martedì 31 ottobre 2017

ORIGIN OF THE PROTO-ORGANISM





Post n.32  English

The universe originated 13.6 billion years ago. It was the Big Bang, the origin of the universe that laid the base for the origin of life that was when the chemical elements were formed.
In the previously published posts, we described the origin of the elements, the origins of inanimate matter, of basic substances for the origin of life, in particular, amino acids, formaldehyde (HCHO) and hydrogen cyanide (HCN). Furthermore, it has also been widely described how the clay, according to the Bernal hypothesis, was able to select, accumulate and protect these fundamental substances. The clays therefore functioned as a physical regulating agent and a fundamental must have been the role of colloidal silica. This hypothesis with a unique model explains, selection, accumulation and formation of polypeptides, and it also shows us simultaneity and localization. In fact, it is of no interest that one of these processes takes place at the North Pole, another at the equator and the other at the South Pole and in completely different chemical-physical conditions. And again, it is not of any interest if at a certain moment the amino acids are selected, from these after a month the levo are selected and after a year we have the catalysis.
We have to ask the question: how did the synthesis of proteins occur on the silica surface?
As we have already explained (post n.26), in an aqueous environment the polypeptide formation reaction is impossible, it is in the double electric layers, a non-aqueous microenvironment which favors the formation of the polypeptides. Moreover, within these compartments a small-scale thermodynamics comes into play, whereby the formation of the polypeptide becomes a spontaneous process.
Then the Levo amino acids accumulated inside the double electrical layer of the colloidal silica, within the clay micro-cavity, give rise to polypeptide chains wrapped around the colloidal silica.
However, the colloidal silica particles have a very short life. If a colloidal silica particle, on which a polypeptide was synthesized on its surface, meets other colloidal silica particles, amorphous silica will form. The electrical interactions between colloidal silica particles are so strong that they deform each other.
The polypeptide, no longer finding the original electrical interactions, detaches from the surface and goes into solution inside the cavity. Since the colloidal silica was helicoidal, necessarily helicoidal will be the course of the polypeptides. These structures are, in aqueous solution, thermodynamically unstable and, due to thermal agitation and impacts with water molecules, they should have decompose into amino acids and fall into energy state 2.



As we saw in post n. 18, the decomposition of polypeptides into amino acids while being thermodynamically possible is kinetically impossible. Water molecules do not have enough energy at room temperature to break all the polypeptide bonds. The decomposition takes place but at a very low speed; an energy barrier therefore prevents rapid decomposition. However, the polypeptides contain positive charges and negative charges. Each polypeptide, before being slowly decomposed by water into individual amino acids and precipitated in State 2 as required by thermodynamics, spontaneously establishes links between the positive and negative charges that stabilize the helical structure. The formation of the stable and ordered structure, called α-helix, frees energy that increases universal entropy. 


The α-helix is ​​therefore located in a hollow of Energy, State 1.
It is probable, however, that the amino acid composition of the α-helices was different in different areas of the planet. As Miller's experiments have shown, some amino acids are formed in particular conditions. For example, Methionine and Cysteine ​​are formed only if hydrogen sulphide (H2S) has been present in the primordial mixture. But this compound could only be present in the vicinity of the volcanoes. Other amino acids need high temperatures unreachable with Miller's experiments (post n. 25). We must therefore take into account the fact that probably the composition of the α-helices, on the surface of the planet, could vary as a result of local chemical-physical conditions.
Consequently, one can only conclude that the polypeptides, produced by ordinary chemical-physical forces and by local chemical-physical conditions, in the form of α-helix, had to be found, in prebiotic times, in great abundance, on the whole surface of the planet, in every cavity, in every pore, in every niche of clayey masses.
As highlighted by Duranti Marcello in "Introduzione allo studio delle proteine" 2015: «Some α-helices contain portions of the cylinder hydrophobic, this gives rise to interactions between hydrophobic amino acids which give rise to super-secondary structures that are the first step towards the tertiary structures of protein».
It is therefore probable that, within some clayey masses, from some α-helices, super secondary structures spontaneously formed and subsequently, with further aggregations, tertiary or globular structures, that is enzymes with broad spectrum of action. The formation of the globular structures causes the expulsion of water molecules, which increases the universal chaos and therefore are thermodynamically more stable.



