martedì 6 dicembre 2011

THE PRIMORDIAL BROTH. The first myth: origin, expectations and failures.

Post n.3 (English)

But when does the theory of primordial broth (or prebiotic broth) begin?
Around 1870 in a letter to a friend Darwin wrote: «If ( and it is an if very big) we could imagine that in a small puddle hot, rich in ammonia, phosphorous salts, light, heat, electricity etc., a proteic compound was formed chemically, ready to pass through variations still more complex[…]». But Darwin’s official position was firm and clear: at the actual state of knowledge it is not possible (ultra vires) to formulate a theory on the origin of life.
In 1924 A. I. Oparin, who at the time was professor of biochemistry at the university of Moscow, translated this idea in a sort of scientific theory and published it in a book: The Origin of Life.

Ev1_03.jpg Aggregati molec. nel Brodo Prim.
According to Oparin, on our planet carbon was linked to metals under the form of saline carbides. These, when they come into contact with water vapour, react giving origin to hydrocarbons and, in successive reactions, to many other organic compounds. When the temperature on the surface of earth lowered to 100°C, water started to condense and all these compounds, contained in the atmosphere, were transported in a “primitive boiling ocean” where they started reacting, forming ever bigger molecules. The successive aggregation of these macromolecules would have given origin to particles of gel, “coacervate”. The organic coacervate would have absorbed and assimilated substances from the ambience and afterwards, dividing themselves, they would have given origin to primitive organisms some of which capable of creating metabolism. The evolution process and natural selection would have given origin, in the end, to all living organisms.
According to Mario Ageno (Lezioni di Biofisica 3, 1984) Enrico Fermi’s student and collaborator of Eduardo Amaldi, and an attentive and deep researcher in Biophysics: «The fundamental idea is certainly very brilliant and it does not lose its interest even today. This, however, must not make us forget that such a “theory” passes in silence all the great problems, all the greatest defiance that the idea of an origin of life from inorganic substances, through natural causes, affronts our mind».
But also Haldane, though expressing a brilliant idea, does not go any further.
In 1929 J. B. S. Haldane, without knowing the ideas of Oparin, publishes a brief article on the origin of life.
According to Haldane the primitive atmosphere did not contain oxygen but, probably, H2 (hydrogen) H2O (water), NH3 (ammonia) and CH4 (methane) as the atmosphere of Jupiter, Saturn and Uranus. More complex molecules would have been formed in the atmosphere as an effect of solar radiations. These organic compounds, transported by the rain, would have accumulated in the primitive ocean, where, by reaction, they would have formed complex molecules, giving origin to a “hot dilute broth” and here the first organisms would have had their origin. The hot dilute broth was immediately translated into “primordial broth”. When the metaphor is born, theory begins.

