to a state function reduction at either boundary of CD - passive boundary. Neither the passive boundary nor the members of state pairs at it appearing in the superposition of state pairs are affected in repeated state function reductions. One has what I have called generalized Zeno effect identified as conscious entity - self.

    At the opposite boundary the states evolve: every state function reduction at active boundary is preceded by a unitary time evolution ending to a localization of the active boundary of CD, which can be also seen as a state function reduction (see this). The temporal distance between the tips of CD increases in this process and gives rise to clock time and experienced flow of time.

    Eventually the first reduction to the opposite boundary occurs and the roles of active and passive boundary of CD are changed. One can say that time reversed zero energy state is obtained and begins to evolve. The first reduction to the opposite boundary would mean death of the conscious entity defined by the sequence of state function reductions at the same boundary and generation of time reversed re-incarnation of self.

  2. Violation of T - to be discussed below - would also imply asymmetry between selves and their time reversals. For instance, the average duration for the state reduction sequences keeping boundary fixed could be different and second causal order could dominate giving rise to a dominating arrow of time. Since these reduction sequences are identified as correlates for conscious selves, the time reversed re-incarnations would live much shorter time. Biological systems might be an exception: in TGD inspired theory of consciousness sensory perception and motor action are time reversals of each other.
  3. Fermionic oscillator operators associated with induced spinor fields allow to represent WCW gamma matrices as their linear combinations: Fermi statistics is geometrized. Fermionic oscillator operators define also quantum Boolean algebra in the sense that fermion numbers 1/0 correspond to the two Boolean values. One could say that quantum logic is square root of WCW Kähler geometry. This allows to interpretation the S-matrix for fermions as quantum Boolean map between quatum Boolean algebras at opposite boundaries. This is obviously important when one talks about quantum computation.

    In the approach to twistor amplitudes (see this, this, and this) fermions are localized at the boundaries of string world sheets defining light-like curves at the 3-D light-like orbits of partonic 2-surfaces, at which the signature of the induced metric changes from Minkowskian to Euclidian and has a vanishing determinant so that tangent space is effectively 3-D. The interpretation is in terms of strong form of holography (SH) stating that the data determining both space-time surface as preferred extremal and modes of the induced spinor field in the interior of space-time surface. SH predicts that both the bosonic and fermionic 4-D actions reduce to 2-D effective actions for string world sheets.

    The implication is that fermion states at the boundaries of CD are localized at discrete points of partonic 2-surfaces. One has of course amplitude over different locations of fermions at partonic 2-surfaces. The presence of fermionic string world sheets correlates the fermions at different partonic 2-surfaces and serves as correlate for entanglement in fermionic degrees of freedom.

  4. The twistor lift of TGD (see this) has led to a rather detailed understanding of discrete symmetries CP, P,T. If M4 factor of imbedding space - or more precisely CD - is endowed with a generalized self-dual Kähler form J(M4) (analogs of magnetic and electric fields of same magnitude and direction), new violations of CP, P and T occurring in long scales and having no counterpart in standard model emerge. The reason is that CP, P and T do not respect the self-duality of M4 Kähler form. The violations of Poincare invariance are avoided if one assumes moduli space for CDs containing the Lorentz boosts and translations of CD.

    The first guess is that T leaving the center point of CD invariant applied to the CD maps the 3-surfaces at the boundaries of CD to each other. The violation of T however implies that the image of the pair need not allow preferred extremal (space-time surface) connecting its members.

    One can however define the temporal mirror image of pair by mapping only the 3-surface at the passive boundary to the opposite boundary: preferred extremal property would determine the 3-surface at the passive boundary. This could imply that the sub-WCWs formed by pairs and the time reversals are disjoint and form different sectors of WCW (see this). This realization of T allows also the possibility that the dynamics of preferred extremals is not strictly deterministic (true at least for p-adic space-time sheets).

