giovedì 1 ottobre 2015

THE ORIGIN OF PROTEINS: The molecular asymmetry problem (part six)

Post n. 24 (English)

As we already explained, in reference to the molecular asymmetry problem, Mario Ageno in "Lezioni di Biofisica", 1980 wrote: "This problem has troubled the minds of a large number of researchers from Pasteur’s time until today and it seems not to have received a fully satisfying answer, which colleagues deducted molecular asymmetry existence of the biosphere with the fundamental principles of physics or biological theory.”
By measuring the potential flow (The origins of proteins: The molecular asymmetry problem, part three) it’s been shown that, within the electrical double layer of Destro quartz the Destro amino acids accumulates, and Levo amino acids in Levo quartz. Today we are therefore in the presence of a process that connects deductively the separation with the fundamental principles of theoretical physics. 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 Levo silica accumulate on its surface the Levo amino acid? And then: what happened to the Destro amino acid?
Unfortunately, it is not possible to prepare diaphragms of colloidal silica and so we can't use, even for the colloidal silica on the equipment that we have used for the measurement of the potential flow of the quartz. 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, is then the following: Prepare a solution of DL amino acid (50% Levo and 50% Destro), 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, that passes through the filter, will be lower and therefore will be highlighted by the polarimeter during observation.
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. But 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 "Elettrochimca" 1963, 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 in "Trattato di chimico-fisica" 1963 can be due to:
1) A reduction of the thickness of the double electrical layer;
2) The double electrical layer is still wide enough but the dielectric constant and the viscosity inside isn’t constant.
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 range went 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, ie. around 12g / L NaCl.
Therefore, if the salt concentration is increased, the tendency to zero of potential is due to point 1), ie the disappearance of the double electrical layer, the amino acid cannot being accumulated on the silica surface, so in the laboratory nothing can be put in evidence.
But if, as highlighted in point 2) the double electrical layer is still extended, the specific amino acids may be retained by the silica and the filtered output therefore has 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.
 
www.tecnolab.bs.it
The DL wing (50% Right 50% Levo) does not deviate polarized light, Levo Ala 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 Alanine D (-). This means that when the DL Alanine comes into contact with the silica, L Alanine (+) is retained inside of the double electrical layers of silica while the D Alanine (-) is not retained, it remains in the solution. The colloidal silica then behaves like quartz, separating the Destro from Levo.
One wonders: why only Alanine and not the other amino acids? As we have already seen (Origins of proteins, part three) each amino acid in relation to quartz, is accumulated in the double electric layer at a specific potential. Thus, only at specific potential the amino acid is accumulated in the electric double layer and removed from the solution. In addition, 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.
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 Levo remained on the surface of the earth, held back by the silica within the double electric layers, resulting in L polypeptides and the Destro 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 Levo 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 the Levo, separated from Destro 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 crustal regions that preserve ancient continental 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. 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
 
Le Scienze 1984
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 which in its short life only exists as Levo and may have accumulated on its surface the Levo amino acids in the prebiotic era.
If this were, the polymerized filaments discovered by Barghoorn could have been Levo 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, silica deposits mainly on the mainland and Levo 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 in "Polvere Vitale" in 1998 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 "L’evoluzione chimica e l’origine della vita" Le Scienze, Gli albori della vita 1984: "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, "Da dove viene la vita" 2000, 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. 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.
                                                                                         Giovanni Occhipinti

 Translated by: Sydney Isae Lukee