miller2.gif Schema dell'esp.di Miller

Around 1950 with H. Urey and S. Miller, an operative program of research starts. In particular, using a mixture of gas like that suggested by Haldane, S. Miller, adding energy (electric charges) succeeded in producing amino acids, which are part of proteins, and many other organic substances.
Haldane’s theory hence seemed to be confirmed: a primitive atmosphere without O2 (oxygen) and the formation, in the atmosphere, of substances fundamental for the origin of life and their accumulation in a “primordial broth”, where life would have had its origin. In this period is born pre-biological chemistry, which has the intent of individuating, over and above the amino acids already discovered, the formation of the molecules fundamental for the origin of life, and their synthesis in the ambiance similar to that of the earth at the period of the appearance of life.
The discovery created a great enthusiasm among scientists and it seemed that, very soon, they would have succeeded in unveiling the mystery of life. But the great problems, passed under silence by Oparin and Haldane in the theory of Primordial Broth, were insurmountable.
But what are, in the end, the great problems that the theory of prebiotic broth passes under silence?
In the last article “Origin of life : myths and perspectives”, these problems have been already described and illustrated. In this article I consider them again, eliminating the illustrations, but adding, in colour, some comments of noted scientists and the solutions, where they exist, that the theory of prebiotic broth proposes.
1) The first organisms could not do without two fundamental macromolecules: Proteins and Nucleic acids (perhaps the RNA). The nucleotides, which constitute the nucleic acids are made up of Phosphate, Ribose and Nucleobases. They have never been found in experiments like Miller’s, even if a few researchers try very hardly to make a few experiments credible.
In “Polvere vitale,1998” Christian De Duve affirms on the subject: «[…] chemists have had a certain success in the production of the five components of the RNA, but with a scarce rendering, and in conditions of time very different from a prebiotic scene, and different for every substance. If one wishes to combine the components in the right way, one is faced with other problems, of such size that no one has ever tried to do it in prebiotic context».
Hence nucleic acids were absent in the prebiotic broth.
2) As illustrated in the article “ The origin of life: myths and perspectives”, the molecules of amino acids of which proteins are made, exist under two forms, Right (D) and Left (L), and they are one the mirror image of the other. If amino acids are prepared in laboratory, for example Alanine, that which one obtains is 50% D Alanine and 50% L Alanine. Also the amino acids discovered by Miller in his now famous experiment were half Right and half Left, and as such also found in the meteorites. Hence in the prebiotic world, the amino acids must have been half D and half L.
The question is that the proteins of all living organisms are made up of amino acids L.
How was it possible? And what became of the Right?
Perhaps light fluctuations lightly favoured the amino acids L. But according to Dickerson (Le Scienze, Gli albori della vita, 1984): «[…]it is possible that at a certain period there was a primitive life, or the ancestors of it, based both on amino acids D and on amino acids L with a probability of 50%, and that, in the end, the amino acids L prevailed over the others».
It is already difficult to imagine the origin of one primitive life; to imagine two, one D and the other L is really hard.
3) The amino acids of which are constituted our proteins are only 20, but in Miller’s experiments, about 60 different amino acids were found. How did the choice come about, and why only 20 amino acids?
The explanation more often given is the most obvious: there were false departures that were extinguished, because they could not compete with the organisms which on the other hand survived.
4) The reaction between amino acids for the synthesis of proteins, all take part with the elimination of H2O. In a watery ambiance, that is the primordial broth, this reaction is practically impossible.
According to S. Fox, the proteins would have formed close to volcanic zones at a temperature of 200°C, and only afterwards they would have been transported by the rain into the broth, where would have been formed microspheres resistant to the destructive action of water. In alternative it has been imagined, that the primordial broth was in reality puddles of water near the ocean and subject to continual evaporation. It has also been thought to resolve the problem imagining secondary reactions between amino acids with compounds rich in energy, but these passages multiply enormously the number of reactions. To obtain a polymer of 40 amino acids hundreds of reactions would have been necessary, and this appears not very credible.
In fact the question is still open.
5) The primitive atmosphere certainly did not contain O2 (oxygen) and hence the shield of O3 (Ozone) was absent. The ultraviolet rays, in larger quantity than the actual ones, attained the surface of the earth. In a primitive ocean, these attained the depth of 10 meters. Diffusion, thermic agitation and currents would have in the end carried all the organic substances to this zone and they would have been destroyed.

