Continuity between molecular evolution and darwinian evolution

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2A01:E35:1398:B70:22CF:30FF:FE80:2C75 (discuss) 19:47, 29 May 2014 (UTC)Mekkiwik

Continuity between molecular evolution and Darwinian evolution

20.7.13  Paris  

Introduction

Suppose that we have described and demonstrated experimentally the different stages of the scenario to move the mineral world to the living world. This is what I call molecular evolution. The question that then arises is how can we move from molecular evolution to Darwinian evolution based on the infinite reproduction of a sequentially (linearly) structured information , while molecular evolution has apparently not structured information.

At most, the mineral can organize itself as in a crystal, or in general by gathering similar entities: the water molecules come together to give the liquid, Zn sulfate molecules to precipitate in ore. It is known that the classical properties of the chemical elements that can purify a particular molecule. Each molecule has an intrinsic high purity is its timely information. These molecules are usually small (a few atoms) and are never a permanent group constituting an identifiable entity in time: all crystal crumbles with time and fortiori not be reproduced and does not multiply.

- - - - - - - - - - - - - following items with abstracts - - - - - - - - - - - -

• Constraint-freedom, action-reaction distance, reproduction, organization.
• Constance-variability, action-reaction between the body and the external environment or between macromolecules, organization, identical reproduction.
• What is missing for the prebiotic is information (and its management = organization). The result of molecular evolution is the establishment of the information.
• The passage of the Constraint-freedom to Constance-variability allows greater efficiency of action-reaction (renewable through information rigidity), complexity of the organization (more suceptible destruction, but renewable the reproduction of information) and the perfection of reproduction. These two processes CL and CV coexist in time and space. If the C-V can lead to astronomical complexity, however, it may disappear if Darwinian evolution disappears after a natural disaster or even this complexity. CL process can still reproduce Darwinian evolution even if it takes billions of years. But the duration may be limited if one takes into account bacteria and viruses. Just as the conditions of molecular evolution exist, ie the prebiotic petroleum.
• There is currently hierarchy between these processes in the following order (for the two evolutions, molecular and Darwinian)

1. C-L
2. organization
3. action-reaction
4. reproduction

Quantum mechanics involved in the action-reaction and crystallization in particular viruses for HGT (horizontal gene transfer)

All this is not possible in a mold of mineral surfaces (stiffness).

- - - - - - - - - - - - - end of abbreviated items - - - - - - - - - - - - - - - -

The strength of the postulate of pocket prebiotic petroleum as the starting point of the origin of life

Compared with the RNA world that requires monomers and mineral surfaces which are closer to the mineral.

 

24-7-13 Paris

•  Evolution is the appearance, what we see from the outside.
• But from molecular point of view, what are the physical constraints that can move from one organization with 2 dimensions, free, without information (liposome) to a rigid organization, with one dimension, containing information (DNA)?

1. In the liposome main physical strength is hydrophobicity plus hydrogen and ionic bonds at the head.
2. In DNA the main physical strength which still allows freedom is the hydrogen bond (note 5/28/13: plus aromaticity, electron synergy). Molecular evolution has created the meantime a chain of rigid and permanent covalent bonds (stable) instead of RNA.

The only constraint that can put side by side two or more nucleotides is chelation peptides themselves in zwitterionic bond with PLDs, as the establishment of hydrohile head with Serine.
This chelation leads a virtuous circle because it causes not only more efficient catalysis but also an organization more and more complex bringing closer certain molecules. This is the contrainst-liberty as with aa/PLD.
   This chelation is much more flexible than between aa/metal-ion because it uses only hydrogen bonds or, at the end, an ester bond (or phosphoester) movable by physico-chemical equilibrium.

Another constraint of global type is quantum synergy created by the physical organization of cytoplasm: cations K+ constitute a sphere parallel to PLDs of the membrane and DNA chains would end up cornered in the center of the cytoplasm. Circular DNA is the ideal geometric shape as the sphere is to the liposome.
   Does this arrangement PLD-K+-DNA has an influence or using only the establishment of linearity and sequenciality DNA?

The RNA instability creates numerous catalyst combinations and catalysis itself is very powerful and fast and can be structured in space and time due to peptides: it is the evolution to the ribosomes and ribozymes.
    This structure is very effective in creating rigid structures such as enzymes but is not flexible enough to continue functionally as the liposome or stable enough to store forever information as DNA. Indeed RNA is very labile and even more enzymes.

The DNA has a very different relationship with the peptides. I resumed here (prebiotic chirality) the assumption that it is the dNTPs that began the evolution of nucleic acids.

1. DNTPs have, as monomers (or oligomers have little), the role of coenzyme, may be less effective than NTPs, but it is interesting for the early molecular evolution, because the events will slowly and the information recorded in the oligomers thus more stable and more permanent.
2. In addition, the molecular evolution of this relationship peptide/DNA go towards the replication and transcription and not to the translation: evolution in continuity with the reproduction of prebiotic liposomes. But in addition, with transcription that involves two relationships aa/DNA and aa/RNA, this development gives rise to the mRNA. From this point of view is the DNA prior to RNA.
3. Viruses are crystals, where backup information because ribosomes are more difficult to make.