    In absence of T violation T operation would also permute the values fermionic states partonic 2-surfaces at the boundaries of CD but if T is violated, can map only the state at the passive boundary to the opposite boundary and determine the state at original boundary from the hermitian conjugate of S-matrix in opposite time direction. The fermionic state at the opposite boundary would be superposition of states having only same total quantum numbers as the state at the passive boundary. The quantum numbers of individual fermions would not be sharp for non-trivial S-matrix if the zero energy states and their T images correspond to same sector of WCW.

    If T is not violated, zero energy states and their T-images would not correspond to the same sector of WCW. Obviously they would correspond to opposite causal orders, see below) This would force to give up the assumption that states at passive boundary are state function reduced. If T is violated globally, the zero energy states and their T-reversals would correspond to disjoint sectors of WCW, and the sectors would only correspond to different arrows of time. This option gives hopes about WCW localization the outcome of the measurement of causal order.

    The union of sub-WCWs with opposite arrow of time is a space with fixed causal order plus additional binary digit characterizing the causal order. The state function for this binary digit could fix the causal order and quantum computation generating superposition of causal orders should generate entanglement with this bit.

  5. What about the situation for a union of CDs? Different CDs should be able to have their own arrow of time. For instance, there are reasons to think that in living matter one can have subsystems with non-standard arrow of time. Also phase conjugate laser ray could be also example of this. This requires that WCW spinor fields associated with a union of CDs form a tensor product. Causal order need not be same for all CDs but characterizes the sub-WCW associated with CD forming a Cartesian factor of WCW so that WCW spinors for the CDs form tensor product.
3. Two views about SWITCH and superposition of causal orders

One can imagine two approaches to the identification of SWITCH operation and superposition of causal orders.

3.1 Option I: Unitary SWITCH as time reversal

The first option corresponds to corresponds to unitary "time travel" option.

  1. As already proposed, SWITCH as a unitary operation could correspond to T. Time reversal operation T applied to the 3-surfaces at the boundaries of CD would naturally change the causal order for the zero energy state. If T is violated the state and its T-image belong to separate sectors of WCW. One could also have a superposition of zero energy states related by T and having different causal orders and localizable to the two sectors of WCW.
  2. Is it possible to perform SWITCH as a unitary (as a matter fact, antiunitary) operation? If T maps the disjoint sectors to each other and maps fermionic time evolutions to their time reversals, SWITCH maps the two sectors of WCW to each other.

    Can one realize SWITCH mathematically as a unitary operation between fermionic state spaces. This seems possible: the tensor product of S⊗ S on tensor product of fermionic Fock spaces would realize this map. Whether SWITCH can be realized physically is of course another question.

3.2 Option II: Non-unitary SWITCH as the first state function reduction to the opposite boundary of CD

Could non-unitary SWITCH be realized as the first state function reduction to the opposite boundary - death of self followed by a re-incarnation as time-reversed self? In this case SWITCH is neither unitary nor deterministic. This SWITCH corresponds to non-unitary "time travel" option in the sense that self identified as passive boundary makes a time travel to the opposite boundary of CD by re-incarnating in non-deterministic manner.

What about the superposition of self and time reversed self as a superposition of causal orders? Schrödinger cat would be more than a catchy metaphor: it would indeed be a superposition of cat and re-incarnated cat! Should one take this seriously?

If the CDs with different arrow of time correspond to different sectors of WCW, different causal orders correspond to states localized in these sectors. A superposition of causal orders would correspond to WCW spinor field having component in both these sectors. If the state function reduction to opposite boundary of CD takes place at the level of entire WCW - or more realistically, for a Cartesian factor of WCW, it must be accompanied by a localization to either sector of WCW in order to avoid paradoxes.

I have already earlier work with TGD inspired ideas related to quantum computation. For more than decade ago I developed rather speculative model topological quantum computation in TGD framework (see this). One speculation about super-effective quantum computations is inspired by the analogy of selves with quantum computations halting, when the self dies and re-incarnates as time reversed self with clock time running in opposite direction at opposite boundary of CD (see this). This would mean using the non-unitary SWITCH realized as state function reduction in quantum computation.

