Giovanni Occhipinti
Chapter 4.
Organizing principle and molecular asymmetry
4.1 Unique model and Bernal theory
As we have explained in the previous chapters it is therefore to be considered that in the prebiotic era, starting from simple molecules such as methane, ammonia, water and other simple molecules thousands of organic compounds were formed and among them were amino acids too. The presence of amino acids in the prebiotic era was confirmed by the analysis of meteorites dating back to the time of formation of the solar system. In particular, in the carbonaceous chondrites there was a presence of amino acids similar, in quality and quantity, to that found by Miller in his experiment.
Since amino acids are the constituents of proteins, it is reasonable to conclude that in the first prebiotic era the first fundamental macromolecules to appear were just proteins. The formation of these complex molecules is therefore an important step towards the origin of a primitive cytoplasm and therefore towards the origin of life.
Now, we must keep in mind that the four problems already highlighted, insurmountable for the primordial soup theory, are interconnected and it makes no sense to imagine to solve them with different models. It cannot be thought that the first problem occurred by chance, for the second based on an evolutionary process, the third a deterministic process, due to a puddle in evaporation and finally for the fourth the location.
On these issues Giuseppe Galletti and Valentina Sorgi in "Astrobiologia: le frontiere della vita" 2009, identified the centrality of the problem when they claim: «These features should be explained, possibly with a unique initial model».
In addition to these four specific points, there are other general questions that need be answered.
A) As Miller's experiment showed, in the prebiotic era there were many other organic substances. Most of these substances were definitely useless, if not harmful and would jeopardize the formation of polymers.
B) The concentration of amino acids, dissolved in water, was certainly very low and, in such conditions, the synthesis of the polymers would have been impossible.
It is therefore logical to conclude that in the prebiotic era, chemical and physical constraints of the prebiotic environment worked as an “organizing principle” for selection and concentration of substances essential for the origin of life and subsequently catalyse the formation of the macromolecules necessary for life.
It is also not possible that one these processes took place in the North Pole, another at the Equator and another at the South Pole. These processes must be located in the same place and therefore in the same environmental conditions.
But the location alone is not enough. As suggested by Paul Davies (quoted work) in relation to these issues, selection, concentration and catalysis must take place simultaneously. You cannot think that amino acids at a given moment are selected, then the Left are selected after a month and after one year the catalysis occurs.
Ultimately, the unique initial model must contain: selection, concentration and catalysis, and all must have be simultaneous and localized processes.
Science has long highlighted that the planets, the stars and the entire universe are the product of chance and natural laws: chance and necessity. And no doubt that the evolution of living organisms is the result of chance and necessity too.
Did chance and necessity govern the first steps of the origin of life, specifically, the synthesis of biopolymers?
If the steps listed above are part of a unique coherent model, there are two possibilities: either the events were all random or were all deterministic. Introducing here and there, with discretion, some random event, or to use the new terminology some "frozen accident", it is just an expedient ad hoc to support theories which lack credibility. But there is no possibility, that chance has separated the Left from the Right and by chance the 20 amino acids have been chosen out of the 60 available and casually the synthesis of proteins has been produced and by chance the ultraviolet rays have not destroyed them and again by chance all these passages took place in the same place and at the same instant; unless invoke the miracle. Therefore, the events that led to the origin of the proteins must have been all deterministic events.
But is there a theory that provides us which chemical physical constraints of the prebiotic environment have functioned as an organizing principle and which allows us to build a coherent model through exclusively deterministic, simultaneous and localized processes?
Yes there is.
In a century of research on the origin of life, the only scientist who suggested a solution was JD Bernal in the essay "Le basi fisiche della vita", reported in "L’origine della vita" 1957 by Bernal, Haldane, Pirie and Pringle. As is known, the clays are formed by various overlapping crystalline layers.
Each layer consists of two sub layers, one of silica tetrahedrons (Si2O52-)n and the other of octahedrons of hydrated alumina [Al2(OH)42+]n.
Without going into details, due the presence of electric charges the various layers or under layers are neutralized at a distance. Between one layer and the other or between an under layer and another there are empty spaces whereby water molecules or molecules that exhibit electric dipoles like the fundamental constituents of the macromolecules, where they can settle. It is calculated that in a cm3 of clay the surface of these empty spaces is equivalent to almost the area of a football field. Bernal suggested that the clays could select and concentrate the essential ingredients for the origin of life and subsequently catalyse the formation of the macromolecules necessary for life. He also suggested the importance of Quartz in the selection of primitive molecules. Quartz in fact is found together with clay and presents, just like amino acids, a D and L form, and could have caused a preferred adsorption, separating the Right from Left. Since inside the clay there would be simultaneity and location, the hypothesis of Bernal gives us, in fact, a consistent model.
4.2 The problem of molecular asymmetry: theoretical part.
As we have highlighted amino acids exists in two forms, D and L, one a mirror image of the other. Living organisms use only the L-form, therefore life is asymmetrical.
Molecular asymmetry, which as we shall see also concerns other compounds, was discovered by Pasteur in 1848. A lot of effort has been made since then in order to understand why life uses one form and not the other and when the separation occurred.
A summary of the most significant attempts to solve the problem was made by Mario Ageno in (quoted work). He anticipates the conclusion of these efforts, saying: «This issue has plagued the minds of a large number of researchers, since the times Pasteur to until today and does not seem to have yet received a fully satisfying answer that is, that deductively connect molecular asymmetry existence of the biosphere with the fundamental principles from the physics or biological theory».
One of these attempts that Ageno had excluded as the assumptions were of doubtful validity, was taken over in 1990 by R. A. and R. A. Hegstrom and D. K. Kondepudi, in an article in Le Scienze, "La chiralità dell’universo". As the authors illustrate, the chemical compounds originated through electromagnetic interactions of the atoms of which they consist. During these processes, it is said there is a conservation of parity, that is, if a compound is formed its mirror image has the same chance to form.
The particles making up the atom, protons, neutrons and electrons, are held together by different forces. Two of these forces, the weak nuclear force and the electroweak force (unification of weak nuclear force and electromagnetism), do not retain parity.
In the crust of our planet, there are elements whose atoms decompose and emit radiation (radioactive decay). During radioactive decay, electrons are also emitted at high-speed, β-rays (beta rays). Without going into detail, the weak nuclear force is responsible for this decay, and since it does not preserve parity, more left-handed electrons than right-handed ones are emitted. When the β rays hit the chiral molecules they decompose them, but being the majority left-handed, the rays preferentially destroy one form, leaving an excess of its mirror image. It is therefore thought that the weak nuclear force was responsible for the asymmetry of life.
It was discovered that the difference in decomposition rates is of the order of one part in 109, that is one part of 1 000 000 000 (one billion).
The second force, the electroweak force does contribute to the formation of the compounds. Since even this force does not maintain parity, it has been calculated that during their formation, in the prebiotic era, Left amino acids had to be the most abundant than the Right by the order of one in 1017, we save ourselves from write a 1 followed by 17 zeros. Even though these are tiny contributions to determine molecular asymmetry, Kondepudi and a co-worker, Nelson, tried to prove theoretically that amplification processes under certain conditions exists. He envisions a pool where competing Right and Left form and writes: «And the pool should be large enough and sufficiently well-mixed (the reshuffle should concern approximately a surface of 10 square kilometres and a depth of several meters) to eliminate the effect due to random fluctuations. If all these conditions are fulfilled, the weak nuclear force should be able, in a period between 50 000 and 100 000 years, to strongly influence the symmetry breaking process». Kondepudi and Hegstrom conclude: «We exhibited numerous models to demonstrate how a chiral asymmetry could have developed in biomolecules. [...].However, none of these showed us a particular group of prebiotic compounds with all the properties required by these models».Ultimately, the conclusions reached by Mario Ageno are still current.
The molecular asymmetry problem is taken up again by Robert M. Hazen in 2001 with an article in, Le Scienze: "Vita dalle rocce". As the title indicates, Hazen turns his attention to the mineral world and prefigures a single model. That is, he imagines that concentration, selection and synthesis may be occurring in small pockets of air or feldspar rocks of volcanic pumice. For these events, the author does not take into considerations deterministic events and indeed states: «The chance could have produced a combination of molecules that would eventually deserved to be called “living”».
The Arab Phoenix rises again.
Hazen tackles the molecular asymmetry problem turning his attention to the crystals of calcite, limestone and marble, because these crystals form pairs of specular faces. As he explains, the calcite crystals were immersed in a solution containing an amino acid 50% Right and 50% Left 50%. After 24 hours, the crystal was extracted and washed, and the solution analysed. The left-handed faces of calcite mainly selected the L amino acid with an excess of 40% and vice versa. Hazen does not pose the problem of seeking the physical causes of this phenomenon and says: «Strangely the most terraced faces were the most selective. This fact led us to predict that the edges of the terraces could force the amino acids to line up in neat rows on their respective faces». Since the faces of the crystals of the left-handed and right-handed are equal, he concludes: «It was by pure chance that the molecule destined for success developed in a crystal face that preferred the left-handed amino acids to the right-handed counterpart». Ultimately a single model but random… and again, the Arab Phoenix re-emerges.
Hazen returns to the topic in one of his essays, "Breve storia della terra" 2017 where he writes: « The most common minerals in every rock and in every soil are rich in surfaces where atoms form "supports" at molecular scale, some turned to the left, others to the right. […]Our experiments have shown that some left rotatory molecules can aggregate only on one type of crystalline surfaces, while the mirror images, the mirror counterparts right rotatory, easily aggregate on both types of mineral surfaces» It is not known the nature of the "supports" but the result of the experiments is interesting.