GNA: Glycerol instead of ribose. More stability than with ribose (RNA) or d-ribose (DNA). The work was far since with a eukaryotic DNA polymerase was able to synthesize the GNA. But efficiency is only valid for purines (A, G), it is much lower for C and zero for T.
   Glycerol-P is my favorite for the initialization of metabolism (prebiotic chirality) and this is the most simple sugar derived from DHA formose reactions, hydrogenated during the formation of the PLD.
   To start a prebiotic it is not necessary that the GNA is as perfect as the DNA. The DNA may appear in a second time when the d-ribose, requiring a single step, appear. GNA will certainly be more effective than DNA in catalysis (but less than RNA), especially as poly P-G exist and have an important role in the membrane and form a stock of poly-P in the current living world.
   When will appear ribose-P, requiring five steps, then the organization of the whole will be advanced and strong to accommodate the frenzy of RNA.

TNA :Works are similar to that of GNA and even earlier, but the tetroses require at least three steps for their synthesis.

[ note on 4.8.13 : meantime I read the wikipedia article on DNAzymes. To add to the role of coenzyme monomers dNTP, paragraph before GNA. ]

[ note on 29.8.13 : Two successive bases are separated by a further carbon in the sugar-P skeleton with DNA and RNA than for TNA and GNA. The distance between the bases must be very important for aromaticity. The bases are separated by water molecules or other small molecules. They are side by side and therefore their electron clouds, 'pi', can come into resonance creating immense physical forces on the chain reaction causing the repair enzymes. We are no longer in the liquid state but in a liquid crystal state. ]

Constraint-freedom:

4.8.13

1. Thermodynamics:

• Open system, random collisions = liquid solution. We are talking about free energy and enthalpy wich do not take account of entropy. This is the principle of freedom.
• You can reach a highly organized state, increasing hydrostatic pressure and decreasing temperature: It's crystallization. It is the mineral, frozen like death. This is the principle of constraint.
• An intermediate situation exists where the two principles coexist. This is a mineral surface (more or less ordered crystal) contacted with an aqueous solution. At the interface, the crystal-network imposes its order and allows chemical reactions in solution, reactions which may not take place in a single solution. This is due to the physics of the mineral surface with vast fields of electro-magnetic, electrical or ionic strengths.
     However, it is still in an open system, the organization stops a few molecules of the surface inside the mineral is not communicating with the rest of the aqueous solution. A large number of experiments in the literature show the synthesis of numerous organic molecules with inorganic surfaces.
• The principle constraint-freedom (the previous two together in this concept) is represented by the movement of the molecules in solution wich are constrained by the mineral surface to establish covalent bonds. It is this mixture of order and movement that I take as a starting point of molecular evolution with liposomes./li>

2. Liposomes:

[in the introduction 20.07.13 finish with the announcement of chapters CL / CV, action / reaction, organization, replication continuity between the current cell and liposomes. In the articles "chemo-osmosis" and "chirality" I approached these concepts from the perspective of processes that define the liposome as the first prebiotic entity defining the biological being and initialize the prebiotic metabolism. In this article I try to raise these concepts at common fundamental principles and continuity between the prebiologic entity and the current living biological cell. ]
   I studied in "chirality" movement of PLDs in the liposome. This is what made ​​me discover the possibility of establishing chirality for a mechanical cohesion of the liposome as a whole. I also made in this section the parallel, described in the previous paragraph, with the mineral surfaces for catalysis and initialization metabolism. The concept of constraint-freedom was there but not explained. Here I will explain and compare to mineral surfaces in the preceding paragraph (thermodynamics) to reach the level of fundamental principle.