This allows to imagine a series of quantum computations at opposite boundaries proceeding as a sequence of re-incarnations so that the size of CD and thus clock time would grow in opposite directions during subsequent incarnations (see this). Although the re-incarnation as time reversed self could have long life-time, it would not be seen by an observer near the former re-incarnation and the re-re-incarnation would appear at clock-time, which need not be much later than the time of previous death. One could imagine that the time-reversed selves could have very long life-time or that the self could die and re-incarnate very many times without any-one noticing it! The large amount of time spent in time reversed mode could explain the miraculous cognitive feats of mathematicians like Ramajunan and also the magic computational abilities of idiot savants able to factorize large integers without any idea about the notion of prime.

4. Higher level quantum computations and ZEO

From the article of Rubio et al one ends up to an article Quantum computations without definite causal structure by Chiribella et al (see this). The article considers a rather far reaching generalization of quantum computation. Ordinary quantum computation is a time evolution of quantum states followed by a state function reduction. Since the outcome of state function reduction halting the quantum computer program is non-deterministic, the extraction of the result involves statistical averaging over a large enough number of quantum computations to get the outcome, say prime factorization or a period of periodic function.

The notion of classical computation is generalized by Church. The computation need not be a function but can assign function to a function. One can continue this abstraction hierarchy indefinitely and it is realized formally in terms of so called Λ calculus (see this). Could this hierarchy be extended to quantum computations? The quantum computation in question would be kind of super-computation assigning to quantum computation a quantum computation and entire hierarchy of quantum computations.

In TGD this kind of hierarchies emerge naturally. At space-time level there is hierarchy of space-time sheets: space-time sheet is (topologically) condensed to a larger space-time sheet and contains smaller space-time sheets condensed at it. The hierarchy of infinite primes corresponds to an infinite hierarchy of second quantizations and could relate to this hierarchy (see this). In each scale space-time sheets would be particles consisting of smaller particles consisting of ... Even galaxy could be seen as elementary particle in some scale characterizing the galactic space-time sheet.

The analog of quantum computational hierarchy emerges quite concretely in ZEO. The simplest zero energy states have positive and negative energy states with opposite total quantum numbers at the opposite boundaries of CD (intersection of future and past directed light-cones). One can have CDs within CDs. Furthermore, the positive/negative energy states assignable to the boundaries of CD could be also zero energy states associated with smaller CDs near the boundaries of CD. The simplest zero energy states correspond to quantum evolution representing ordinary quantum computation. Higher level zero energy stats would represent time evolution assigning to a quantum computation represented as zero energy state at the boundary of CD a second quantum computation at opposite boundary of CD.

The fermionic representation of quantum Boolean algebra makes this hierarchy quite concrete. At lowest level unitary evolution connects positive and negative energy fermionic states at opposite boundaries of CD and unitary S-matrix characterizes the computation. Higher level computations connect zero energy states assignable to sub-CDs near the boundaries of CD.

See the chapter Topological Quantum Computation in TGD Universe and the article Quantum computations without definite causal structure: TGD view

Viruses as fragments of topological quantum computer code?

I was listening a highly interesting talk about viruses in Helsinki by Dr. Matti Jalasvuori, a molecular biologist working in the University of Jyväskylä as a researcher (see this). He has published a book about viruses in finnish titled "Virus. Elämän synnyttäjä, kuoleman kylväjä, ajatusten tartuttaja" (see this).

I learned an extremely interesting new-to-me fact about viruses. They might be far from a mere nuisance, In TGD Universe they could be quantum memes, short pieces of a code of quantum computer code, wandering around and attaching to the existing quantum computer code represented by DNA! Replication of viruses would be replication of memes. If the infected organism survives the virus attack by taming the virus and making it part of its non-coding DNA, it will gain more strength! If my computer survives the updating of the operating system, it works better!

Some basic facts

Viruses are very small, few nanometers is the size scale. Virus contains short pieces of RNA or DNA coding for the virus, in particular the protein shell around it, which virus must have in the "non-living" state outside the host cell to which it can penerate. Inside its host this shell melts and virus attaches to DNA and is able to to replicate. The copies of virus leave the host cell to search for their own host cells.