In 1984, it became clear to me that Bernal's theory was the only theory that indicated us a credible path to understanding the origin of life and that the molecular asymmetry problem was one of the fundamental steps. Bernal in his theory suggests a path where the laws of inert matter can penetrate those of living matter.
He, however, does not indicate the physical forces in action and so, as he himself writes, it does not indicate the stages of the path due to lack of necessary research.
So, what can these forces be?
4.3 The electrochinetic potential
A capacitor consists of two metal plates (armatures), located at a distance of a few centimetres, one of which is positively charged and the other negatively.
If the two plates are connected to a voltmeter, we will measure the potential difference of the capacitor from which one can also deduce the energy of the capacitor.
Water molecules are made up of hydrogen and oxygen and have a charge shift inside them.
In particular on the hydrogen atoms a portion of positive charge is localized δ+ and on the oxygen atom a portion of negative charge δ-. In general, molecules, which have inside them a charge separation, are called polar and their polarity is measured by the dielectric constant.
Imagine we have a plastic bag full of water. If it is inserted inside the capacitor, the positive part of the molecule will orient towards the negative plate of the capacitor and vice versa.
As shown by the image, the potential difference of the capacitor decreases and consequently also the energy of the condenser is reduce.
In conclusion, what is important to emphasize in this context is as follows: Since the energy of the condenser is reduced when a polar substance is inserted, if we slowly place this substance into the capacitor, it will be spontaneously sucked inside. A process that follows the 2nd law of thermodynamics, like the stone that rolls down the hill when pushed.
Also the amino acid molecules exhibit a charge separation and are therefore, polar substances. In aqueous solution, they appear as dipolar ions with a very high dielectric constant.
The question to be asked is the following: are there natural capacitors that in the prebiotic era may have sucked and accumulated within them the amino acids removing them from the solution? Certainly, they must be capacitors that act on a molecular level.
It was discovered that these natural capacitors exist.
Between 1890 and 1930 they have been discovered and studied, by Helmholtz, Gouy and Stern (Trattato di chmica-fisica, S. Glasstone 1963 pag.1280), double electric layers generated from silica, silicate and glass, all substances that present residual electric surface forces.
Phenomena within these double electrical layers were called electrokinetic effects. The glass, for example, initially neutral, in contact with H2O easily loses the positive ions of the surface (Na+,Ca++,...) and then remains negatively charged.
If a Na+Cl- solution is put in contact with the glass, the Na+ ions originate an ion layer in the proximity of the negative part of the glass wall. A part of the ionic layer is firmly attached to the glass wall while the other part is widespread toward the solution. We can imagine, in the spread out part, two hypothetical plates passing respectively through points A and B. Within these hypothetical plates, on the left there are more positive charges that the right and, accordingly, between points A and B there is a potential difference called electrokinetic potential. The double electric layer is then similar to a capacitor (more precisely a micro capacitor) and as such was studied. The distance between A and B, for low concentrations, is of the order of 0,6x10-6cm (Giuseppe Bianchi, Elettrochimica, 1963 pag.426). Micro capacitors of this type retain a row of dipoles of about 10 molecules of water, they act at molecular distances.
Therefore, there were natural capacitors in the prebiotic era, which may have attracted and accumulated within them the amino acids removing them from the solution.
The potential between points A and B cannot be measured directly; however, forcing the solution through a capillary or a diaphragm, a portion of the diffuse part of the double ionic layer is dragged, while the remaining portion remains attached to the surface. These ions measured at the ends of the capillary are named: the flow potential. The flow potential of course depends on the content of the solution.
As we have seen, these micro capacitors act at molecular distances and therefore there is a problem of how to imagine the electric field inside them.
In a macroscopic capacitor like that in the figure, the electric field is uniform and is represented by parallel and equidistant force lines. In such systems, the arrangement of the charges is a uniform distribution on the two surfaces of the capacitor.
In a micro capacitor such as that described above, the + charge is not evenly distributed on a surface but is spread, while the negative charge still presents a fairly uniform distribution on the glass surface.
As a first approximation, we could still consider the electric field uniform and represent it with parallel and equidistant force lines.
But, we can still speak of a uniform electric field with parallel and equidistant force line, if in addition to the positive charges also the negative charges are not equally distributed on a surface?
The crystalline quartz is made from helical structures whose constituent units are tetrahedron of SiO4. These helical structures can develop, clockwise D or counter clockwise L and give origin to crystals that are the mirror image.
When one of the forms is placed in contact with a solution, micro capacitors are generated on the surface and thus electric fields, whose force lines cannot be parallel and equidistant.
This is because:
a) The dipoles xδ+ yδ-, of the Si-O bond, don’t lie on the same plane,
b) Do not have the same orientation,
c) Act at small distances, i.e. at the molecular level, where their belonging to a helical complex must be decisive.
The force lines inside a capacitor of this type, for distances of the molecular order, one could imagine a helical shape, like the hole of a right or left hand screw, according to the structure used.
4.4 Amino acids and their dipoles
The amino acids, constituents of protein, are dipolar substances presenting a group (-COO-) and an amino group (-NH3+). Their dipoles are stronger than those of water molecules. They have a tetrahedral spatial structure with the carbon atom in the center. But each atom or atomic group bound to the central carbon atom, has polar covalent bonds and thus is a dipole. It is clear that if the D-form is the mirror image of the L-form, also the dipoles of the D-form will be the mirror image of the L-form dipoles. Since the carbon atom has a spatial structure, at the molecular level the dipoles of the two different structures can be imagined helical in shape, just like an oriented clockwise or counter clockwise screw.
In laboratory, in order to measure the polarity of the molecules, capacitors with high potential, of the order of a few Volts, and a distance of a few centimetres between the plates are used. In these tests, we can call macroscopic, the helical nature of the dipoles of the individual molecules are not highlighted, when we measure the resultant of the dipoles.
But, if the amino acids are immersed in suitable micro capacitors generated by the quartz where: the hypothetical distance between the plates is of the molecular order, the electric field inside them is helical and the potential is of the order of mV (millivolts), then it must be possible to highlight the helical structure of the dipoles from their molecules.
4.5 The molecular asymmetry problem: experimental part.
I have built an appliance for the measurement of the potential flow. I will spare you problems and errors as, having in mind macroscopic capacitors while operating with microscopic capacitors.
(Appendix 2)
As we have already mentioned, micro capacitors contain a row of about 10 molecules of water.
The purpose of these measurements were to verify Giuseppe Bianchi’s claims, (quoted work pag.470), states: «Species with lower dielectric constant have a tendency to be ejected from the double-layer to be replaced by species with a higher dielectric constant» In our case, the amino acid molecules will replace the water molecules. Furthermore, as emphasizes the author, this is a phenomenon «[...] which corresponds to a decrease in the energy of the system».
The decrease of energy is expressed in an increase of the thermal agitation of molecules of water expelled from the double layer, which is, an increase of Entropy. At the same time, the amino acid molecules will be accumulated and sorted within the double electric layer. Chaos from order.
The substitution of water molecules with the amino acid molecules, then leads to a decrease of the system energy. This reduction is shown through a reduction in the electrokinetic potential, and then by the potential flow. In summary, if the solutions containing the amino acid present a potential difference lower than that of the reference solution, it means that the amino acids have been subtracted from the solution, sucked-in, and accumulated within the micro capacitors.
Before moving to the experimental data, we have to specify the following:
A) The amino acids of the proteins of all living organisms are 20; all have the same composition, except for the R residue.
For example:
For glycine instead of R, you have to put H.
For valine instead of R, we must add a CH3 group.
It is therefore obvious, as illustrated by the image of some amino acids, if you change R, necessarily, both the size and the polarity of the amino acid molecule change.
To return to the metaphor of the helicoid crew, this means that in order to vary R for each amino acid, the helix of our hypothetical screw, the diameter and pitch changes; In conclusion, twenty amino acids for twenty different helicoidally screws.
B) The quartz crystal, in the short term is insoluble in water. But prolonged contact with H2O, gives rise to a slow surface chemical reaction with the formation of silanol groups and the -Siδ+ -Oδ- dipole is replaced by -Oδ-- Hδ+ dipoles which lower the potential.
The formation of silanol groups defines the electric field on the surface, giving rise to new electric fields and helical field lines with different amplitudes and new distances between the coils in the double electric layer. Thus, our hypothetical screw hole has changed diameter and pitch.
This fact, as the graph shows, is manifested by a decrease of potential flow in function of time.
This decrease in potential does not occur continuously in the solution, but discretely. In particular, if you use the appliance or leave it on standby for some time, the potential is lowered with jumps of about 0,20mV. This means that on the surface of the quartz grains a number of Si-O-Si bonds are at the same energy, and at the same time react with water and giving rise to groups of silanols.
The potential flow of the capillary diaphragm of quartz in contact with the reference solution varies from a maximum of 10.10 mV to 7.50 mV. Below the potential value of 7.50mV, it is not stable. The flow potentials are therefore within an interval of about 2,60mV. Later, we will address the meaning and the consequences of that range.
The device for the measurement of the potential flow is connected to a Schlumberger digital multimeter. The potential flow of solutions of the following amino acids with respect to the reference solution we measured.
Val L 10-3M Valina
Ala L, Ala-D 10-3M Alanina
Phe L, Phe-D 0.5⋅10-3M Fenilalanina
Leu L, Leu D 10-3M Leucina
Met L 0.7⋅10-3M Metionina
Ileu L 10-3M Isoleucina
Trp L 0.8⋅10-3M Triptofano
Pro L 2⋅10-3M Prolina
The amino acids have been dissolved in the reference solution.