• While mineral surfaces are planar and infinite, the liposome has two spherical surfaces defining a closed thin aliphatic thickness that enables communication between inside and outside. (to be developed, medium closed plus diffusion).
• The mineral surface of the liposome is composed of only the phosphate PO4 ion, inorganic molecule like SiO4 example. But these phosphate ions are attached to the free PLDs and moving all the time. While the mineral surfaces in the ions are fixed in a plane and that the liposome is then closed.
• Each PLD has a zwitterionic head (2 ions) with P ^- and an amine ⁺ or almost zwitterionic, with P ^- and OH glycerol (hydrogen bonding), or it may, on the inner surface wear even 2 anions P ^- and COO ^- and a cation NH3 ⁺ in the case of PLD PS. Mineral surfaces essentially containing inorganic ions of a given electric charge, anionic or cationic. And in general it has no zwitterionic entity, even if zones with different charges were side by side.
• Thus the concept of constraint-freedom, in the liposome, is doubly present and the molecules of the aqueous solution that are constrained by the ionic surface apparently rigid, and the P ^- ions, which may be to move in a two dimensional space.
• However this principle C-L can prove defective if in the liposome surface freezes. It can freeze or become rigid (crystal), such as mineral surfaces, in 2 cases:
• Homogeneity of hydrophilic heads leading to crystallization. By numerical simulation I saw that one liposome made by only PG PLD likely to crystallize with the generalized hydrogen bonds as in the ice. The anionic surface becomes only (P ^- ) as a mineral surface. So far life.
• The conditions of T and P are such that the zwiterrion becomes ionic bond, as in a crystal. This is the case of high pressures. And even lower pressure PLDs can not move and liposome loses his freedom and becomes like a mineral surface with the free single aqueous solution.
• Thus we see that the C-L principle should be generalized, at least at the beginning of molecular evolution. Requires that 2 parts C and L are intimately linked: C is represented by the surface, but in this surface entities are free. Here we touch the organizing principle that I develop further. And then we can design molecular evolution as an organization increasingly rigid or complex without exceeding a certain threshold. That's what I'll demonstrate with DNA and transcription factors after declining 3 other principles of organization, action / reaction and reproduction.
• C-L principle in the liposome is due to the lower forces, VdW forces. According to the previous pragraphe we see that the C-L principle will evolve involving bonds becoming stronger, in ascending order: VdW, hydrogen, acid anhydride, ester, amide, ether.

3.Darwin's natural selection:

6.8.13 Mont d'est

• The Darwinian evolution is observed at the macroscopic level, the level of multicellular and unicellular species, whether procarryotes or eukaryotes. It is defined by the constancy of the characters in the species, and variability among individuals. At the molecular level, it is subtended by the DNA. But the DNA molecule is an almost crystalline, since it consists of two linear strands held together by hydrogen bonds between all nucleobases whose number, in base pairs may exceed 10 million in prokaryotes.
• From this point of view, it has nothing to do with the liposome, intimate mixture of constraints and freedoms. Yet its macroscopic manifestations, constancy and variability are equivalent molecular behavior of the liposome, respectively behavior constraint and freedom.
• The result of molecular evolution is precisely to reproduce in DNA these two fundamental principles in an organization more and more structured. Molecular and Darwinian Evolutions would thus based on the same basic principles of evolutionary C-L (C-V), organization (memory, information), action/reaction (control channels) and reproduction (replication).

the organizing principle:

1. Thermodynamics:

• ionic bonding (electronic bond) in the crystals. In liquid ions are surrounded by a cloud of H2O. Instead of an ionic bond we have a group of H2O oriented from the -, linked with the H of H2O, to the +, linked with the O of H2O. The cloud is spherical. So positioning of ion + and - must have the same configuration as in a crystal. If one starts from a dry crystal water, and we added a little water, this water will be inserted between the + and - but will not destroy the relative positions. Only distances and amplititude vibrations change. In solution (plenty of water) the + and - do not move independently of each other and keep more loosely structure dry thanks to the crystal oriented H2O clusters.
• K+, NH4+ (-NH3+) are similar in size. So their clouds of H2O are also similar and they would gather. And even more so if the majority anion is also the same size. This is the case of -PO4=. This would explain why K+, by resemblance with -NH3+ and -PO4=, is inside the cell and Na+ and Cl- outside:
• Number of internal ions (e.coli), K⁺_i = 10⁸ Na⁺_i = 10⁶ ~ Cl ^-_i       Na⁺_x/Na⁺_i = 20.
• Ionic radii (pharmacorama): Na⁺_r = 97 pm K⁺_r = 133 pm (+40%) NH4⁺_r = 145 pm (+5%) Cl ^- _r = 181 pm (free and unique). Ca⁺⁺_r = 99 pm Mg⁺⁺_r = 66 pm. Polarizability is given as a result the number of electrons: Na⁺ = 10e, K⁺ = 18e.  Problem of ionic radius of NH4+ : Atkins De Boeck Supérieur 1998 page 265, 137 pm. Wiki english, 175 pm. others: equal to K⁺_r.
  

  Element	Li +	Na +	K +	Mg ++	Ca ++	Fe 3+	F -	Cl -
  Ionic radius A°	0,68	0,97	1,33	0,66	0,99	0,64	1,33	1,81
  Enthalpie of Hydration Kj/mol	-519	-406	-322	-1921	-1577	-4430	-515	-381

• =PO4^- fixed and large, bond P-O^- = 156 pm to which we must add the radius of O (wiki). (phosphate-verre 145 see annexe 3.1)
• Ca++ : H2O molecules must create two clusters aligned, but in opposite directions, to attach to Ca++ (electron repulsion of the oxygen atoms). In a solution, while keeping the configuration of a loose crystal with anion, the cation, by its double charge, swirl and will therefore disrupt other ions H2O environments and will be more readily chelated by molecules with two atoms electron donor (anion or electron pair). And especially since the ionic radius of Ca++ is great. In the case of Mg++, the ionic radius is 50% smaller, so its swirl is less disruptive and more difficult to chelate. So that in E.coli there are only 40 cations Ca++ free against 2000 (?) Chelated while Mg++ cations are at 4,000 and all free.
• The organization of H2O and solutions in general......

