domenica 11 settembre 2011

THE ORIGIN OF LIFE: Myths and perspectives

Postn.2 (English)

The sedimentation of small granules of calcite and silicates, on colonies of microorganisms, gives origin to stratified structures called stromatolites. These structures can be found, today, in various regions of our planet, but the most extraordinary are to be found in Australia.
In a zone of Australia, called North Pole, also structures similar to stromatolites, dated 3,5 years ago, have been found. They are, probably, the most antique traces that life has left on our planet.

STROMATOLITE TODAY                                                       STROMATOLITE NORTH POLE

We know that our solar system originated 4,6 milliards of years ago, from the condensation of a cloud of gas and dust. Hence we have about 1 milliard of years empty between the formation of our planet and the appearance of the prokaryotes about 3,5 milliards of years ago. Our planet was at the beginning very hot and hammered by impacts of meteorites and asteroids. Its surface was fused.
When these phenomena started to decrease, after about half a milliard years, the earth rapidly cooled, water was able to condensate and give origin to the oceans. Then, approximately between 4 milliards of years ago and 3,5 milliards, the fundamental substances which gave origin to the first cells (prokaryotes), must have been formed.
The following is the task of prebiotic chemistry, that is, to discover how life could have originated from lifeless matter.
Prokaryotes, though simple, have nonetheless very complex cells. It is not possible that life had its origin directly from prokaryotes. Before the prokaryotes there surely existed organisms, called proto organisms, much more simple and elementary. But how simple?
All organisms are “machines” more or less complex, but none can do without 2 fundamental macromolecules: nucleic acids and proteins (enzymes). These 2 macromolecules are moreover interdependent in the sense that the nucleic acid (often identified as software)contains the program of how to synthesize the proteins. But nucleic acid needs proteins (hardware) to be synthesized. For this reason they are interdependent: one always needs the other.
The proto organism, although very simple had to contain both. Hence we must search for the fundamental molecules, that is the constituents, that gave origin to these macromolecules. These constituents are nucleotides for acid nucleic and amino acid for proteins.


NUCLEOTIDE                                                                                     AMINO ACID L

The first theory on the origin of life out of lifeless matter, dates from around 1930 resulting from the work of Oparin and Haldane, and it is known as: the theory of the prebiotic mixture. In particular Haldane imagines a primitive atmosphere without oxygen made up of H2, H2O, CO2 and presumably CH4, and NH3. From these substances, in the presence of external energy, the substances fundamental for the origin of life would have formed. Transported by rain and rivers, they would have united in a primitive ocean. This primitive ocean has functioned as a mixture of a cultivation for the following synthesis of macromolecules and at length for the appearance of the first living organisms.
In 1953 S. Miller, imitating a prebiotic ambiance, as suggested by Haldane’s theory using CH4, NH3, H2, H2O and as a source of energy electric charges, succeeded in synthesizing many organic substances and among these many amino acids some of which components of our proteins. This experiment seemed to be a confirmation of the Oparin-Haldane theory in its global aspect. Very soon however some obstacles against the theory of the prebiotic mixture resulted insurmountable.
1) Nucleotides, constituents of nucleic acids, are made up of Phosphate, Ribose and nucleobases. These substances have never been found in experiments of Miller’s sort and hence nucleic acids were absent in the prebiotic mixture.
2) The amino acids formed by a prebiotic way were surely chiral. Of these there exists a L (left) structure and its specular image D (right).
                                         Ala L                              Ala D

Now, in all living organisms, the amino acids which take part in the formation of proteins all have the L structure.

Ala L

The molecular disorder of the prebiotic mixture, with a great number of different organic substances, would have impeded the formation of polypeptides of amino acid L. This disorder would have produced crossed reactions between amino acids L and D and reactions with other compounds present in solution. How did the choice of the amino acids L come about and what happened to the D?
3) In Miller’s experiment about 60 different amino acids were found, but in living organisms the amino acids which form the proteins are 20. How did the choice come about in the prebiotic mixture?
4) The reaction between amino acids for the formation of the proteins and the most important macromolecules necessary to life occurs by the elimination of H2O.