As can be seen from the graph, “misure quarzo Destro”, D amino acids solutions, on capillary diaphragm D crystalline quartz, relative to the reference solution, lower the potential flow only at particular potentials. Such reduction is between 0.30 mV ± 0.05 mV for all the amino acids used. This means that at these potentials the corresponding D amino acids, from the solution are sucked inside the micro capacitors. For example:
The potential flow of the reference solution is 9.70 mV; at this potential Ala D solution gives 9.40 mV. If an L- form of Ala solution is used, no change is observed in potential relative to the reference solution.
From the graph “Misure quarzo Levo” it is clear that L amino acids solutions in capillary diaphragms of crystalline L quartz compared to the reference solution lower the potential flow only in well-determined potentials. The reduction is between 0.30 mV ± 0.05 mV for all the amino acids used. This means that only in these specific potentials, the corresponding amino acids are sucked in and accumulated within the micro capacitors and therefore subtracted from the solution.
For example:
The potential flow of the reference solution is 9.70 mV; at this potential, a solution of Ala L gives 9.40 mV.
The potential flow of the reference solution is 9.50 mV; at this potential, a solution of Phe L gives 9.20 mV.
The potential flow of the reference solution is 8.70 mV; at this potential, a solution of Trp L gives 8.40 mV.
At potential differences other than these, the amino acid solution gives the same potential flow of the reference solution, this means that the amino acids remain in solution, for example:
If the reference solution gives a potential of 8.70 mV and instead of Trp L, Ala L is used, the potential flow will show 8.70 mV.
If at the same potential, for example 9.70 mV for Ala L, a solution of the D-form of Ala is used, no change will be observed in potential relative to the reference solution.
The opposite is observed when a D quartz diaphragm is used.
Such behaviour must be the logical consequence of what was said in the theoretical part. The crystalline quartz in the double electric layer generates the helical lines of force equivalent to the bore of a screw. In the amino acid to the four different atoms or atomic groups, bound to the carbon atom in a tetrahedral structure, are associated four dipoles with a helical structure. For this reason, the amino acid is comparable to a screw. Still referring to our metaphor, if the screw finds its proper hole then the amino acid accumulate in the double electric layer; there is a decrease of the energy of the system, and a reduction of the potential can be observed. If the hole is not the right one, either the screw goes in and out right away because the hole is wider, or it doesn’t enter at all, because the hole is too tight, the potential remains constant and the amino acid don’t accumulate on the surface. If the screw has an opposite direction, as in the case of the D-form, it cannot enter, and even in this case the potential remains constant, the amino acid remain in solution. Therefore, only at a specific potential the amino acid is accumulated in the double electric layer and removed from the solution.
The metaphor of the hole and the screw must be understood as Erwin Schrödinger, one of the fathers of quantum mechanics, states in his essay "Che cosa è la vita"1944: «In the light of current knowledge, the inheritance mechanisms are closely linked, indeed are founded on quantum theories [...]. The great revelation of the quantum theory consisted in discovering, in the book of nature, signs of discontinuity in a context in which anything other than the continuity seemed absurd [...]. Based on facts that we cannot discuss here, we must admit that a small system may, for principle reasons inherent to its very nature, possesses only certain discrete amounts of energy, which are called energy levels of their system. [...]. The result is that, if a number of atomic nuclei, with all their bodyguards are to be joined to form a "system", they cannot assume, because of their nature, any arbitrary configuration among all those that can be imagined. Their nature allows them to choose only within a very large but still discrete series of "states". Generally, we call these states with the term "levels" or "energy levels" because the value of energy is one of their most important features. [...]. Between the discrete series of states of a certain set of atoms there may be (but not necessarily), a level lower than all the others, in which the nuclei are closely spaced. In such a state the atoms constitute a molecule».
So every molecule has its own energy content defined, discrete, i.e. a quantum structure. But if the energy is discrete, since the bonds between the atoms are electromagnetic in nature also the electromagnetic field associated with the molecule must be discreet. And for the amino acids, the electric field associated with the molecule must also present a D or L orientation. We will get back on these concepts.
Finally, it seems that a physical agent, quartz, in the prebiotic era, can connect deductively the separation of Right amino acids from Left with the fundamental principles of physics. It can therefore be assumed that these double electrical layers have worked as electrochemical filter, selecting and accumulating the amino acids, on the quartz surface, and then on the earth’s surface.
But we must not forget that the crystalline quartz, which is found in nature today, is 50% on the right and 50% on the left and this was to be the situation even in the prebiotic era. On the other hand we now know that, in the prebiotic era, the amino acids were 50% D and 50% L. Then, if the Left quartz has accumulated Left amino acids, the right quartz will have done the same accumulating the Right amino acids. In these conditions, there would be L polypeptides, D polypeptides, subsequently a D life, and an L life.
However, D life does not exist, in reference to amino acids only an L life exists. So the question remains: how did Left survive and what happened to the Right?
Chapter 5.
The problem of molecular asymmetry: the disappearance of the form D.
Theoretical part
5.1 The problem of molecular asymmetry: The relationship between quartz and amino acids
It seems a strange thing, that Left quartz accumulates on its own surface the Left amino acids and Right quartz, the Right amino acids. The obvious question is: what is the relationship between the quartz structure and molecular structure of amino acids? None.
A beam of natural light is made from a very large number of rays whose electric vector oscillates in all directions. Schematically represented in figure 4.1a.
If such a light beam hits special crystals, called polarizing prisms, or
Polaroid filters, all the rays, except one, are deflected or absorbed. The electric vector of the only outgoing beam always oscillates in the same direction and the plane (x 'x) on which lies the propagation direction and is called: the plane of the polarized light, Figure 4.1b. Similar light beams are called: linearly polarized light.
In nature, there are several substances and minerals which, if crossed by a beam of polarized light, have the property to rotate the plane of polarized light, rightwards or leftwards. An analyser placed inside a device called polarimeter, whose visual field is divided into two semi-circular parts, allows us to observe this deviation. This property is called optical activity and depends on the molecular structures for substances. For the crystals, it depends on the crystalline structure, that is, the arrangement of atoms, ions or atomic groups within the crystal.
In the inorganic world, the most common mineral that has optical activity is the quartz. The quartz crystals were initially studied with respect to their external "habit", that is, with respect to the arrangement of the faces on the crystal itself. Since the external "dress" comes in two different forms, one a mirror image of the other, it was assigned the morphological designation, Right (D) and Left (L). At the beginning of 1800s, when J. B. Biot analysed quartz with polarized light, he did not know its internal structure, its crystal structure yet. Now, since the quartz morphologically Right rotated on the Right and quartz morphologically Left on the Left, he gave the denomination D and L.
At the end of 1800s, X-rays were discovered. The X-ray analysis of the quartz showed that it is composed of tetrahedral structural units with the silicon atom in the centre and the oxygen atoms at the vertices.
These structural units are linked together to form right-handed and left-handed helices.
The analysis highlighted a fundamental fact: in quartz, optically and morphologically "Right", the helixes are left-handed and in quartz optically and morphologically "Left" the helixes are right-handed.
Therefore, when we say that L quartz absorbs on its surface the L amino acids, it is actually the Right-handed quartz structure that accumulates the L amino acids.
The name assigned to Biot nevertheless benefited and is universally used.
As we said, there are several substances, such as amino acids, which in solution rotate the plane of polarized light. The same sense of rotation adopted by Biot for quartz was also adopted for substances, but was given the + sign if turned Right and - if it turned Left. This rotation has no correspondence with the designation L and D for amino acids. The denomination is related to the molecular structure that has been determined through universally accepted sequence rules, but arbitrary. There is in fact an L (+) Valine as well as the L (-) Proline.
With these clarifications, we return to our main problem.
The two molecular forms of amino acids, Right and Left, have the same chemical physical properties, and it was believed that they were inseparable.
Meanwhile, through the double electrical layers we have made a first step. Quartz separates the Right amino acids from Left and connects deductively this separation with the fundamental principles of physics. However, since in reference to the amino acids, there is only an L-life, there must exist, in the inorganic world, an asymmetric substance only with an L-form that has retained and accumulated on its surface only the L amino acids.
5.2 Molecular asymmetry: Water
The idea of existence of an asymmetric mineral, in the inorganic way, was born from reading Encrenaz Thérèse’s article, “L’acqua nel Sistema solare”, Le Scienze (2001). It highlighted how the water molecules are not all the same but there are of two types: ortho molecules and para molecules.
The nuclei of atoms, such as electrons, rotate around their own axis clockwise or counterclockwise. Due to this rotation, called spin, the nuclei and the electrons behave as tiny magnets. The spin effect is most visible in the permanent magnets. In a permanent magnet, the spins of some electrons of the atoms that constitute it all have the same orientation. Since each electron can be considered a very small magnet, the cumulative effect of all the spins gives rise, at a macroscopic level, the properties of the magnet.
The nuclei of the hydrogen atoms constituting the water present, as other atoms, nuclear spins.
The water contains two hydrogen atoms, their spins may eventually go half in one direction and half in the opposite direction. Well it was discovered that in 75% of the water molecules of our planet, the spins of the two hydrogen atoms have the same direction of rotation, meaning, they are parallel. They are called: ortho molecules. In the remaining 25%, they are antiparallel and are called para molecules.
Even pure hydrogen presents ortho molecules and para molecules with the same percentages. Although the magnetic field associated with the nuclei is very weak, several researchers have shown how, in pure hydrogen, the para hydrogen presents vapour pressure, boiling point and specific heat different from that of normal hydrogen (Samuel Glasstone, trattato di chimica fisica, 1963 page 100).