2. The organization of the liposome:

7.8.13 Mont d'est

• Recall liposome formation with the postulate of prebiotic petroleum, where the article on prebiotic chirality.
• Phase separation due to VdW forces
• K+
• invagination and non self-assembly
• Implementation of constraint-freedom: anhydride bonds of fatty acids where the PLDs with 2 alkyls
• Forming heads: ester bonds, DHA-P, PS and PE PG PLDs (formose reaction)
• Chirality + cohesion + dipole + length of alkyls + pressure
• Initialization of metabolism where dATP = A + P + glyceraldehyde-Acetaldehyde (but no ATP)
• dCTP, CTP, Ser: gathering ADN ARN Proteine.
• Diffusion of small molecules + indole + bases .... where specific chemistry inside = sugars + α helix screwed to the membrane
• Hanging aas by hydrophilic heads where pseudo-peptides, channels
• Enzymes in or attached to the membrane. Free enzymes? where central metabolism
• Consequences: small aas (DHA Ser Gly Cys Ala Thr), hydrophobic aas caught by the outer face (FWA ... GP)
• Problem of other aas EKQRH:
• E    to form a ring (wiki aas)
• Q   inside E + NH3
• K    neutral form becomes almost aliphatic
• R    ornithine first input (as K), then adding inside carbamoyl-P.
• H    be remaining H

3. Organization of ADN

8.8.13 Mont d'est

• I seek here to identify the principle constraint-freedom (and not resume that is, as we have seen, due to the sequence of bases and their modifications). That's how I discovered the chirality with the liposome describing its organization and its formation.
• The first observation that appears to priori trivial, is that the bases are in the form of a linear sequence, bases can never interact remotely as between aas in a protein which is also linear. Base interacts only with its two neighbors, the front and the rear, strengthening the structure by the VdW and aromatic forces. And no base should be free (unpaired). This sequentiality is enclosed in a strong-box by the strict pairing between two complementary strands through hydrogen bonds, much stronger than VdW and aromatic bonds to which they be added. It's almost a crystal. These are the attributes of a storage medium. This memory is strict record of all steps of the many life processes that occur over time and not in 3-dimensional space. It is a relentless logic and is linear. It can not be 2-dimensional. For a given process the number and arrangement of bases should always be the same.
• We reach the maximum principle of constraint. I say maximum and not total because the hydrogen bonds can be done and undone easily. It would be total, if instead of hydrogen bonds had covalent bonds. And this will be a crystal, so a mineral.
• The principle of freedom is thus introduced by hydrogen bonds. They are essential for the memory can be read and the process of life can continue. But they require opening the bases to interact with the outside world (outside the chromosome). This then connects us to the principle of action/reaction as to the hydrophilic heads liposomes interacting with its environment. But the principle of freedom also extends in the case of DNA to attacks from the outside environment: break the backbone or bases by radiation or foreign molecules in metabolism. But even molecules of central metabolism can attack the bases at the opening of the hydrogen bonds. Maintenance of the integrity of the sequence of bases is the guarantor of the principle of freedom. But it goes beyond the correction of errors since this freedom to create other arrangements and hence introduce variability of Darwinian evolution. As the constraint DNA crystallization introduce constancy of Darwinian evolution.
• Maintenance of the integrity of DNA is a full metabolism.
• Consistency and variability also exist at the atomic level, but they do not result from C-L principle, but the quantum state of the atoms. They are also only 2 elements, phosphorus and nitrogen.
• Phosphorus is consistency since almost, phosphorus is always present in the form of a tetrahedron H3PO4 in the living world. And even in the mineral world most mineral phosphorus are made of this molecule. It is unusual to find only phosphorus without oxygen, as is often the case with As wich is in the same column as phosphorus.
• Nitrogen is the variability. Indeed, the amine -NH3+ has the unique distinction among the elements of conformational change periodically with a frequency of 24 GHz. This configuration change is of great importance at the hydrophilic head of PLDs and aas. Importance for the cohesion of the liposome through the chirality, and its approach by aas.
• The second observation is that the bacterial chromosome is very long, up to 10 million bp not to mention some of eukaryotic chromosomes may reach 500 million bp. And as it is a double helix, any process to open it causes huge topological deformations. And even impossible to determine, as in the case of replication. That is why that involved special proteins, gyrase, topoisomerase, which recognize these distortions, cut it at some phosphodiester bonds and weld it afterwards. These deformations are possible only if the structure is flexible. For this there are only properties of bases which can be adapted, the skeleton being imposed by the sugar-P (P-dR for living beings other than virus). These properties include the number of types of bases and these bases properties. As the lipid bilayer where we associated the two principles of constraint and freedom.
• The number of types of bases in DNA can only be 4. When comparing the functional RNA after post-transcriptional modifications, where the number of types of bases in the tens, one may wonder why DNA is limited to two types of base pairs. This is the principle of constraint which limits as seen in the linear DNA. But it is also the principle of freedom that limit, because the metabolism of the maintenance of the integrity of DNA, guarantor of the principle of freedom itself, becomes either too complex or unreliable with respect to integrity.
• But one might ask why not be limited to one single base pair? It may very well point logically constitute a memory with 2 bases as in computer with zero and one. Only the topological viewpoint constraints are the same for AT and TA for example. So for the topology we have uniformity. And who says uniformity said quantum and thus crystallization and rigidity. Also the minimum imaginable is 2 types of base pairs. This satisfies the principle of constraint that must be maximum. The passage 3 types of base pairs may be prohibitive for chromosomes 10 million base pairs as was seen for the maintenance of the integrity. This may be possible, however, at the begining of molecular evolution with small strands of a few hundred base pairs.
• For very long chromosomes can improve the flexibility of the two types of base pairs by selecting the properties of the bases. As before this is not the intrinsic properties of two types that should be taken into account, but only the difference in flexibility. If this difference is too large we touch up the principle of constraint, against the maintenance of the integrity of the DNA should not change much. But even for the latter the intrinsic properties of the base remain paramount. This is particularly the case for the choice of dT instead of dU.
• The third observation is that there are proteins that are as opening the double strand to initiate transcription called transcription factors. They have no classical enzyme activity of etablishing or breaking covalent bonds. The radicals of their aas must establish ionic and hydrogen bonds with the backbone of P-dR, behaviors that are close to the sugar-P encapsulation of the central metabolism. But they must also establish hydrogen bonds with the four nucleobases. Which is much less common in the central metabolism. Then these proteins must move to establish more links to progress. Since DNA is a double helix, these proteins should also have alpha helices and as these have a right helicity, they can move along the DNA as a corkscrew is pressed. We then find another use and the chirality of sugar-Ps and that of aas for the penetration of alpha-helices in the membrane. Thus the origin or rather the need (constraint) to have these aas we now know. These are QRSL (see Tables counts of aas for transcription factors, in preparation):
• R for electrical charge + to hold on to DNA skeleton with electrical charge -. R can also create hydrogen bonds with bases.
• Q principally for its hydrogen bonds with bases.
• S and L for alpha helices.
• Hydrophobic aas for hydrophobic relations with bases
• K is less represented than in the free protein
• K and R dominate in the ribosome (with E?).
• Then we may explain the length of these aas by alpha helix and interaction with DNA and RNA.