In prebiotic condition, in ambiance with water this reaction is practically impossible.
5) The atmosphere did not contain oxygen and hence the shield of ozone was absent. Ultraviolet rays, much more numerous than the actual ones, attained the surface of the planet. In a primitive ocean these attained the depth of about 10 m, destroying any form of life. Diffusion and thermic agitation would, sooner or later, have carried all the substances in this zone and they would have been destroyed.
Prebiotic chemistry has not succeeded in resolving any of these problems, but for every one of these it has always found an answer ad hoc. And so after 60 years of research, we are still at Miller’s experiment.
Meanwhile the prebiotic mixture has become a myth: the first myth of the prebiotic mixture.
Many researchers, who accept the theory of the prebiotic mixture, hasten to point out that their view on the problem of the origin of life is essentially deterministic. But in the prebiotic mixture life could have had its origin only through a fortuitous event and highly improbable: a casual event. It would be more logical to speak of a “miracle”, because, starting from inorganic material, to synthesize complex biomolecules, a succession of steps are necessary which are not reproducible through a casual process. Case does not have memory and cannot give origin to congruent processes.
According to certain scientists, in a sufficiently long time, also events which seem miraculous become possible. And so also this time we have the ad hoc answer: long lengths of time. And so we give our confidence once again to case.
And case becomes: the second myth of prebiotic chemistry.
And as case can manifest itself only once, one concludes that all living organisms descend from a unique common progenitor.
The common progenitor has become: the third myth of prebiotic chemistry.
Prebiotic mixture, case and common progenitor are three myths of which we must free ourselves so as hot to remain for another long period of time with Miller’s experiment.
And yet a theory, different and more credible than that of the prebiotic mixture, existed already before Miller’s experiment. In 1951 J. D. Bernal suggested that the argil could have selected and protected, from ultraviolet rays, the substances fundamental for the origin of life. Afterwards the argil could have catalyzed the formation of the macromolecules necessary to life. The physical-chemical mechanism which sustained such processes was already known. Between 1890 and 1930 double electric strata generated by silica silicates and glass, were discovered and studied. They are all substances which present superficial electric forces. Such double electric strata are assimilable to capacitors and as such they are studied around 1915 by Helmholtz, Gouy and Stern. It is known that capacitors attract inside them, substances which have an elevated dielectric constant. Amino acids in solution give origin to dipolar ions with an elevated dielectric constant. A study of the interaction between double electric strata and amino acids has been effectuated at Magistri Cumacini, Como.
The experimental indications seem to confirm Bernal’s brilliant idea. Crystalline quartz is made up of helical structures whose constitute unities are tetrahedrons of SiO4. Such helical structures can develop in a right direction (D quartz) or in a left direction (L quartz) and give origin to crystals which are the mirror image one of the other.

When one of the forms is put into contact with a solution on the surface micro capacitors are generated, and hence electric fields, whose lines of force must be imagined with an helical form, that is like the hole of a screw oriented in a right or left direction

Simulation on computer; electric field near the surface of the quartz

Amino acids, which make up proteins, are substances with an elevated dielectric constant; they are chiral, that is each one of them presents itself under two forms, Right and Left, which are one the mirror image of the other, and they are not superimposable. Every atom or group of atoms, presents covalent polar links and hence is an electric dipole.

Because the asymmetric carbon atom has a spatial structure, the dipoles of the Right form and those of the Left form, being one the mirror image of the other, we must imagine them with a helical form, that is like a screw oriented to the Right or to the Left.
The experimental data on the interactions between diaphragms of quartz and amino acids, the discovery that silica gel rotates the plane of polarized light and probably presents a single helical structure directed on the left, these facts seem to confirm the role of firm land in the origin of life. These data indicate that probably silica gel maintained on firm land the amino acids L whereas the D was transported by water and rivers into the primitive ocean where it was destroyed.
On firm land, also, the choice of the natural amino was made.
The existence of a chemical-physical system of recognition and complementary nature between triplet of nucleobases and amino acid is possible. This could make clear both the interdependence between nucleic acid and proteins and a primitive mechanism of synthesis of the proteins. This type of direct recognition between triplet and amino acid could have functioned before the appearance of the actual mechanism, very elaborated, which includes the participation of tRNA, Ribosomes and enzymes.
The origin of life hence appears no longer a miraculous event, but a deterministic process, which does not leave any space for a unique progenitor common to all living organisms. As already said, double electric strata, have been observed in the presence of sand, argils and silicates in contact with solutions. In some of these the electric fields give lines of force parallel and equidistant. On the other hand the greater part of the molecules, necessary to the formation of the macromolecules fundamental to life, present covalent polar bonds, hence linear dipoles and dielectric constants which cannot be neglected. As Miller’s experiment has demonstrated, the primitive atmosphere must have been the site of synthesis of a great number of organic substances. The greater part of these would have been useless and an obstacle to the formation of the fundamental polymers. Order has the priority. It is necessary to think that a first step must have been the separation of the organic substances. It is hence possible to make the hypothesis that the double electric strata functioned as an electrochemical filter, selecting and accumulating on firm land, as in Bernal’s hypothesis, the substances necessary for the origin of life, whereas all the molecules not necessary were transported into the primitive ocean. And it is inside these double electric strata, the D and L once separated, and shielded from ultraviolet rays, according to the laws of nature, that life must have made its first steps.
Oceans and marshes were nothing else but containers of molecular residues where was reversed all that was not necessary to the formation of the macromolecules fundamental for the birth of life. The prebiotic mixture never existed (or else it was prebiotic porridge!). Hence life could not have had its origin in the sea and that because, as affirmed above, of the obstacles which are against the theory of the prebiotic mixture. On the other hand it is on firm land that life found the ambiance of its origin, many origins, all almost similar, because similar were the physical-chemical conditions.

                                                                      Giovanni Occhipinti

Translated by Silvia Occhipinti, 25.08 2012
To know more:
Prebiotic chemistry and origin of life
ISBN 978-88-488-1152-1


Nessun commento:

Posta un commento