In the water molecule hydrogen is bonded to oxygen, and due to the effect of the strong electronegativity of oxygen, the hydrogen electron is moved towards oxygen.
In the ortho water molecules, ¾ of water on our planet, the small magnetic fields are parallel, they sum and tiny permanent magnets oriented in the same direction rise.
Water is therefore, asymmetric.
Now, the water is the source of survival of living organisms. It was and is decisive for the evolution of the surface of our planet and, for four billion years, has stabilized the temperature within a range compatible with life. Without water, the earth would be a barren rocky planet. A question spontaneous arise: is it possible that the water asymmetry played a role in the asymmetry of the molecules essential for life?
Apparently, the two types of asymmetry seem different, one a magnetic type and the other of a structural type. But the molecular structures are formed by atoms linked through electrical interactions, and so both asymmetries are of electromagnetic origin. How these two asymmetries were able to interact is not simple to understand, but this cannot prevent some experimental attempt. The history of science is full of phenomena whose theory has been understood long after their discovery.
The asymmetry of water, however, may not have acted directly on the choice of the asymmetry of life. If we put in water a racemic amino acid, that is 50% Right and 50% Left, no deviation of the plane of the polarized light is observed. The water does not have a particular preference for one of two forms.
But then, how it may have determined this choice?
5.3 Molecular asymmetry: Colloidal silica
As Miller has shown, the primitive atmosphere was the site of synthesis of the amino acids that were dragged by the rain on the planet's surface. Amino acids, as water, were then distributed across the planet's surface. The water’s asymmetry must, therefore, have acted on a substance that was also distributed across the planet's surface. One of the minerals that was and is present almost everywhere is silica. Silica is also one of the clay components, and so we fall under the Bernal theory.
Quartz is an important component of the earth's crust, but even more important are the silicates that cover over 90% of the earth's crust. Metamorphic rocks are sediments of silicate that have suffered environmental damage. The clayey minerals, diffused on the whole surface of the planet, are silicate rocks, which have undergone such metamorphosis reacting with H2O and CO2 (carbon dioxide). Clay is one of the components of farmlands. One of the components of this metamorphosis is amorphous silica or silica gel. In nature amorphous silica often gives rise to a mineral called opal. The X-ray analysis showed that it is always present in the tetrahedral structural unit and contains microcrystals, named crystallites, of tridymite and cristobalite, which are polymorphic forms of quartz. The oldest opal also contains microcrystals of quartz and in fact, with the passage of geological Eras, it is transformed into chalcedony which is a mass of microcrystalline quartz.
The X-ray analysis showed the presence tetrahedral structural unit and also microcrystals of cristobalite in amorphous silica prepared in the laboratory and dried (silica gel). The amorphous silica, in the laboratory, is obtained by reacting, in aqueous solution, sodium silicate (soluble glass) and hydrochloric acid.
Na2SiO3 +2HCl + H2O → 2NaCl + H4SiO4 (ortho silicic acid)
The ortho silicic acid thus obtained polymerize and gives rise to first colloidal silica (sol).
The colloidal silica particles (sol) are not visible and do not stay long in suspension in the solution. After several minutes, they slowly aggregate to form flakes, visible to the naked eye, which precipitate giving rise to a precipitate of amorphous silica (gel). The formation of the colloid is not instantaneous. From H4SiO4 a certain amount of colloid, slowly forms an amorphous silica aggregates while another colloid begins to form. The concentration of the colloid in the solution is not always constant.
The formation of silicic acid in nature follow different chemical reactions, but the formation of the sol before and then the gel is identical to the experiments in the laboratory.
As already mentioned the amorphous silica is one of the components of the metamorphosis of the rocks and is spread practically all over the entire surface of the planet. The silica that precedes the amorphous silica is the colloidal silica. Like all colloids, it is not even visible under the optical microscope. However, even if invisible, the particles are still very large and therefore have very large surfaces. A colloid in solution is then considered a two-phase system, which has the same properties of a liquid in contact with a surface. On the surface of the particle in contact with the liquid medium we can have, phenomena of adsorption, formation of the electrical double layer, etc.
There are no known polarimeter observation researches of siliceous solutions. To be kept in mind, however, that until the 90s the most used polarimeters had a sensitivity of 0.1 degrees, with 10cm polarimetric tubes, with inclined position and manual sliding. With these polarimeters, it was impossible to bring out small deviations of the plane of polarized light. The new digital polarimeters with an automatic slide (type Polax-2L), have 20cm polarimeter tubes in a horizontal position. The deviation of the plane of polarized light is then doubled. They also have a sensitivity of 0.05 degrees and thus also the sensitivity is doubled.
Measurements of the water glass solutions, at various concentrations and times, were made with the polarimeter Polax-2L. Once the technique was standardized, it was observed that such solutions have optical activity. In particular, the silica in solution rotates the plane of polarized light to the Left.
This deviation will disappear after about 5-10 minutes.
The fact that after a certain time the deviation of the plane of polarized light disappears, this means that the colloid is to have such a characteristic. The amorphous silica, which subsequently is formed by the aggregation of the colloidal particles, forms a cloudy solution without any deflection of polarized light. The addition of ethyl alcohol to the solution substantially increases the deviation of the polarized light. It is well known that ethyl alcohol retards the aggregation of the colloidal particles and so the concentration in the solution is temporarily increased. (Appendix 3)
It therefore appears that, even if of short life, we are in the presence of an asymmetric mineral: the colloidal silica.
As already stated, the amorphous silica presents microcrystals of tridymite and cristobalite. The colloidal silica, which precedes the amorphous silica, rotates the plane of polarized light to the left. It therefore seems that the orthosilicic acid, polymerizing, forms, during its brief existence as a colloid, helical structures of Left quartz type. These structures are transformed into microcrystals of tridymite and cristobalite in amorphous silica and, after geological years, into chalcedony quartz crystals.
Now, if the colloidal silica in aqueous solution gives rise to helical structures, they are as likely to form both Right and Left structures. If the structures are only Left type, this can only be due to the asymmetry of the water.
But how does the water asymmetry determine the asymmetry of the colloidal silica?
5.4 Molecular asymmetry: Water, colloidal silica and the Earth's electromagnetic field
The colloidal systems are influenced by several independent factors, and today we still cannot define a complete theory of colloid stability. In order to study the colloidal systems it is therefore necessary, as suggested by various researchers, to standardize the technique and predefine a certain interval before the observation. For several colloids such as silica, H2O gives a considerable contribution to their stability.
It is known that the water molecule has a polar covalent bond, due to the strong electronegativity of oxygen and is therefore a dipole;
As a result of this bond, the water molecules are oriented in all directions, with the hydrogen to oxygen forming larger molecular aggregations (clusters).
The study of ice, through X-rays, has shown that these molecular aggregates give rise to crystals formed by tetrahedral structural units, at the center one oxygen atom and at the four vertices other oxygen atoms. Each oxygen is bonded to four atoms of hydrogen, and then presents a coordination number equals to four. Each molecule is then linked by means of the hydrogen bonds with four other molecules forming a more expanded structure. The directions along which the 4 links are located depart from the center of the atom of oxygen and go towards the vertices of a tetrahedron.
It is likely that this almost crystalline structure is present even at ordinary temperature and up to 37°C and that this structure is the responsible for the high specific heat of water at these temperatures. Above 37°C, the specific heat of water has in fact its minimum value. The most likely hypothesis is that over this temperature, the coordination number is two and the tendency to coordination number four is lost and the almost crystalline structures collapse definitively.
It is important to make it clear that measurements of silica solutions at the polarimeter have also been made at various concentrations and temperatures. Experimental data indicate that by increasing the temperature up to 34°C the deviation of the polarized light is constant. Beyond 34°C, the deviation decreases drastically to zero between 38-40°C, the asymmetry of the silica has therefore disappeared.
As already said, the most likely hypothesis is that at the temperature of 37°C the almost crystalline structures of H2O collapse definitively. The experimental data shows that around the same temperature the colloidal silica does not deviate any more polarized light. It seems clear, however, there is a direct relationship between the clusters of H2O and the structure of the colloidal silica (Sol); once the Cluster is destroyed, finally the asymmetry of silica disappears.
So in addition to the asymmetry of water where, as we have seen, dominated by ortho molecules in parallel spin,
also clusters seem to contribute to determining the asymmetry of the colloidal silica.
Moreover, it is remarkable that molecules and structures connected to life have the same structural units: the quartz consists of tetrahedral structural units, but as we have seen elsewhere, also the amino acids have tetrahedral structural units. We later discovered that the silica and then the water present tetrahedral structural units. Now, if the first clue is by chance and the second one is coincidence then the third clue usually indicates a pattern. The tetrahedral structural unit, energetically very stable, must somehow also have a role in the guidance to the final geometry of the colloidal silica.
We can conclude that there are three contributing factors that tend to help determine the asymmetry of colloidal silica: water asymmetry, clusters and the tetrahedral structural unit.
As already said, the tetrahedral structural unit of the silica places the silicon atom in the center and the oxygen at the top. Through the bonding of these structural units following the reaction:
Fig.1
From the first of colloidal silica formation where, as seen in Fig.1, many of the oxygens are still linked to a hydrogen atom. Because of the different electronegativity between oxygen and hydrogen, there is the formation of a dipole, and on it water with its characteristic bond orients itself and binds.
Fig. 2
The silica is then surrounded by a large number of H2O molecules, which gives it a certain stability in the colloidal state.
In fact, most of the H2O molecules around the colloidal silica are oriented in the same way that is with the positive charge on the outside.