The tertiary structure will now occupy State 1, with a lower energy than that of two or three single α-helices and will therefore be thermodynamically more stable.
What has been described up to now, that is the origin of the polypeptides, is in principle accompanied by experimental data. The path followed by the polypeptides towards the origin of the proto organism, and so towards the origin of life, is a true mystery for science. Now, to engage in the search for such a path one risks, as Schrödinger wrote, to cut a bad a figure. But since I am not an academic, I don’t risk to cut a bad a figure, so then I’ll try.
Not having available experimental data, to understand the origin of the proto-organism, only through a credible narration we can proceed, making the effort in logic and imagination.
So, let us imagine a niche, a micro-cavity inside a clay mass, where a few hundred α-helices have accumulated. Some α-helices gave rise to super secondary structures and subsequently to tertiary structures. The tertiary or globular structures contain within them hydrophobic groups and, on their surface, hydrophilic groups with residual electric charges. Therefore, tertiary and α-helical structures were certainly surrounded by clusters of water to form a complex interactive protein system.
If we want to make an extreme summary, we would imagine that residues with negative charges are found on the surface of a polypeptide, they would be wrapped around a cloud of water molecules with Hδ+ oriented towards the negative.



In the contact zone between the two water aggregates, water will disposed itself in such a way as to minimize the electrostatic repulsion.
Within the cavity, all the components of the interactive system would have to be included, therefore, within an ordered macrostructure, “almost crystalline", of water and the interactive protein system would assume the appearance of a gel.
To this macrostructure, we can extend the concept expressed by Peter W. Atkins with reference to the α-helix reported in Post n. 18: The ordered disposition of all the molecules of this gel macrostructure is prefered to an irregular cluster because that corresponds to the situation of greater chaos of the universe. The macrostructure is certainly endowed with a minor chaos due to the ordered arrangement, but the universal chaos is greater because of the energy that is released when the strong hydrogen bonds are formed.
Like the stone on the hill that sinks more and more after each storm, so does the macrostructure into an energy pit, represented by State 1, gaining a great chemical stability.



This interactive system between protein molecules operates, therefore, within the second principle of thermodynamics, by which order generates chaos, the formation of complex structures to produce entropy.
Within this gel structure the components of the system communicated through the electromagnetic force generated by the surface potentials. Now it is evident that if from the external environment one or more molecules rich in energy come into contact with the gel of the micro cavity, the nearby polypeptide begins to destabilize by changing its shape. This change induces the water that surrounds the polypeptide to take another arrangement. This new arrangement will force all water molecules of the gel to re-orientate electrically, passing the information to all the macromolecules of the system that, in large or small size, will be subject to changes their shape. The energy accumulated by a single polypeptide is discharged and shared by the whole complex interactive system. The new arrangement of all the other macromolecules making up the gel will send a feedback signal that will indicate to the first macromolecule whether to reject or absorb, to synthesize and what to synthesize. Only systems that succeed in developing a communication system that minimizes errors will flourish. The complex interactive system is now an entity and presents a rudimentary homeostasis that is the ability to maintain a more or less constant uniform chemical equilibrium in a changing environment.
But the homeostasis so defined is only an idea, a concept.
How can we physically represent this entity, and what really is homeostasis?
The formation of molecules from atoms always involves electrical charges. Around the molecule of a compound, we must imagine an electromagnetic field with its own specific energy content, which differs from other compounds. This electromagnetic field defines the properties of the compound. For example, in a droplet or a glass of water, the electromagnetic field surrounding all the molecules defines the liquid state of the water at room temperature.
The electromagnetic field that surrounds the molecules of an amino acid confers its solubility in water. When tens of amino acids bind to form an enzymatic protein, the electromagnetic field around its molecule not only defines the intrinsic properties such as solubility, but also gives a function: the enzymatic function, that is that the enzyme, through its electromagnetic field, recognizes and splits or binds specific molecules. When hundreds of enzymes are surrounded by clusters of water they give rise to an interactive protein system, at the bottom of an energy pit and therefore very stable, the electromagnetic field around and inside this system organizes and controls the system itself and identifies it as an entity.
Now, the electromagnetic field of the protein entity certainly generates properties and functions, which to a macroscopic level manifests itself as homeostasis. However, if the entity is under the controls of the electromagnetic field, we can to define homeostasis as: the response of the electromagnetic field around and inside the entity due to changes in the external environment and the internal medium. However, homeostasis is an emergency state associated with a complex interactive system whose energy is at the bottom of the pit and in chemical equilibrium. Homeostasis, through chemical reactions and feedback cycles, tends to preserve this balance. Since this entity presents homeostasis, we can identify it as a primitive protein cytoplasm.
Emergence must always be understood in the meaning given by Ernst Mayr (cited work): "The occurrence of unexpected characteristics in complex systems". «It does not include any metaphysical implications». «Often in complex systems properties that are not evident (nor can be predicted) even knowing the individual components of these systems appear».
In reality, this is also true for simple systems. The water consists of Hydrogen and Oxygen. Knowing the properties of these two gases, no one can predict the properties of water. And this is true of all chemical compounds. Only that chemistry has managed to associate laws to the properties of simple systems and their transformations. In contrast, for complex systems that lead to life, which do not have specific properties, we associate concepts.
The homeostasis defined as the response of the entity's electromagnetic field around and inside due to changes in the external environment and the internal medium is not a concept any longer, but it assumes a chemical- physical meaning.  
The second fundamental step towards the origin of the proto-organism is the formation of short RNA molecules.
How did the formation occur?
The RNA consists of nucleotides (post number 31), the latter are formed by the link between a phosphate group (H2PO4-) and a nucleoside.