The principle of action/reactionn

10.8.13 Paris

1. Thermodynamics:

• Hierarchically the principle of C-L is first compared to the principle of organization as we have seen previously. Constraint is produced by a pervasive and isotropic strength. It is represented by the hydrostatic pressure in the hypothesis of pocket prebiotic oil (ref.). So the origin of the organizing energy to molecular evolution in this type of hypothesis.
• We can see constraint as a control. But it has a notion of finality: it controls a process to arrive at a pre-determined goal. If we now remove the concept of finality control is a specific action in space and time, which may have no specific purpose. To this action a particular entity that reacts with a reaction, an opposite strength to return to its starting equilibrium.
• Classical physics study forces with the notions of action/reaction, from a human point of view. We start with a solid object big enough that we can handle: these are the contact forces. But we can also study the gravitation and electromagnetism by invoking a force that acts at a distance and propagates in a vacuum. Here as solid objects are used.
• Then applied these principles to any physical process. Applied to gas it gave thermodynamics which is doing quite well. Applied to the light, against this led to paradoxes that resolved with quantum mechanics, which combines in a single equation particle and wave (concept of material point or solid). But applied to liquids, these principles of solid state physics gave hydrodynamics, very dark matter as it does not account (simplification) of the electro-magnetic and chemical forces between material points with which a liquid is modeled. The results of thermodynamics and those of quantum physics, applied to liquids, led to modern chemistry oversimplified quantum mechanics. Yet molecular evolution does not allow simplification as relations between the countless molecules involved are beyond comprehension and even possibilities of digital simulations. Similarly, the principle of action/reaction of classical physics (material point) is no longer relevant in a liquid. And even remote action of the electro-magnetism is no longer possible, because there is no vacuum in a liquid. It takes a powerful external process liquid to act remotely on all its molecules, but in fact transmit the action closer and closer. A given molecule of the liquid can act on another molecule via its neighboring molecules. There are currently more contact force (it must be a solid body) or remote action. There are currently more than the attraction of the atomic nuclei and the repulsion of the electron clouds of the molecules. The resultant of these two forces is balanced by the hydrostatic pressure in the molecule of a given point. As the hydrostatic pressure varies with the distance the molecule will still motion. The distance between the centers of two molecules is a measure of the hydrostatic pressure, which is none other than the expression of the gravitation. And as the source of this pressure is more than matter (electromagnetism) gravity would be electro-magnetic in nature without electric or magnetic fields. Thus gravity always attracts toward the center of a mass of matter, since the gradient of the pressure is directed toward the center.
• 11.8.13 Paris
  [ Note: add the principle of initialization
• Initialization is imperfect: with foreign molecules (bases .... His) and synthesis of small molecules 1st (Ser, Gly, Asp). For DNA trapping aNs by transcription factors, self-duplicating some aNs ---> oriC, but also origin of the production process by fragment and not sequencely nucleotide by nucleotide and errors correction giving processes of initialization DNA synthesis, replication and metabolism of DNA maintenance (Darwin variability ).
• Slow evolution initiated by the principle of constraint/freedom and the principle of organization and finally the principle of action/reaction.
• This principle of initialization concerns 6 metabolisms:

1. Organization of communication between interior and exterior through the membrane: channels, diffusion, hydrophilic heads, membrane proteins.
2. The central metabolism: see prebiotic chirality.
3. The DNA restorative maintenance.
4. Post-transcriptional modifications.
5. The post-translational modifications.
6. The construction of the bacterial cell wall.

A priori initializations metabolisms could start with chemical reactions or possibly with a coenzyme (metal) plus some aas.

These metabolisms have their own existence as in automobile there is subcontracting completion or completions. The main process is the liposome, DNA, RNA and finally proteins. Main processes and metabolisms cooperating a virtuous circle. ]

2. The liposome:

• Quantum mechanics, volume of the liposome and hydrostatic pressure.
• Local action when a chemical bond forms (covalent or hydrogen) due to local pressure which brings the atoms or molecules involved.
• The organizing power of the cloud of water molecules around a molecule (or ion) varies greatly from one entity to another. Ions of transition metals are particularly organizers that the number of electrons of the 4d layer increases. This is because their electron cloud of layers 1+2+3 already contains 18 electrons. And this is why P, K and S are the first organizers of the structure: P for the membrane, K inside, and S for catalytic clusters (+ Mo).
• Transmission:
• Then change due to local action is transmitted radially. Tracking change step by step can also cause local action.
• The environment close to local action respond (reaction) causing a second change that is transmitted radially in his turn.
• The remote transmission of these changes corresponds to the theoretical principle of classical physics of remote action (note that most cases in classical physics we do not talk to remote reaction. Action/reaction is often contact point). Any action at a distance can be an organizer. The establishment of a chemical bond is not explosive. Or it is in synergy with the existing organization, or the 2 principles of constraint/freedom and organization include it in their process or dynamically by giving movement to certain structures or improving the overall organization. It is like a part of a scaffold is removed: it is provided for positioning a structure properly and slowly, or it is not the case and the part is reset or changed by another more appropriate. The scaffolding is well imaged as local actions (establishment of chemical bond) produce changes of low amplitude compared to an organization the size of the liposome.
• The loop: action/reaction, organization and contraint/freedom is virtuous. It is endless and produces other structures which settles this loop: liposome, DNA, nuclear membrane, organelles, organization and so on .... not to mention the reproduction that duplicates existing structures (liposome, DNA ).
• Dipoles, chirality and the transmission through the membrane:
• 2 chains: There is no vacuum in the liquid. As against the membrane consists of two inside layers of aliphatic chains, one opposite the other. Should they touch to communicate? One has the impression that there is no process (at the head) that can remove 2 chains to create a vacuum. In this case the interpenetration of the two chains can not be coincidental and would rather annoying, because if it was widespread it would take away the freedom to structure: 2 sheets move independently of each other, which ensures autonomy of the internal environment (cytoplasm). So if there is remote action in a vacuum, it should be very short or even the process of heads (including the chirality) constantly cancel this distance. It should be noted that the length of aliphatic chains is very controlled and varies with the hydrostatic pressure, the temperature range where bacteria are living close. At boundary temperatures they respond with a consolidation of the wall and archaea the nature of the chain unsaturated equips many to respond to vibrations due to temperature and goes up to eliminate the freedom of two independent chains to constitute a single, polyunsaturated in some archaea. Is the disappearance of the degree of freedom that makes me think that the bacteria appeared before archaea. Because it touches on the principle of constraint/freedom.
• Transmission: It is much faster than in a disordered liquid (or more complex). It will be even faster than local action puts into play a proton H +. The aliphatic chain is made of 16 or 18 C and therefore 32 H or 36, identical. The principle of indistinguishability of quantum mechanics (fermions, photons) that in principle the proton should move at the speed of light. But this is not the case, even an electron passing an electron cloud to another as H must pass from one to another carbon, without establishing covalent bonding. From this point of view, in archaea the maximum transmission through the membrane takes place by electrons passing a double bond to another. This transmission should be faster. This is due to the rapid changes due to temperature.
• Dipoles and chirality:
• The dipoles of hydrophilic heads are very powerful and those two layers directed towards each other, a spaced, mutually repel. That is why the short chains in water provide pipes with heads inside and channels to outside, instead of giving bilayers. When the chains reach a certain length repulsion is balanced by the very low dipole of chains. Exceeded a certain length hydrophobic attractions become a brake travel and the weight of the whole tends to precipitation (waxes). The length of the chain should normally increase with hydrostatic pressure tends to bring closer the heads (ref.). This is what is observed in bacteria 500 bars. These considerations of repulsion are valid whatever the nature of the head. In the case where there is the carboxylic acid, the heads react creating anhydride bonds between two heads and chains can be shorter. In the liposome P has a much more powerful dipole than the carboxyl, but it is balanced by the amine arm PLD neighbor. In carboxylated bilayers, the movement of two fatty acid linked by anhydride bond is chaotic. All local action attract the couple outwardly of the bilayer, it would react with the hydrophobic binder strength of the fatty acid in question with its neighbors. This has two consequences: local action must be strong so insensitive to weak actions; Then when the action occurs, it disrupts the entire bilayer. A local action which pushes the head toward the inside of the bilayer is opposed by the reaction of the dipoles.
• The chirality of the amino arm (or glycerol) can react quickly without involving the neighboring hydrophobic forces and thereby becomes more sensitive to small local actions which hydrogen bonds are the most numerous. It is this degree of freedom that brings fluidity and sensitivity necessary to the organizing principle. I showed the necessity of chirality L in "prebiotic chirality" (ref.), but I had used the concepts of classical physics. Here L chirality is even more appropriate with the principle of action/reaction in liquid medium.
• The electric potential:
  The electric potential was invoked abondantly to explain the chemo-osmotic at the level of liposome. Only this notion is, in the article by Mitchell (ref.) who founded this discovery, classical physical type. As also in my article prebiotic chemo-osmosis (ref.). Protons are viewed as electric particles gathering together on one side of the membrane, and one can imagine the establishment of an electric field across the membrane. But according to the preceding paragraphs, as there is no void, there is no electric field and which piles up on the face of the membrane that are H+ ions surrounded by a cloud of water molecules. The forces which bind the water molecules on the surface do not cross the membrane, since there is no water between the aliphatic chains. The electric field has moved (electrons) along the C and H atoms, to land in the hydrophilic head and the water molecules, of the opposite face. Here there is the establishment of a constraint on 2 sides.
    The principle constraint/freedom then occurs either by migrating cations from the outside inwards with their clouds of water or by organizing the hydrogen bonds between the hydrophilic head and hydrophobic amino acids, all 2 zwitterionic, to penetrate these amino acids in the membrane constituting channels without covalent bonds.