The repulsion between the positive charges delays the aggregation of the colloidal particles and the formation of amorphous silica (silica gel). Water molecules that are found around the colloidal silica are not single molecules; they always belong to the water cluster that preserve tetrahedral structural units.
So, how do the three factors listed above lead to the asymmetry of the colloidal silica?
We try to give an answer.
We know that if current flows in a wire, around it generates a magnetic field. If small magnets, placed on a plane, surround the wire, they will be oriented around the wire so as to form a closed circumference.
If, however, no current is flowing in the wire, the small magnets should slowly arranged themselves to minimize the energy of the whole, as represented in the figure.
But this arrangement is not realistic because all the magnets must be aligned with Earth's magnetic field (indicated by the large arrow).
Now, let us imagine having a glass of water and we agitate it vigorously with a stirrer so as to destroy all clusters. What happens as soon as you stop stirring the water? The predominant force is the dipole-dipole interaction between the water molecules. Under the effect of this force, the clusters of water with their tetrahedral structures would rebuild.
The tetrahedral structure within the clusters is the most stable structural unit. But this stability is achieved not only because -Hδ+ are geared toward -Oδˉ and also taking into account the effect of the spin, even if that contribution is very small. The direction of rotation of the hydrogen nucleus, which generates a small magnetic field, can rotate clockwise or counterclockwise, this direction is referred to as spin up and spin down. Imagining the tetrahedral structure out of context, there is no doubt that the increased stability is obtained when within it, the four hydrogens have 2 spin up and 2 spin down, as indicated by the small arrows in the figure; in this way the very small magnetic fields associated with them cancel each other and the structure is more stable.
The tetrahedral structure in formation is, however, surrounded by Earth's magnetic field. If the barycentre of small magnetic fields were coincident, Earth's magnetic field would not have any influence on them. The nuclei of hydrogen inside the tetrahedral structure, however, are at a distance of approximately 4Å and are more subject to the effect of the Earth's magnetic field than to their mutual attraction. It is possible that the Earth's magnetic field requires the formation of structures with ortho-water molecules and hydrogen magnetic fields aligned with them.
Certainly, this is not to say that the Earth's magnetic field shifts the axis of spin as in NMR resonance. The water molecules, due to the thermal agitation effect, are oriented in all directions. Here we only want to emphasize that probably, due to Earth's magnetic field, only the ortho water molecules oriented in the direction of that field, become part of the tetrahedral structure, so as to make the structure slightly more stable.
For simplicity we will indicate, using a single arrow above the structure, the small magnetic fields of nuclear spin oriented in the direction of Earth's magnetic field.
It is important to highlight that the tetrahedral structures impose bond angles between the atoms, of about 110°. Since the link between Hδ+ of the colloidal silica structure and Oδ- of water tetrahedrons are predominant, small magnetic fields associated with the hydrogens inside the tetrahedrons cannot be aligned with Earth's magnetic field. This provision can be represented with the tetrahedron of the water that, due to the bond angles of the tetrahedral structures, assume a different orientation (Fig. A). As a result, the magnetic fields associated with the tetrahedron are no longer aligned with the Earth's magnetic field and will be subjected to different actions by the Earth's electromagnetic field.
Now, imagine for a moment that the whole structure is rigid except at the point of conjunction between the silica tetrahedrons. As can be seen (Fig. B), in the lower tetrahedral structure of colloidal silica, under the action of Earth's magnetic field, the clusters linked to -OH in position 1 and 3 are subject to a counterclockwise push while those in position 2 will undergo a clockwise push; the counterclockwise prevails.
On the contrary, in the upper tetrahedral structure of colloidal silica, the clusters in position 4 and 5 will suffer a clockwise push, and the clusters in position 6 on in a counterclockwise direction; in this case, the push in a clockwise direction prevails.
The final result is that the thrust will drag the lower tetrahedral structure of the colloidal silica by rotating it counterclockwise, and the upper structure zone rotating it clockwise.
Ultimately the tetrahedral structural units of the silica, when binding to create colloidal particles, could have any orientation, and any contribution, even if very small, may determine a preferred direction. This contribution could be given to the combined effect of Earth's magnetic field and the three factors listed above the asymmetry of water, the formation of clusters and the tetrahedral structural unit.
It is therefore possible that this combined effect impose a preferred direction and are at the base of the origin of the asymmetry of the colloidal silica.
5.5 The problem of molecular asymmetry: the disappearance of the Right form.
Experimental part
By measuring the potential flow it’s been shown that, within the electrical double layer of Right quartz the amino acids Right accumulates, and Left amino acids in Left quartz. Today we are therefore in the presence of a process that connects deductively the separation with the fundamental principles of physic. We also found that the colloidal silica is left-handed. So the question is: does colloidal silica have the same behaviour of the Quartz? Can the colloidal Left silica accumulate on its surface the Left amino acid? And then: what happened to the Right amino acid?
Unfortunately, it is not possible to prepare diaphragms of colloidal silica and so we cannot use, even for the colloidal silica, the device that we used to measure the quartz flow potentials. We must necessarily use a different strategy.
A colloid in solution is a two-phase system, which has the same properties of a surface in contact with a liquid. On the contact surface of the particle with the liquid we can have, adsorption phenomena and the formation of a double electrical layer. The strategy to be used, in summary, it is then the following: Prepare a solution of DL amino acid (50% Left and 50% Right), which on a polarimeter, does not divert polarized light. In the same solution water glass is added (Na2O · 2SiO2 · 2H2O) to produce the colloidal silica, filter and observe the polarimeter. If one of the two forms is accumulated on the silica surface it will remain in the filter together with the silica, its concentration in the solution, which passes through the filter, will be lower and therefore will be highlighted by observation on the polarimeter.
However, in order to put in evidence a deviation of the measured polarized light, we need a good amount of adsorbed amino acids and consequently we have to produce a considerable amount of colloidal silica. However, here lies a problem. As can be seen from the reaction,
Na2SiO3 +2 HCl + H2O → 2 NaCl + H4SiO4 (ortho silicic acid)
The production of a considerable amount of colloidal silica also produces a considerable amount of salt (NaCl).
Now, according to Bikerman as reported by G. Bianchi (quoted essay), with an increasing salt concentration in the solution, the electrokinetic potential tends to zero. In particular, for a unit salt charge, the electrokinetic potential is zero when the salt concentration reaches 3-4 g / L.
This decrease, as highlighted by Samuel Glasstone (quoted treatise) can be due to:
1) A reduction of the thickness of the double electrical layer;
2) The double electrical layer is still extended but the dielectric constant and the viscosity vary within it.
Unfortunately, it is not possible to prepare in laboratory a substantial amount of colloidal silica with a salt content below 3-4 g/L. After several attempts, the concentration chosen was 1,1g/ 50mL of water glass (Na2O · 2SiO2 · 2H2O) adjusted between pH 6.8 -7.4 with HCl 8N. In these conditions, the amount of silica is large; it forms after about ¼ h and after 3-5 h may be filtered with a medium-fast Wattman filter. The salt content is however of about 0,60g / 50mL, i.e. around 12g / L NaCl.
Therefore, if increasing the salt concentration, the tendency to zero of potential is due to point 1), i.e. the disappearance of the double electrical layer, the amino acid cannot being accumulated on the silica surface, so in laboratory nothing can be put in evidence.
Nevertheless, if as highlighted in point 2) the double electrical layer is still extended, the specific amino acids could be retained by the silica and the filtrate have a lower concentration.
The chosen concentration for the amino acid was 0,30g / 50mL approx. There is not a specific reason for doing so. For amino acids, an average molecular weight of 100 uma, the 10-2 M concentration appears too diluted, while the 10-1 M concentration is too concentrated: we chose for an intermediate concentration.
The polarimeter used is a Polax 2L. Amino acids examined were alanine, valine, and threonine; other amino acids were not available in sufficient quantity. Of these, only the alanine gave positive results. (Appendix 4)
The DL Ala (50% Right 50% Left) does not deviate polarized light, the Ala L deflects to the right (+), while the D Ala deflects to the left (-). From the experimental data it is clear that the solution of DL Alanine, after getting into contact with the silica and filtration, it deflects the plane of polarized light to the left, therefore it contains a greater amount of Ala D (-). This means that when the DL Alanine comes into contact with the silica, L Ala (+) is retained inside of the double electrical layers of silica while the D Ala (-) is not retained, it remains in the solution. The colloidal silica then behaves like quartz, separating the Right from Left.
But because only Alanine and not the other amino acids?
As we have already seen each amino acid in relation to quartz, is accumulated in the double electric layer at a specific potential and removed from the solution. Then, it is very likely that the double electric layer of silica is very widespread as mentioned in point 2), and that high salt concentration requires only specific potential, corresponding to Alanine. The experiments were done in the course of one year at an average temperature of 20 °C. When in late spring and early summer, the temperature reached 24°C and the experiment was repeated, no deviation of the polarized light was observed. It is likely that in these new conditions, the colloid had a new stability, the double electrical layer varies drastically and consequently the potential is not the specific potential of Alanine.
5.6 Still on the terrestrial electromagnetic field
In the theoretical part, we hypothesized that the Earth's magnetic field had played a role in the asymmetry of the colloidal silica. So then, eliminating the Earth's magnetic field, the asymmetry of the colloidal silica should disappear. In truth, a close colleague of physics, Professor Clemente Cattaneo, asked this question. As Clement illustrated to me, the earth's magnetic field cannot be completely eliminated. Anyway, we decided to try.
My relationship with Magistri Cumacini, the High School where I taught for almost thirty years, is still ongoing. A group of teachers, now retired, work at the reordering and cataloguing operations of the school library. The kindness and the interest of the Engineer Enrico Tedoldi, Headmaster, who granted us permission to carry out the experiment, was ever present.