Usually viruses are regarded as a nuisance. But a new more holistic vision is evolving about viruses and their actual role. Viruses have been present perhaps even before the cell was present in its recent form, they might have been crucial for the emergence of life as we know it and would be also now. The system would consist of various kinds of cells, not necesary those of single organism. The contain several kinds of DNA and RNA: cell nucleus and mitochondria contain their own genomes; there are circular plasmids, and also viruses.

There is a continual exchange of information between cells including viruses as form form of information exchange. In this framework virus represents a meme represented by its DNA ,which does not code for protein shell. This meme wants to replicate and must use the genetic machinery to achieve this. But does virus do this to only replicate and produce more nuisance?

The organism manages to survive the virus attack if it is able to transform the virus so that it cannot replicate. One manner to achieve this would be transformation of the DNA portion due to the attached virus DNA (possible reverse transcribed from the RNA of virus) to a non-coding DNA often referred to as "junk" DNA. Non-coding DNA includes both intragenic regions - introns - and intergenic regions containing for instance promoters and enhancers crucial for the control of gene expression as proteins (see this). Introns are portions of genes, whose contribution to mRNA is sliced away in translation to proteins. The decomposition to introns and translated regions is dynamical, which gives rise to a rich spectrum of different translations of the gene.

In fact, most of non-coding DNA might be due to viruses! The portion of non-coding DNA increases for speciei at higher evolutionary level. For our species it is estimated to be 98 percent! Most of our genome is "junk" as many biologists still would put it. But can this really be the case? On might think that immune system would have invented some mechanism to prevent the infection of DNA by junk DNA? The size of the trash bin cannot be a measure for evolutionary level! It is also known that virus infections force the organism to change and in some cases to become a better surviver. Viruses would drive evolution.

One can speculate that during the very early period in evolution there were only viruses and proto-cells. There is no need for them to be coded by genes. Self-organization can produce cell membrane like structures: soap films represent an example. The DNA fragments could survive inside these proto-cells but according to simulations done by the Jyäskylä group in which Matti Jalasvuori is working, eventually the evolution would lead to the emergence of parasitic DNA strands, which would soon begin to dominate and kill the protocell.

Viruses might solve the problem. Viruses would attract DNA fragments and replicate with themto build a protein wall around the fragment containg also a piece of DNA of proto-cell. Viruses would leave the proto cell before its death and find another protocell. Gradually genome would be formed as viruses would steal pieces of DNA fragments from protocells. One step in the later evolution could be the elimination of the part of virus coding for the protein shell and the use of the rest as protein coding DNA. For eukariotes the transformation to non-coding DNA including intronic and intergenic DNA becomes possible.

Viruses as pieces of quantum computer code?

Computational thinking would suggest that viruses might make possible the emergence of new biological program modules allowing to use existing program modules coding for proteins more effectively. The different slicings of mRNA dropping some pieces away would correspond to different manners to transform DNA sequences to proteins. But what about intragenic portions of DNA: are they just junk?

Could the non-coding DNA and viruses have a much deeper purpose of existence than mere replication? In TGD Universe this kind of purpose is easy to imagine if the system formed by DNA - say intragenic portions of DNA - and nuclear membrane (or cell membrane) system serves as a topological quantum computer. DNA codons would be connected to lipids of the lipid layer of cell nucleus by magnetic flux tubes carrying dark charged particles. These connections could be also to cell membrane and even to cell membranes of other cells.

The braiding of the flux tubes would define the space-time realization of a quantum computer program. This would represent a new expression of DNA and would explain why so small differences between our DNA and that of our cousins give rise to so huge differences. What is important that genetic code would not be terribly important: it is braiding that matters now. The realization as quantum computer programs would give rise to cultural evolution, the realization as proteins to biological evolution. There would be a transition from the level of genes to that of memes.