The RNA consists of nucleotides (post number 31), the latter are formed by the link between a phosphate group (H2PO4-) and a nucleoside.
The constituents of the nucleosides are: a sugar, the D-Ribose, belonging to the family of sugars (below in the figure), and one of the four nitrogenous bases: Adenine (in the figure) and Guanine, belonging to the Purine family; Uracil and Cytosine belonging to the Pyrimidine family. The problem that arises is, understanding if these constituents were present in the prebiotic era.
In relation to the nitrogenous bases, in 1961 Juan Orò, one of the most engaged chemists in prebiotic chemistry research, succeeded in synthesising Adenine by heating a high concentration of (HCN) hydrocyanic acid at 70 ° C in the presence of ammonia (NH3). In this experiment several organic substances were obtained and among these adenine. Later, Orò was able to synthesize guanine too. Regarding these experiments C. Ponnamperuma in "Origin of Life", 1984 comments: «[...] the concentrations used by Orò were far too high to correspond to a prebiotic situation. If the experimental conditions were really similar to the prebiotic ones, for example, if lower concentrations had been used, then these reactions would be of great help in understanding the origin of the purines in the conditions present in the prebiotic phase of the Earth».
Unfortunately, after these experiments and for over 50 years there are no significant experiments.
As explained in post no. 7, the reason is probably to be found in the arrogance of the supporters of the "RNA World" who have transformed a hypothesis into a confirmed model, considering the research on nucleic acid constituents superfluous.
After this long period, it seemed that research on the origin of the nucleic acid constituents had fallen into oblivion, until two Italian scientists, Ernesto Di Mauro and Raffaele Saladino, reopened the game.
Their experiments described in the essay "From the big bang to the mother cell, the origin of life" 2016, are of considerable interest. First of all because, instead of using HCN (Hydrogen cyanide) which is a gas, they obtained the nitrogenous bases using the HCONH2 (Formamide) which has a boiling point above 200 ° C, and which was certainly present in the prebiotic era because it was produced by reaction between HCN and H2O. Moreover, these experiments take place using clay or minerals certainly present in the prebiotic era. These experiments are fully part of the Bernal theory. In fact, Bernal hypothesized that clay could function as a regulatory principle to select, accumulate, protect and catalyze the fundamental substances for the origin of life. So we find ourselves, in prebiotic times, the necessary bases for the nucleic acid right inside clayey masses, where the primitive protein cytoplasm originates.
In relation to Ribose it should be pointed out that its molecule, like the molecules of amino acids, has a Destro and Levo shape, a mirror image of the other, but only Destro is used in nucleic acids. Ribose, like Arabinose, Xylose and Lisose, is a pentamer of formaldehyde (HCHO), in the sense that it is made of 5 molecules of formaldehyde but is, in an aqueous solution, an unstable compound. Around 1880 A. Butlerov treated formaldehyde in a strongly basic environment; he succeeded in synthesizing Ribose, a reaction known as the reaction of the formosa. This reaction does not work in prebiotic conditions, besides together with the Ribose a mixture of other sugars are formed, including the other three pentamers, which would have impeded the formation of the nucleic acid (post n.10). In the absence of valid research, in 1994 L. Orgel on The Science, "The origin of life on earth" wrote: «First of all, in the absence of enzymes, it is problematic to synthesize ribose in adequate quantities and with a sufficient degree of purity».