After measuring the magnetic field in the laboratory, corresponding to 0.16 Gauss, Clemente prepared the necessary equipment. This is consisted in a 20 cm of 150 solenoid coils, traversed by a continuous current of 17mA, which generates a magnetic field of approximately 0.16 Gauss. By placing an inversed field compared to Earth’s, we definitely reduced if not cancelled out the field in the area. Unfortunately we could not assess the variation of the field produced by the metal parts of the polarimeter, but we are certain that the influence is negligible compared to the field created by the solenoid. We found that a sensitive compass did not undergo significant deviations within the polarimeter, which is made up of prevalently aluminium, stainless steel and plastic.
With a direct polarity the field was, however, increased.
For the experiment were used Na2SiO3 (soluble glass) in H2O and CH3CH2OH (ethyl alcohol), magnetic stirrer, polarimeter "Polax 2L". In Polarimeter, the metal staff of the test tube was replaced by an identical wooden support.
We do not know how much the circuit lowers the Earth's magnetic field. However, the results of the measurements showed that there is no decrease in the deviation of the polarized light of the colloidal silica, which exceeds the sensitivity limit of the polarimeter. Clemente asked himself another question: If the magnetic field contributes to the asymmetry of the colloidal silica, by increasing the magnetic field, the deviation of the polarized light must increase.
Here we played on reliable data: placed the solution under four times the Earth's magnetic field. As it often happens in researches, the unexpected occurs: The deviation of the polarized light was not increased, but had disappeared. The colloidal silica lost its asymmetry.
In order to draw definitive conclusions of the magnetic field at different values, a number of tests should be done and a graph plotted. I however do not have more than one laboratory, and it is not correct to abuse of the kindness of others. The tests described above are therefore a clue, a strong clue of the role played by Earth's magnetic field.
It is possible that without the presence of a magnetic field, there is no asymmetry of the colloidal silica. The appearance of a magnetic field imposes, through the tetrahedrons of water, a slight rotation on the siliceous structures, and therefore the appearance of the asymmetry of the colloidal silica. It is likely then that beyond a certain value, a strong magnetic field does not induce a rotation, but imposes a strong alignment of the small magnetic fields of water molecules destroying the asymmetry of the colloidal silica.
5.7 Molecular asymmetry: Barghoorn and the primitive filaments
It is clear that these results cannot lead to definitive conclusions, but they are a strong indication of how the facts might have gone. The DL amino acids synthesized in the atmosphere and carried away by rain, reached the earth's surface and were separated from the colloidal silica. The Left remained on the surface of the earth, held back by the silica within the double electric layers, resulting in L polypeptides and the Right ones dragged into the primordial sea.
In the prebiotic era, the atmosphere contained no oxygen and therefore the ozone layer was absent. Ultraviolet rays, in much greater quantities than in the present days, reached the planet's surface. In a primitive ocean, they reached a depth of 10m destroying all life forms in formation and the organic substances necessary to its origin too. Diffusion, thermal agitation and currents would eventually lead all substances in this altitude of the ocean and would be destroyed.
It can therefore be assumed that the bilayers have worked as electrochemical filter, selecting and accumulating the Left amino acids, while the Right transported from waters in the primitive ocean were slowly being destroyed by ultraviolet rays. It is within these double electric layers, separated the Left from the Right and away from UV rays, according to natural laws, that life made its first steps.
So, is the asymmetric colloidal silica the agent we have been looking for almost two centuries? Is this the missing link to solve the molecular asymmetry problem of living organisms in the prebiotic era, that is, before life originated?
Of course, 3.5 billion years ago, in contact with the silica something must have happened.
There are regions of the earth's crust that preserve very ancient rocks called old shields. The formation of the Fig Tree in South Africa is among the oldest of these old shields. Its sediments and its rocks have been dated to 3.2 to 3.5 billion years ago. We are at the lower limit of that billion years void, between the formation of the earth 4.5 billion years ago and the uprising of the first living organisms, estimated 3.5 billion years ago.
In 1965 E. S. Barghoorn, "I fossili più antichi" Le Scienze, Gli albori della vita 1984, picked up flints from different locations of the Fig Tree and here is what he wrote: «By examining thin sections under the microscope, we observed that the rock matrix presented
abundant laminations of dark and substantially opaque organic matter [...]. The deposition process of the organic substance was placed within a silica-rich matrix, before it crystallized in flint [...]. The electronic microscope also revealed the organic substance in the form of irregular, thin filaments [...]. The filaments were definitely simultaneously with flints formed [...]. It was suggested the hypothesis that they can be polymerized filaments of organic matter abiotic, coming from the prebiotic soup».
Colloidal silica is an asymmetric mineral that in its short life only exists as Left. In prebiotic times, it may have accumulated the amino acid Left on its surface.
If this were, the polymerized filaments discovered by Barghoorn could have been Left amino acids polymerized and remained imprisoned inside the silica matrix for 3.5 billion years. Such an event could definitely separate the D amino acid from L putting them in completely different chemical and physical conditions.
In fact, at that time, the silica was deposited mainly on the mainland and Left amino acid would be concentrated in specific areas, protected from ultraviolet rays and away from other reagents.
The Right amino acid, transported by waters in the primordial ocean, would participate in a huge number of secondary reactions of no use for the origin of life and slowly would be destroyed by ultraviolet rays.
Christian de Duve (quoted essay) writes: «This strange preference of nature for left-handed amino acids is considered by many scientists one of the most interesting mysteries on the origin of life»
According to R. E. Dickerson (cited article): «It seems that the early selection of the L-isomers over D-isomers were a coincidence. [...] It may be that, in a certain period, there was a primitive life based on both D and L amino acids, with a probability of 50% and that, eventually, L amino acids prevailed over D amino acids».
For several researchers including Paul Davies, (quoted work) the question of the asymmetry of living organisms is also: «A proof of the universal ancestor results from the bizarre question of the so-called chirality of the molecules. [...] Each compound is found with the same chirality, Right or Left, in all living beings. This suggests that they all descended from a single cell, which contained every molecule in the chiral form in which we find it today»
But, perhaps there is no mystery, no double origin and no common ancestor at least as regards molecular asymmetry. It was the chemical physical conditions of our planet, that laid the foundations for the unity of life and the chemical physical selection of amino acids was the first step.
The facts seem to be simpler than might think and regulated by strict determinism, at least in the first stage of the origin of life.
Chapter 6.
The origin of the genetic code: The electrokinetic theory
The origin of the genetic code has been defined: the universal enigma.
To make the reasoning understandable and not to lose the unity of the topic, it will help to repeat what is meant when we say the genetic code, that is the law of correspondence between the mRNA and amino acids for the synthesis of proteins.
The mRNA is the nucleic acid messenger that carries the information for the synthesis of proteins and consists of nucleotides.
The nucleotide constituents are:
The phosphate group: (H2PO4)-.
A sugar, a Ribose, which exists in two forms Right and Left, a mirror image one of the other. Only the Dexter make part of nucleotides: D-Ribose.
The bond between a phosphate group, a ribose molecule and a molecule of any of the four Nucleobases give rise to four different compounds, which are called nucleotides. Of the four nucleotides, as an example, the Adenosine-5-phosphate is shown
(Figures from: "Lezioni di Biofisica" by Mario Ageno)
In the mRNA the name of “triplet” is given to the three adjacent nucleotides and are indicated with the letters of the Nucleobases. For example, in the figure the three nucleotides that expose UAC Nucleobases make up a triplet. If were followed by GUA in the figure, we would be in the presence of another triplet and so on. Starting from this RNA macromolecule, through a process, today quite complex, proteins are assembled. For each triplet (also called codon) corresponds to a specific amino acid, one and one only, and that law of correspondence, represented with 3:1, is called: genetic code. Although in recent decades some exceptions have been discovered, it can be said that all living organisms on our planet use the same genetic code, it is therefore universal.
By having available four nucleotides the total number of triplets we obtain placing them three by three is 43 = 64. Three of these triplets are used as end signal (t.), in theory, the mRNA contains the information for 61 amino acids. Since the amino acids at the disposal of all living organisms are only 20, the genetic code is degenerate in the sense that more triplets are coding the same amino acid.
For example the triplets posing in 1st, 2nd, and 3rd position: GUU, GUC, GUA, GUG, all encode the same amino acid: the valine (Val).
Let us see now, very briefly, how the synthesis of proteins in living organisms works today.
(Figure prepared by: "Lessons of biophysics") Mario Ageno
A particular sequence of nucleotides of the DNA (gene), containing the information for the synthesis of a well-determined protein, is transcribed into mRNA. This molecule, as the punched tape of an old electronic processor, slides inside an organelle, the Ribosome. It reads the information contained in mRNA and for each triplet of consecutive mRNA Nucleobases (codon) it matches the specific amino acid. The amino acid, however, does not enter directly in the ribosome, it is transported by a particular type of nucleic acid, the tRNA. The tRNA contains at one end a triplet of Nucleobases (anticodon), complementary to the codon, and at the other end the specific amino acid. Through the participation of enzymes the amino acids Pro, Phe, Ala, Ser and so on, are therefore bound in the right order to form the protein (as in the figure).
As we said this is an extremely simplified representation of the process. Just consider that the bacterial ribosome consists of two subunits: the first is linked to thirty-four proteins and the second to twenty-one proteins; both contain nucleic acids. Such a complicated structure definitely was not present in the prebiotic era. Also, in the cell, for each amino acid an adapter is present, a tRNA, with a specific enzyme, meaning other 40 molecules and if you add the enzymes participating in the whole process we reach 50 compounds. Such a complex system is unimaginable at the dawn of life. All scientists who deal with the problem, believe that in the beginning a protein synthesis process surely existed in a much more simple and rudimentary form.