3. The principle of action/reaction with DNA

• While the 4 principles of C/L, organization, A/R and reproduction exist at the outset of molecular evolution, as snippets for the liposome to DNA or the principle C/L nor the organization can not be there and actually work, since this DNA does not yet exist. At most we can say that the future of the liposome is to move towards more stress with less freedom but adequate to maintain molecular evolution.
    But we do not know how. The only possible initiation can only come from the liposome and dynamically by continuity of these processes. This initiation may be the fact that the principle of A/R of the liposome. However as soon as the formation of the bilayer, the liposome define (even headless phosphate) an area of ​​the interior space that has the property of constraint (freedom being not reduced to a point space), since the ionic heads that of them are carboxylic or P converge their clouds of water molecules toward the center. This is a quantum property of the bilayer. Then all of the interior space is organized as anions P of the internal sheet are necessarily balanced by K+ lined up in sphere parallel to the liposome. And to balance them it takes P to the center. I mentioned P and K because they are the organizers as we saw at the beginning (and perhaps simply if the amino arm is glycerol, so no zwitterion). However, the zwitterionic head PLDs provide more freedom in the center, necessary for initiation of DNA structure.
  So it is the A/R of the liposome which will initiate the establishment of DNA. We have seen that the organizing principle of the DNA base sequence is storing the manufacturing steps of the living. So the process of A / R of the liposome will be also recorded.
• They are the initial stages of setting up DNA?
  This is making me clearly that the central piece of the puzzle that is the ribosome can not perform its translation process if the amino acids used for protein must be involved in a strict and a constraint way in this process. Now we know that the binding protein/RNA is done by hydrogen bonds, which would be suitable for initialization of DNA that functionally uses hydrogen bonds.But RNA can not be a memory because it is transient and very labile. For it is against renewed indefinitely from DNA that plays the role of memory support.
  I turned then to proteins that bind to DNA and to make it as simple as possible (principle of initialization), they should not have catalytic activities, while proteins of the ribosome can have. Transcription factors were all shown.
• Does transcription factors perform all functions of the principle of A/R?
• It takes the whole process of action of liposome can be realized. Indeed:

1. We know that dR-P can be initialized by the emerging central metabolism due to the liposome.(ref. chiralité prébiotique).
2. We know that the nucleobases are hydrophobic and can cross the membrane.
3. We know that proteins can be formed according to the principle of initialization. However, these proteins must contain the amino acids necessary for DNA recognition. Thus I admitted EQRKHL amino acids can be produced by the emerging central metabolism or transported by diffusion through the membrane hydrophobic form:

• E  by cyclizing and once inside reappear be aminated to
• Q  (E+NH3) by the emerging metabolism.
• K   given its length and if NH2 is not protonated can pass the membrane.
• R  would be the product of ornithine, would pass as K and would be transformed into R with carbamoyl-P and NH3 of the nascent central metabolism.
• H  would pass (with C?) by chelating transition metals including Zn.
• L  I also recognized in prebiotic chirality (ref.), hydrophobic amino acids that are introduced into the membrane and then pass into the cytoplasm, by the principle of A/R of the liposome, and in particular L.