In 2008 in “The origin of life", Christian De Duve takes into consideration the researches of Prieur (2001) and Ricardo (2004) who using the borates managed to stabilize the Ribose and limit to the formation of other sugars. Ricardo, in "Planetary Organic Chemistry and the Origins of Biomolecules" 2015, describes in detail the mechanism of reactions and the function of boron, but also reports Hazen’s criticisms which defines boron as an "exotic" element to be part prebiotic chemistry. Christian De Duve also reports a work by Ricardo e al.2004, which obtained four pentose (both Destro and Levo) by making glyceraldehyde to react with glycolaldehyde. Also Di Mauro and Saladino pickup on the works of Pieur and Ricardo but add that similar results were also obtained by employing Zirconate. Now, the fact is that the zirconates are anything but "exotic", they, even if in small quantities, are distributed across the whole surface of the planet and mainly in sedimentary and metamorphic rocks. The clay, in relation to the composition, distinguishes itself as kaolinite, beidellite and montmorillonite. In the beidellite clay, a quantity of zirconates was found to be above the planet's average. And so we find ourselves once again within the Bernal theory. So, in prebiotic times, besides a primitive protein cytoplasm contained in the clay cavities, it is probable that dozens of nitrogenous bases and dozens of sugars, both Destro and Levo, were spread inside clayey masses. From this mixture of nitrogenous bases and sugars, diffused in the clay masses, only four bases, Adenine, Cytosine, Guanine and Uracil and only one sugar the D-Ribose were co-opted within the rudimentary protein cytoplasm.
Why these and not the others, what constraint imposed this selection?
To select these compounds there must have been a homeostasis of the primitive protein cytoplasm.
The Homeostasis responsible for maintaining chemical balance allows, within the protein cytoplasm, the diffusion of only substances that maintain this equilibrium.
As we have already mentioned, homeostasis, could be the response of the electromagnetic field of the entity with respect to changes in the external environment and the internal medium. So, let us try to give a physical explanation to the events.
Imagine having a glass of water and adding sugar. We can simplistically say that the electromagnetic field around the sugar molecules is compatible with that of the water molecules and therefore the sugar dissolves in water. If instead we put a drop of oil in the glass, the electromagnetic field around the molecule of the oil is not compatible with that of water, the oil does not mix with water and collects on its surface. Now, let us imagine how the electromagnetic field generated, around our protein entity, comes from hundreds of α-helices. These α-helices consisted of L-amino acids and all had a right-handed pattern. The electromagnetic field around the protein entity had to comply with the right-hand helical trend of the α-helices and therefore had to necessarily be right-handed. If the protein entity had been made up of left-hand α-helices, the electromagnetic field would have been left-handed which means the mirror image of the electric field of the right-handed entity. Now, since the molecules of D-Ribose and L-Ribose are one image of the other, their electric field must also be the mirror image of the other, which are, right-handed and left-handed. Then, when in the prebiotic era D-Ribose molecules and L-Ribose molecules tried to spread inside the cavity where there was a right-handed α-helix entity, the homeostasis would co-opt the D-Ribose, because complementary to the electric field of the entity, while its mirror image, L-Ribose would be rejected.
In addition to the Ribose, in the clay masses there were certainly other sugars similar to Ribose, Destro and Levo too, such as the Arabinose. D-Arabinose, like D-Ribose, was certainly complementary to the electric field of the protein entity. Why was D-Ribose chosen and not D-Arabinosio?