bocche idrotermali.jpg

To resolve this problem, one imagines that the first organisms had their origin fixed to the bottom of not very deep lagoons no higher than 10 meters. For some researchers the problem does not exist, because life has had its origin in the deep of ocean bed near the hydrothermal sources.
Now, it is evident to all, that all the hypotheses, made to fill this void, are in reality modifications ad hoc, often even in contradiction one with the other and without any possibility of experimental verifying. In “Le radici della biologia” Mario Ageno writes «We can hence say that at the beginning of the ’80´s research on the origin of life was in a crisis».
In reality we can say that, since research has not even scratched the surface of these problems, the balance of theory on prebiotic broth is a fallimentary balance and so after the first 30 years we are still with Miller’s experiments.
But in 1983 a great discovery revitalizes against the theory of the prebiotic broth. Cech and Altman discover the “Ribozymes”. Nucleic acids and proteins (enzymes) are macromolecules fundamental for living organisms and without doubt, in a primitive organism, they could not be absent.
Now, whereas nucleic acids contain the genetic information for the construction of proteins, these last are necessary for the construction of the nucleic acids. Nucleic acids and proteins are in this way interdependent, the ones are necessary to the others. And that which in Biophysics is called “The problem of the egg and the hen”, which appeared first?
Thomas R. Cech and Albert Altman discovered that some types of RNA (Ribonucleic acid) are capable of behaving both as nucleic acids and as enzymes (that is they are egg and hen at the same time) and they have been called “ribozymes”. The “RNA world” was born, that is it was thought that life had its origin, in the Primordial Broth, through the synthesis of an RNA molecule reproducing itself, and that this molecule, evolving, had learned to synthesize the proteins.
Also the “RNA world” inspired much enthusiasm, but the big problems mentioned above were the object of silence once again, and so after about ten years, and in spite of contribution of many eminent researchers, the “RNA world” revealed itself, for the theory of prebiotic broth, another failure. Towards Christian De Duve synthesizes (Polvere Vitale 1995): «It is honest to say that a mechanism which can explain in a satisfactory way the prebiotic synthesis of RNA has not yet been found, in spite of considerable efforts made by some of the best chemists in the world. Even the most faithful partisans of the “RNA world” have expressed pessimistic opinions on the future perspectives of this line of research».
And hence what do we do?
One elaborates an ad hoc solution. Some scientists have already created it: before the RNA world perhaps there existed a “preRNA world”.
This continual search of ad hoc solutions only demonstrates that at the beginning of the new millennium the theory of Prebiotic Broth is in deep crisis.
Experimental research has shown, in conclusion, that in the prebiotic broth life could not have had its origin, and hence the prebiotic broth never existed.
And then today, on the origin of life, which is the theory most accredited? The theory of prebiotic broth.
Now, it is just to ask ourselves: how it is possible, after 90 years of its elaboration and after 60 years of experimental failures, one still insists on the theory of the prebiotic broth?
Across the years and up to our days, the prebiotic broth has passed from puddles to ocean, then to marshes and returning, with the help of volcanoes, to ocean. Then it passed anew to hot puddles evaporating, to return once again ocean but in the ocean beds near the hydrothermal sources, whereas in the “RNA world” it is impossible really to understand what this is all about (hydric basins).
John Horgan in one of his articles, (Le Scienze Quaderni n. 89) writes «None of these theories is credible enough to be considered a paradigm, but, on the other hand , none has been proved false, and this troubles Miller, a person famous for being a rigorous experimentalist, but also a fairly intransigent person». If Miller felt only disturbance, over and above the virtues mentioned above, he must have been a mild person; actually not very credible theories are elaborated and then one asks others to demonstrate that they are false.
But what science is this?
And Horgan continues «This way of proceeding, Miller protests, strengthens then the conviction that in the origin of life, only a marginal fringe of the scientific world is interested, as though it were a discipline unworthy of serious research».
From this affirmation one can only deduce, that there are no institutions who pay serious research and research over a certain time on the origin of life, and that which is published is only the fruit of a marginal research.
But what is intended by “marginal”?
In “Polvere Vitale” concerning the theories of origin of life, Christian De Duve affirms: «That which we have instead is a variety of theories, influenced by the scientific specialization, the philosophical attitude and the ideological propensity of their authors».
And it is like saying that a theory is elaborated when a researcher, at the margin of his research speciality, discovers an indication which links him to the problem of the origin of life. And so, the astrophysics think that life comes from space and they find aliens even on the Earth. The geneticists take as certain an “RNA world”, forgetting that it is only a hypothetic world. Those whose occupation is a metabolism, give the importance to the origin of proteins. Naturally, those who have discovered the hydrothermal sources affirm that life had its origin in the ocean beds. And all those who are disconcerted by the result of the research and the evolutionists, prefer speculating and dusting up the “magic” word: chance.
According to Paul Davies (Da dove viene la vita, 2000): «Many researchers have trouble in admitting in public that the origin of life is a mystery, even if in closed doors they confess their disconcertment. Such uncase seams to derive […] from the fear of opening the doors to religious fundamentalisms and the pseudo explanation given by “The god of the lagoons».
That the prebiotic broth is also considered, by some, as a sort of fortress to be defended?
And so between failures and fears the prebiotic broth has become a myth where the research on the origin of life is drowning.

                                                                                  Giovanni Occhipinti

Translated by Silvia Occhipinti: 08.09 2012
To know more:
Prebiotic chemistry and origin of life
ISBN 978-88-488-1152-1




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