The first to develop a theory on the origin of the genetic code, a year after the discovery of the double helix of DNA, was George Gamow in 1954. He proposed a direct interaction between the nucleic acid triplet and amino acid. In truth at that time, the role of mRNA had not yet been discovered. Moreover, Gamow did not propose any chemical physical mechanism to the law of correspondence between triplet and amino acid, and therefore was easily to demolish his theory. In fact, if we consider the sequence of four nucleobases UUCG, UUC encodes an amino acid while UCG encodes another amino acid, how the choice would be made. Without a chemical physical mechanism, given four Nucleobases one can jump from one to another triplet and give rise to completely different proteins. The Gamow's theory, however, remained an attractive idea.
In 1966, Woese, with other researchers, published: "The molecular basis for the genetic code". The work involves a chromatography research on paper to study the interaction between triplets and amino acids. Not being able to directly use neither the three nucleotide, that is a triplet, nor just the nucleobases, Woese and colleagues chose the Pyridine as a solvent, a compound close to the Pyrimidine, founder of uracil and cytosine nucleobases. The authors conclude that there is a hierarchy in the nucleobases of the triplet, regarding the choice of amino acids, defined in terms of polar or non-polar interactions. In particular, the choice of amino acids is mainly determined by the nucleobase in 2nd position. The nucleobase in the 1st position is seen as a disturbance that chooses between similar amino acids, while the third position interacts weakly on the choice of amino acids and therefore plays a minor role.
Analyzing the issue, Jacques Monod in "Il caso e la necessità" in 1970 concludes with this alternative:
«A) The structure of the genetic code can be explained in chemical terms or more exactly stereochemistry; if a certain codon was chosen to represent a given amino acid, it means that between them there existed a certain stereochemistry affinity;
B) The structure of the code is arbitrary from the chemical point of view; the code as we know it today, comes from a series of random choices that gradually enriched it. The first hypothesis seems by far the most attractive, because it would explain the universality of the code and then because it would allow imagining a primitive translation mechanism in which the sequential alignment of the amino acids in the polypeptide structure would be due to a direct interaction between the amino acids and the replication structure itself ". Monod therefore reports a conclusion of F. Crick in 1968: «Several attempts in this direction have actually been made, but they have a negative balance at least for now». F. Crick had long proposed as a hypothesis "the frozen accident." According to this hypothesis, the origin of the genetic code would have been a random event that once occurred has frozen, that is, he could not go back.
In 1984 Mario Ageno (quoted work), examines the formal structure of the genetic code, which shows, as we shall see, a certain centrality of the bases in the 1st and 2nd position in the allocation of amino acid. He also reports an Orgel proposal: «So, U in the 2nd position would have meant hydrophobic amino acid, A is a hydrophilic amino acid, while C and G always in the 2nd position would have meant intermediate hydrophobic amino acids between the first two groups». However, after examining the work done at the time, Ageno says that no progress has been made since Crick's conclusions in 1968. In researches after 1984, metabolic or coevolutionary processes that still require the presence of other molecules mainly tRNA as adapters, were privileged. Among these researches caused some initial interest the works of Yarus M. “RNA-ligand chemistry: a testable source for the genetic code”, 2000 and Yarus M1, Caporaso JG, Knight “Origins of the genetic code: the escaped triplet theory”, 2005. In them it is assumed, at least for some amino acids, some direct stereochemical interaction between codon and amino acid and subsequent evolutionary processes have brought the code to minimize errors in translation. It seems that these errors due to incorrect reading are in the ratio of 10: 1: 100 for errors relating respectively to the 1st, 2nd and 3rd position. The authors extended, the hypothesis already advanced by C. R. Woese in 1965 for the UUU triplet, to all triplets containing a pyrimidine 2nd position.
It is established that, once the process of the cell evolution began, the genetic code will have undergone some changes. As reported by Eugene V. Koonin and Artem S. Novozhilov in "Origin and evolution of the genetic code: the universal enigma", 2009: «Today, there is ample evidence that the standard code is not literally universal, but is subject to significant changes, without changes to its basic organization».
The issue is that evolutionary processes assume the existence of a cellular life. But in the presence of cells, if evolution had contributed to the origin of the genetic code, every living species would have developed its own genetic code and it would not be universal. The origin of the code must necessarily precede cellular life and Darwinian evolution. The era of the origin of the genetic code is the prebiotic era. Ultimately, after more than sixty years of research, it seems proven the centrality of the nucleobases in the 1st and 2nd position in the selection of the amino acids, with a predominance of the 2nd nucleobase, but we don’t know the origin of the genetic code yet.
How was it possible?
I think these attempts to understand the origin of the genetic code all contain a fundamental error.
As we have seen, the term "triplet” illustrates very well the structure of the genetic code, but hides a fundamental fact overseen by all: we know the properties of the amino acids but do not know the properties of the triplet. So in the end, we found ourselves comparing the chemical-physical properties of the amino acids with some letters of the alphabet (U, A, C, G). But there is more: each nucleobase of the triplet is linked (see picture above) to an asymmetric molecule, the Ribose with Right structure. The Ribose then binds to a phosphate group to form three nucleotides. The link through the phosphate groups of the three nucleotides form a trinucleotide that presents three nucleobases, that is, the triplet. So the triplet properties are not those of the triplet but ones of the whole trinucleotide. We can express it this way: the trinucleotide have specific properties that vary with the triplet. It is the whole trinucleotide that specifies the amino acid and not the triplet alone. The ratio 3: 1, three bases, one amino acid, is conceptually incorrect. The right representation would be: one trinucleotide one amino acid, 1:1. We can leave, for convenience, the representation 3: 1, but it must be understood in this way: The trinucleotide that presents the three nucleobases encodes for a specific amino acid. And it is also wrong to say that the constituents of nucleic acids are nucleotides, because the nucleotide do not represent anything; the constituents of nucleic acids are the trinucleotides. The trinucleotide can be considered an entity in itself, which interacts with the other trinucleotides in the mRNA but which must already have its own peculiarity.
At least do we have an indication of the existence of this peculiarity?
In reference to the law of correspondence, Mario Ageno (quoted work) wonders if the genetic code has been from the beginning 3:1; is it possible that in primitive times it was different, for example 2:1? He excludes such a possibility because, in that case, all metabolic processes made with a code 2:1 would be lost in the transition to a code 3:1 and evolution would have had to start again, but he added: «However, it is possible that at the beginning not all three positions were read: perhaps the first two while the third had the function of spacing». If only the first two positions were read, leaving the third as spacing, then by ordering the four nucleotides two by two, only 42 = 16 amino acids would have been sufficient. According to Paul Davis, (quoted work), grouping the four nucleotides in pairs rather than triplets and use 16 amino acids would have been much easier for the origin of life. Life could have worked just as well with less than 20 amino acids. Probably life would not reach the level of today's complexity, but it would work.
Why was this choice not made?
We can also ask: having 4 bases why not choose a 4: 1 code?
Sure, with such a code can be encoded 44 = 256 amino acids, with the increasing risk of translation errors; but, how did the molecules know about the risk. On the other hand, the choice of code may not have been an evolutionary process because life did not yet exist and therefore neither evolution.
Therefore, there were three code possibilities: 2: 1, 3: 1 or 4: 1, the 3: 1 triplet code predominated. But this means that the trinucleotide that exposes the triplet must have its own peculiarities. That is, the trinucleotide must have at least one property that distinguishes it from other codes.
Having said that, if in beginning there were no evolutionary processes, if there wasn’t a system of tRNA adapters with a specific enzyme for each amino acid because it is too complex, then there must be a stereochemistry affinity, not between triplets (codons) and amino acid but between the trinucleotides and amino acids; a direct chemical-physical interaction that immediately coded the information of the nucleic acid.
So, let us first of all look for some indication of such stereochemistry affinity and, subsequently, which property distinguishes the code 1:1 from other codes.
As we have already amply illustrated, the crystalline quartz in contact with solutions gives rise to double electrical layers on its surface, comparable to micro capacitors. Through the measure of the flow potential, it is clear that amino acids accumulate on the quartz surface with a predetermined potential, specific potential.
Well, between the structure of the genetic code, where the centrality of the bases in 1st and 2nd position is evident, and the specific potentials of amino acids there is a surprising mutual correspondence, in particular:
1) Eight out of twenty amino acids are already encoded by the first two letters (the third is indicated with a dot), that is each amino acid, as seen from the table of the genetic code, is already encoded by a single nucleobase pair in 1st and 2nd position. And are:
Leu – CU∙ Val – GU∙ Ser – UC∙ Pro – CC∙ Thr – AC∙ Ala – GC∙ Arg – CG∙ Gly - GG∙
Of these amino acids, the three at our disposal, for measuring flow potentials, each has only one specific potential.
Pro 10,10 mV Val 9,90 mV Ala 9,70 mV
2) Eight pairs of amino acids are already encoded by the first two letters, which means in eight cases two amino acids are encoded by the same pair of nucleobases in the 1st and 2nd position. And are:
(Phe, Leu) – UU∙, (Ileu, Met) –AU∙, (His, Gln) – CA∙, (Asn, Lys) –AA∙, (Asp, Glu) – GA∙, (Cys, Trp) –UG∙, (Ser, Arg) –AG∙, (Tyr, t) –UA∙,
(Tyr, t) –UA∙; with (t) as the end signal, seven pairs of amino acids encoded by the same nucleobase pair in 1st and 2nd positions remain.