As seen from the image, the D-Arabinose molecule compared to D-Ribose has only one -OH group on the left instead of the right. For this small difference, Arabinosio has a melting point of 157 ° C while the Ribose has a melting point of 90°C. But the melting points are determined by the interaction of the electrical charges of the molecules, that is ultimately the electromagnetic field around the molecules. Thus, the electromagnetic fields of the D-Ribose and D-Arabinose molecules are different. But as we have already mentioned, the specific energy content is associated with the specific electromagnetic field of each molecule of any compound. The molecules of D-Ribose and D-Arabinose therefore have different energy contents. So, if the electromagnetic field around the protein entity has chosen D-Ribose, it means that the energy content of its molecules maintain the balance of the protein entity, while the D-Arabinose molecules would have destabilized it. The homeostasis of the protein entity therefore recognizes differences in the electromagnetic field and the energy level of the molecules. This principle must have worked also in the choice of the nitrogenous bases. Only the electromagnetic fields associated with the molecules of Adenine, Cytosine, Guanine, and Uracil are compatible with the electromagnetic field around and within the protein entity, and their energy levels stabilize the thermodynamic equilibrium. Ultimately, the protein entity homeostasis co-opts the environment molecules based on electromagnetic field compatibility and energy content.
Simplistically, we can conclude that Adenine, Cytosine, Guanine, Uracil and D-Ribose are soluble in the protein entity while all the other nitrogenous bases and sugars are not soluble.
We identified the protein entity that presents homeostasis as a primitive protein cytoplasm.
But the rudimentary protein cytoplasm is a set of enzymes. Within the entity, these enzymes, using the little phosphate available in the solution, bind D-Ribose correctly with one of the bases and phosphates creating the nucleotides. Other enzymes properly bind three nucleotides, giving rise to the trinucleotides. As we have hypothesized in post n. 27, during the prebiotic era there must have been a direct interaction between a trinucleotide and a specific amino acid, a chemical-physical and complementarity system of recognition. Now, when the trinucleotides spread within the entity and meet a α-helix, each trinucleotide pairs with the specific amino acid of the α-helix. When each amino acid of the α-helix is ​​superimposed by the specific trinucleotide, it will be the enzymatic action of the α-helix to bind the trinucleotides giving rise to RNA, ribonucleic acid. Since the RNA was synthesized by a helical enzyme, the α-helix, it turns out to have a helical structure. If there were a hundred different α-helices in the cavity, they would give rise to a hundred different RNA. The nucleic acids replace the silica and with the amino acids in solution they can synthesize the enzymes that for various causes were decomposed. To use the Cairns-Smith metaphor: the armature, the silica, generated an arch, the α-helix, which in turn generated an armature, RNA, which definitively replaces the former. Nucleotides synthesis (ribose + nitrogen base + phosphate group), trinucleotides synthesis and RNA synthesis all occur in the non-aqueous microenvironment of the surface of the enzymes. These conditions allow the enzyme an extraordinary reactivity, different from those in an aqueous environment. Furthermore, in all these synthesis reactions, water molecules, which will increase the universal chaos, are released. Order is created by increasing entropy: Chaos from the order.
Homeostasis maintains balance, but with the appearance of the RNA, the entity is expanded, giving rise to a cytoplasm containing an interactive nucleic acid-enzyme system that sinks even further into the energy pit. Homeostasis maintains equilibrium through the electromagnetic field around and within the entity.
The new entity, which is the cytoplasm nucleic acids-enzymes, is the proto-organism.
In conclusion, since the second principle of thermodynamics is not able to follow the path of maximum chaos represented by the energy level of state 2, it follows the path of possible chaos and digs a parallel energy ditch represented by state 1. Along this path, through various energy jumps, order generates chaos until it causes the origin of the proto-organism. The proto-organism has always been considered as a system far from the thermodynamic equilibrium described by the state 2. In reality the proto-organism is a system far from the maximum chaos but is in equilibrium with the possible chaos and therefore under the control of the second principle of thermodynamics.

So, we are faced with this scenario.
In millions of billions of cavities, niches and inter-crystalline spaces of an unspecified but enormous number of clay masses, an infinite number of polypeptides that give rise to a primitive protein cytoplasm. Nitrogenous base and D-Ribose molecules contained in the clay masses are co-opted within the protein cytoplasm, helical polypeptides that synthesize the nucleic acid. The interaction between nucleic acids and enzymes gives rise to an endless number of proto-organisms.

Giovanni Occhipinti

Translated by: Sydney Isae Lukee

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