I checked that these amino acids EQRKHL are abundant in transcription factors (ref.), relatively compared to free enzymes from the cytoplasm (ref.) and alpha helices of pores and channels of the membrane (ref.).

Some transcription factors may well exist before the onset of DNA as from the principle of A/R of the liposome. Such as peptides chelating Zn or other metals to pass His. These factors are small (principle initialization) and since very organizers containing transition metals we saw very organizers.

It is necessary that the nascent transcription factor can respond to the action of the liposome, in the case one wishes incorporating dNs or olio-dNs. However for evolution to take its course, it is necessary that DNA produces its own action to RNA and it is organized to reach a beginning of constraint.
Indeed we may consider these as traps of dR-Ns or R-Ns when ribose begin to appear in the nascent metabolism. The monomers can be used as coenzymes (first dR-N, see chirality ref.) and oligomers can be combined with certain proteins of the principle of A / R of the liposome to a synergy with the emerging metabolism.

At this point we enter the RNA world very complex and has been studied widely. An entire research will be needed to continue the process of molecular evolution after initialization of DNA. However the assumption that originally AGN are RNA and/or DNA appears very interesting from the point of view of the principle of initialization. For the poly-glycerophosphate appears in the current central metabolism and I showed in prebiotic chirality it appears as 3 due to sequestration DHA stress carboxylated heads.
 However, if this is the case, it must explain why the molecular evolution replaces two molecules evolutionary behaviors that are almost opposite crystallization of DNA on one side and the catalytic and the fragility of hyperactivity RNA from the other side.
 It seems to me quite logical that the object of the principle of action/reaction is distinct from the object principles C/L and organization. That fulfill the AGN. It is as if there were a self-activation, which would snow-ball and block molecular evolution: RNA activating the production of RNA, DNA of DNA and PLD of PLD. This would be very short loops.
 So if it turns out that the AGN is at the origin of RNA and DNA, it is necessary that only the RNA is even more quickly than DNA appears in the nascent metabolism (see prebiotic chirality). RNA replace later AGN much more suited as we saw above.

The hypothesis of transcription factors (pseudo) seems interesting to me because, in addition to performing the functions of the principle of A/R they seem to initiate replication of DNA as the principle C/L introduced the organization and it introduced the principle of A/R. Indeed these factors recognize sequences with repeated patterns and or as palindromes. Transcription factors themselves (Zn fingers, HTH ....) have similar geometries. The synthesis of the DNA sequence, recording the steps of actions and reactions would be caused by agents of the principle of A/R and more, by duplicating the geometries it is easier to make a sequence similar to the previous by changing only a few bases. This not only initializes the organizing principle of the DNA but also initializes the metabolism maintenance.These organizing process of DNA leads to initialize replication through base pairing that are the foundation of the principle of C/L of the DNA process.
 Which is incredible in these factors is that the replication initiation factor recognizes a pattern similar, but smaller it is, only 248 nucleotides in E-Coli. It contains 3 times an oligo of 13 N and 4 times an oligo of 9 N. It is called Oric in E.Coli.

The principle of replication

This principle must perpetuate a given organization with the capacity to perform the previous three principles (C/L, Organization, A/R), but create new ones by duplicating mechanism of DNA. This principle applies to the liposome, but there is rudimentary.
Molecular evolution lead to Darwinian evolution by adding a meta-process heading the other 3, which is the exchange of genes and their mixing by sexuality and viruses (and more polyploidy)
Viruses made ​​of RNA above. Hyperactivity of the NRA disadvantaged until now, but its crystallization in the presence of proteins allows him to approach eternity while reborn when it encounters DNA and the machinery that goes with it to produce, duplicate, and RNA and proteins. Hence it horizontally transferred genes between organisms, even if they disappear, viruses are there to continue the molecular evolution and leave again faster than if starting from scratch.

16.08.13 Villette avec Elsa, dans le métro.

[ DNAzyme, GNA does not take thymidine ]

• Principle of production: It should be put before replication. While the principle of C/L allows continuous mass synthesis, which skips to the principle of the organization of this mass, the principle of production is expected to synthesize molecules on demand in response to an action, and this with using (and context) principle of C/L. This response is isolated and should synthesize small amounts of molecules corresponding to the action. These molecules are moving while remaining within the context C/L and can organize locally and meet other actions/reactions.
• At the 1st stages of E.Coli, molecular evolution in question:: LGA (P?), ethanolamine.