Of these amino acids, the four at our disposal for measuring flow potentials:
Two amino acids, Phe and Leu, have the same specific potential of 9.50 mV.
And other two, Ileu and Met have the same specific potential of 9.30 mV.
3) In addition, two pairs of nucleobases UU∙ and CU∙ encode Leu, the Leu produce two specific potentials, 9.50 mV and 8.10 mV.
We report the Chart already exposed that shows the potential of specific amino acids available at our disposal:
The correspondence between the pair of nucleobases in 1st and 2nd position of the triplet and the specific potential of the amino acids is clear.
A single nucleobase pair recognizes an amino acid: only one potential for the amino acid. Pro 10,10 mV, Val 9,90 mV, Ala 9,70 mV
A single nucleobase pair recognizes two amino acids: only one potential for the two amino acids. Phe, Leu 9,50 mV, Ileu, Met 9,30 mV.
Two pairs of nucleobases recognize an amino acid: two potential for that amino acid: Leu 9,50 e 8,10.
But such correspondence must be mutual, in the sense that: if the potential generated via double electric layers confirm the central role of the nucleobases in the first and second position, then the centrality of such nucleobases confirms their connection with double electrical layers. So then, the centrality of such nucleobases should be of the same nature, specifically electrochemical, otherwise we would find ourselves once again compare properties of amino acids with letters of the alphabet. There is therefore an indication of a stereochemical affinity, which could be the trace of a rudimentary mechanism of protein synthesis, "fossilized" in the genetic code, which has come down to us from the prebiotic era. But how can we explain this stereochemistry affinity?
We have already said that the quartz in contact with a solution gives rise, on its surface, to a double electric layer that has allowed us to know the specific potentials. Finally, we have also extended this mechanism to colloidal silica. Then, remembering that the nucleobases do not have properties but the trinucleotide do, we can extend these concepts to an RNA molecule of the prebiotic era.
The RNA is a large molecule, which in contact with a solution gives rise, on its surface, to double electrical layers. Each trinucleotide finally represented by a triplet, has the property of generating its own specific electric field. Within this electric field, the lines of force must have a helical shape determined by the presence of the Right form of Ribose that is, D-Ribose, comparable to the hole of a screw. If the potential of the trinucleotide electric field is specific to an amino acid, the latter with a left-handed structure, whose electric field has lines of force comparable to a screw, it recognizes it, and being complementary to it, it attaches to the trinucleotide by lowering the system energy.
Within this double electric layer, as we have amply illustrated, amino acids dragged by the "arrow of time", found the conditions necessary to be synthesised in proteins. There would therefore exist a law of correspondence between trinucleotide and specific amino acid, a chemical-physical system of recognition and complementarity. This kind of direct electrochemical recognition, represented by a ratio of 1:1, one trinucleotide, one amino acid, might have worked in the prebiotic era. It may have transferred through evolutionary processes into the current mechanism, which is very complicated that involves tRNA, ribosomes and enzymes.
It is likely that every trinucleotide had the property to delimit its own electric field helical comparable to the hole of a screw. This electric field is mainly determined by the nucleotides that expose the nucleobases in the 1st and 2nd position, with a dominant 2nd position, and at a lesser degree by the nucleotide that exposes the nucleobases in the 3rd position. The electric field of the first trinucleotide of one end defines the electric field of the remaining trinucleotides of the entire mRNA. This means that it is not possible to take a part of a trinucleotide and another part of a trinucleotide from elsewhere to constitute a new trinucleotide and encode a new amino acid. The electric field of a trinucleotide cannot be skipped.
From these considerations emerges the fact that the third nucleobase is not the spacing function as suggested by Ageno. As explained above, the four triplets with the first two letters UU encode the Leu and Phe while the 3rd base distinguishes them. Similarly the four triplets starting with AU encode Ileu and Met and the 3rd nucleobase distinguishes them. Some researches, as we have already explained, show a minor role played by the 3rd nucleobase in the genetic code. The nucleotide containing the third base probably completes and improves the electric field of the trinucleotide, but its contribution to the potential is weak and the appliance for measuring the potential of flow is unable to detect. Now, is it possible that the assumptions presented above have left crystallized traces in the current molecular structures of the mRNA and proteins, traces from the distant past?
Is there any data that we can take as clues to support this hypothesis? We must start from the premise: If an amino acid recognizes a trinucleotide in the mRNA molecule, a trinucleotide recognizes an amino acid in the structure of the ꭤ-helix protein.
1st Clue.
As we have noted, the colloidal silica rotates the plane of polarized light and appears to give rise to structures of Left quartz type. But the Left quartz structures, under the analysis of X-rays were found to be Right-handed helices, and so the structures of the colloidal silica must have Right-handed helices. We also suggested elsewhere that the colloidal silica has retained on its surface the Left amino acids whereby polypeptides can be synthesised. But if the colloidal silica has Right-handed helices also the polypeptides formed on its surface must be Right-handed. In fact, one of the secondary structures of proteins is the ꭤ-Right-handed helix.
Now, if a trinucleotide recognizes an amino acid on the ꭤ-Right-handed helix and we imagine that on it was synthesized an RNA, these too will have a ꭤ-Right-handed helix. In fact, the RNA helix is Right-handed. This analogy may suggest that RNA is Right-handed because it used the Right-handed helix as a template, which is Right-handed because it used the Right-handed colloidal silica as a template. The trend clockwise of these molecules could represent a crystallized trace in their structures, a sign of their distant bond.
However, a single clue is just a chance.
2nd Clue.
But is there some evidence to assume that in the prebiotic era the RNA used the ꭤ-helix Right-handed as template?
The helical structure of proteins, the ꭤ-Right-handed helix, is a periodic structure, consisting of amino acids, which after a rotation, returns to the straight line of his initial position. Each helix rotation contains 3.6 amino acids. To recognize 3.6 amino acids, 3.6 trinucleotides are needed. Each trinucleotide is formed from three nucleotides, so 3,6x3 = 11. To recognize the 3.6 amino acids of a rotation of the ꭤ-Helix it takes 11 nucleotides.
The helical structure of RNA is also a periodic structure consisting of nucleotides that after a rotation return to the straight line of his initial position. And how many nucleotides are included in a rotation of the RNA helix? 11 nucleotides, that is, 3.6 trinucleotides that serve to recognize amino acids 3.6.
Perhaps a geometric illustration is more effective.
If we project on a plane a rotation of dell'ꭤ-Helix we get a circle. By dividing the round angle by the number of amino acids, for each helix rotation we will obtain: 360°: 3.6 = 100°. Each amino acid molecule covers a 100° circular arc where the amino acid properties are enclosed.
If we project on a plane a rotation of the RNA helix, we get a circle. A tour of the RNA helix contains 11 nucleotides, that is, 3.6 trinucleotide. By dividing the round angle by the number of trinucleotide per helix revolution, we will obtain: 360 ° 3.6 = 100°. Each trinucleotide covers a 100°arc, where the properties of the trinucleotide are enclosed as a separate entity.
Then, one trinucleotides and one Amino acids each in their own helix cover an equal arc of 100 °; can this still be considered chance?
However, a second clue is just a coincidence.
3rd Clue
All amino acids contain a carbon atom, which are linked to an H atom, an NH2 group, a carboxyl group -COOH and a side chain R. To distinguish an amino acid from another is just this side chain R. The ꭤ-Helix is a structure stabilized by hydrogen bonds that compacts it, and inside there is no free space. All R side chains that distinguish the amino acid are arranged outside the helix, that is, in the convex part.
The RNA helical structure is also stabilized by hydrogen bonds between the nucleobases. However, in the helix nucleobases are inside the RNA helix, that is, in the concave part. This means that the arc of the RNA which contains in the concave part the trinucleotide and therefore the triplet, may overlap the arc of dell'ꭤ-Helix, which in the convex part contains the amino acids. Trinucleotides and amino acids are, therefore in geometrical conditions that they can interact, the two helices can be overlapped.
But the third clue is a proof
4th Clue.
Let us imagine a 100° RNA arc that contains in concave part of the Helix a trinucleotide. Let us place this 100°arc towards the convex part of a ꭤ-Helix arc, which contains the amino acid side chain (R). Trinucleotides and amino acids can interact but their atoms cannot touch, they are at an average distance of about 4 Å (angstrom).
If three clues are a proof, the fourth clue indicates the certainty.
The theory above shows a correlation between experimental data, the structure of the genetic code and the molecular structure of proteins and RNA.
In physical chemistry, phase is defined as a homogeneous portion of matter limited by defined separation surfaces. So for example: ice in water, fat particles in milk, sand in the water are constituted by two phases, solid and liquid; therefore, they are biphasic systems. The colloidal solutions consist of a liquid phase in which particles ranging in size from 10Å to 1000Å are dispersed. They are characterized by a large surface area and are therefore biphasic systems.
The fundamental macromolecules of life, proteins, nucleic acids etc., fall under the characteristics of the colloids, therefore in solution give rise to biphasic systems.
H. v. Helmholtz, in 1879, (Glasstone 1963) proposed that in the surface of separation between the two phases a double electric layer always forms. The phenomena that are observed due to the presence of the double electrical layer were called, at that time, electrokinetic effects. Since the theory proposed above is based on the properties of the double electrical layer on the surface of the macromolecules, we can call this theory the electrokinetic origin of the genetic code.
The electrokinetic origin of the genetic code postulates a chemical-physical interaction between the ꭤ-Helix amino acids and trinucleotide, and between amino acids and mRNA trinucleotides. It represents a primitive translation mechanism that links the genetic code to the principles of physics and biology, and it is through these principles that the universality of the genetic code is explained.
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