# Continuity between molecular evolution and darwinian evolution

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)
* 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)?
* 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.
* 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:
* 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.

## 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:
* 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:

### 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.
* 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 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):

## 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

### 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:

### 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?

## 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.