Viruses would correspond to pieces of quantum computer code - memes. They would be wandering between cells and infecting them to get fused to the DNA. If DNA is able to transform them to introns it gets the code. Otherwise it dies. Infection is the necessary price for achieving meme replication. Living cells could be seen quantum computer programs updating them continually. Sounds somehow familiar!

See the chapters DNA as topological quantum computer, Three new physics realizations of the genetic code and the role of dark matter in bio-systems, and More Precise TGD Based View about Quantum Biology and Prebiotic Evolution.

How Was Ancient Mars Warm Enough for Liquid Water?

The popular article Mars Mystery: How Was Ancient Red Planet Warm Enough for Liquid Water? tells about a mystery related to the ancient presence of water at the surface of Mars. It is now known that the surface of Mars was once covered with rivers, streams, ponds, lakes and perhaps even seas and oceans. This forces to consider the possibility there was once also life in Mars and might be still. There is however a problem. The atmosphere probably contained hundreds of times less carbon dioxide than needed to keep it warm enought for liquid water to last. There are how these signature of flowing water there. Here is one more mystery to resolve.

I proposed around 2014 TGD version of Expanding Earth Hypothesis stating that Earth has experienced a geologically fast expansion period in its past. The radius of the Earth's space-time sheet would have increased by a factor of two from its earlier value. Either p-adic length scale or heff/h=n for the space-time sheet of Earth or both would have increased by factor 2.

This violent event led to the burst of underground seas of Earth to the surface with the consequence that the rather highly developed lifeforms evolved in these reservoirs shielded from cosmic rays and UV radiation burst to the surface: the outcome was what is known as Cambrian explosion. This apparent popping of advanced lifeforms out of nowhere explains why the earlier less developed forms of these complex organisms have not been found as fossile. I have discussed the model for how life could have evolved in underground water reservoirs here.

The geologically fast weakening of the gravitational force by factor 1/4 at surface explains the emergence of gigantic life forms like sauri and even ciant crabs. Continents were formed: before this the crust was like the surface of Mars now. The original motivation of EEH indeed was that the observation that the continents of recent Earth seem to fit nicely together if the radius were smaller by factor 1/2. This is just a step further than Wegener went at his time. The model explains many other difficult to understand facts and forces to give up the Snowball Earth model. The recent view about Earth before Cambrian Explosion is very different from that provided by EEH. The period of rotation of Earth was 4 times shorter than now - 6 hours - and this would be visible of physiology of organisms of that time. Whether it could have left remnants to the physiology and behavior of recently living organisms is an interesting question.

What about Mars? Mars now is very similar to Earth before expansion. The radius is one half of Earth now and therefore same as the radius of Earth before the Cambrian Explosion! Mars is near Earth so that its distance from Sun is not very different. Could also recent Mars contain complex life forms in water reservoirs in its interior. Could Mother Mars (or perhaps Martina, if the red planet is not the masculine warrior but pregnant mother) give rise to their birth? The water that has appeared at the surface of Mars could have been a temporarily leakage. An interesting question is whether the appearance of water might correspond to the same event that increased the radius of Earth by factor two.

Magnetism is important for life in TGD based quantum biology. A possible problem is posed by the very weak recent value of the magnetic field of Mars. The value of the dark magnetic field Bend of Earth deduced from the findings of Blackman about effects of ELF em fields on vertebrate brain has strength, which is 2/5 of the nominal value of BE. Hence the dark MBs of living organisms perhaps integrating to dark MB of Earth seem to be entities distinct from MB of Earth. Could also Mars have dark magnetic fields?

Schumann resonances might be important for collective aspects of consciousness. In the simplest model for Schumann resonances the frequencies are determined solely by the radius of Mars and would be 2 times those in Earth now. The frequency of the lowest Schumann resonance would be 15.6 Hz.

For background see the chapters Expanding Earth Model and Pre-Cambrian Evolution of Continents, Climate, and Life and More Precise TGD Based View about Quantum Biology and Prebiotic Evolution of "Genes and Memes" .

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