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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.
Without bio-catalysis biochemical reactions leading to the formation of biopolymers and cell membrane would be quite too slow. Here phosphorylation enters the game.
2.5 The difference between organic and inorganic phosphates
Phosphate appears as too variants: organic and inorganic.
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.
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.
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.
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.
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.
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?.
Are all of us artists? I could immediately answer the question: we are artists - all of us. This is what my "Great Experience" taught me about consciousness before I had any theory of consciousness. I started to work systematically with the problem of consciousness - that is to write a book, which is the manner I work - only 10 years after this experience.
What I claim is that the construction of sensory mental images is not a passive process but a creation of an artwork, kind of caricature giving a representation of the sensory input optimal as far as survival is considered. This means decomposition of the sensory input to features and picking up the key features relevant for the survival.
The article with link below is a written and slightly longer version of a talk in which I told about the role of vision in sensory experience seen in the theoretical framework provided by TGD inspired theory of consciousness. I decided to tell about my "Great Experience around 1985 since it divides my life to two parts: life before and after this experience, and because this experience provided fascinating insights to consciousness and perception, not only visual, but also auditory perception and proprioception (body experience). I have told about this experience in my homepage (see this) and in some material in books and articles to be found there (for instance).
There are online books about TGD proper and two published books (Luniver and Bentham). For TGD inspired theory of consciousness and quantum biology see the online books at my homepage and the published book about consciousness and quantum biology (Lambert). The article Philosophy of Adelic Physics published by Springer explains the recent vision about the mathematics forced by consciousness theory.
For details see the chapter Magnetospheric sensory representations or the article Are we all artists?: or what my "Great Experience" taught me about consciousness.
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.