sabato 4 febbraio 2012

ORIGIN OF LIFE: Chance, the second mith.

Post n.4 (English)
From ancient time and until 1800, man believed in spontaneous generation. That is it was thought that life originated itself spontaneously from unliving matter. Preferred places for spontaneous generation were, in particular, mud and organic matter in putrefaction. It was the research of Francesco Redi and of Lazzaro Spallanzani which introduced doubt regarding this belief. Louis Pasteur gave the last blow by demonstrating experimentally, around 1860, that in the actual physic-chemical conditions of our planet life can generate only from life.
If we exclude spontaneous generation, how did life have its origin on our planet?
For more than half a century, after Pasteur, there was not much interest in the problem of the origin of life. The first theory on the origin of life from unanimated matter, as largely illustrated in preceding articles, it can be dated around 1930 as the work of Oparin and Haldane, and it is known as: the theory of the prebiotic broth. In it one hypotheses the formation of substances fundamental for the origin of life in the atmosphere and their gathering in a primitive ocean, primordial or prebiotic broth, where would have formed more complex molecules and from these in the end life would have had its origin.
The now famous experiment by Miller, seemed to be a confirmation of the theory Oparin-Haldane on the whole and hence also of the prebiotic broth which, also today, remains the most accredited theory. Unfortunately, after sixty years, in spite of the contribution of many researchers, the theory of the prebiotic broth has a failing balance.
But if research has given a negative conclusion, how could life have had its origin in the prebiotic broth?
After having analysed if the first to appear were the proteins or the nucleic acids, Paul Davies (Da dove viene la vita, 2000) writes: «All the theories have in common the same idea: once that life had been born in whatever form, the rest came almost by itself, because Darwin’s evolution has been able to make its way. Hence it is natural that scientists try to appeal to Darwinism starting from the very first phase of the history of life: with his entry into the scene enormous progress is possible sustained only by the driving force of chance and selection. Unfortunately, though, so that Darwin’s evolution can begin, it is necessary to have a minimum level of complexity. How was this initial complexity attained? Put against the wall, the greater part of scientists wrings their hands and murmur the magic word: chance».
The word “chance” has however different meanings and it contains for this reason a trap, which we shall clear further. In the context of the origin of life, the meanings which are given to the word chance are essentially two.
1  ) Chance as an event fortuitous highly improbable, almost a miracle; it can happen or not happen and if it happens it will be unique in its species. Let us imagine a person who, stressed by work, decides to go on holidays and buys the last ticket available for an island of the Caribbean. Here, compelled by the waves to promenade at distance from the shore, he goes down in a hole and finds a treasure bidden by pirates. It has a chance of the sort ever happened? It can happen or not happen but if it happens it will be a fortuitous event, with the same characteristics it will never happen again.
2)  The second meaning is a question of probability, hence mathematical, early or late it will happen and also more than once. It is sufficient to remember that the probability to win the pools for one single player is very small, but if the players are millions, almost every week there will be at least one winner.
But when was born this idea of chance? And then life could really have had its origin by chance?
To introduce the concept of casuality in the origin of life, seems to have been Leonard Thompson Troland, American physicist and psycho physiologist, as Iris Fly reports in her essay (The origin of life on the earth, 2002): «It was thought that the gene formed itself in an improvised manner a consequence of a “first event” fortuitous , highly improbable. Troland attended to this situation, affirming that in the great extension of time during which life could have emerged even a highly improbable event could have become possible. All that was requested was a reproduction of one single molecule self-catalytic. (Troland, 1914, 105), A fortunate collision of molecules or a “fortunate chance”, to take the expression often used in what follows». Also Haldane thought that life had a casual origin, but with a different approach. In “Origin of life (Bernal, Haldane, Pirie, Pringle) he affirms: «I have been reproved for having introduced “chance”. By “chance” we intend the partial impossibility to predict an event.[…] on principle the larger part of processes are not unforeseeable, however it is not possible to predict some particular phenomena without affirming that, a particular event, has a certain probability of realizing itself in a definite time».
From 1953, the years of Miller’s experiment, until 1970 were years of intense research and strong enthusiasm, the chance was almost forgotten. But with the failure of the experimental research on the prebiotic broth, the chance revives like a Phoenix.
It was principally J. Monod ( The chance and necessity) not only to reintroduce the chance in the origin of life, but also to make it a philosophy of existence. According to Monod the origin of life in the earth was a unique and unrepeatable event .«The universe was not going to give birth to life, and neither the biosphere would give birth to man. Our number comes out on the roulette: why then should we not perceive the exceptional nature of our condition […]».
Criticism and consensus of this vision are not lacking. In 1980, the origin of life as a fortuitous event was definitely archived by the English astronomer Fred Hoyle, with a metaphor now become classic: «"[…] The spontaneous appearance of an unicellular organism from a casual combination of chemical compounds, is just as probable as the creation of a Boeing 707 as the result of a tornado which crosses a pile of useless metal[…]». Even if there is who attempts again a solution ad hoc : given a sufficient long time, even events that seem miraculous become possible; but no-one believes any more in an event unique and unrepeatable.
Yet the probabilistic sense of the word “chance” remain.
Between 1950 and 1980, after the discovery of the structure of DNA by Crick and Watson, the complexity of living systems was understood. The DNA has formed by tens of thousands of genes and every one of these codifies for a protein. What is then the probability that, in the prebiotic era at least, one protein or a gene of biological relevance has formed? In the actual organisms, a protein (enzyme) is made up  of about 300 residues different from the 20 aminoacids. Since every amino acid is codified by a triplet of bases (three nucleotides), the gene which corresponds will be made up of 900 nucleotides. With these data the number of proteins possible corresponds to 20300, and the number of corresponding genes 4900, which translated respectively 10390 and 10540. With these numbers the probability, in the prebiotic era, of the formation of important macromolecules of biological interest, is zero. Even if we reduce the genes, in the prebiotic era, to 300 nucleotides, the number of genes possible still results enormous: 10180. Someone proposed to reduce the number of nucleotides to 75; the number of genes would then be 1044, a number still too great. In the end, these simple calculations are enough to demonstrate that the probability that in the prebiotic broth,  proteins or functional genes had their origin, is practically inexistent. We are now in the position to abolish the trap of the word “chance” and we do it with the words of Mario Ageno, (Le radici della biologia, 1986): «Event of little or very little probability, practically realize a continual passage from the second to the first category». Hence, when the probability of an event is very little, a probabilistic event becomes thus too fortuitous, almost a miracle. In fact, who still insists with the calculation of probability to justify the casual origin of life, only imagines constructing a Boeing with a tornado.
Around 1980 the theory of the “RNA World” begins, that is it was thought that life had its origin through the synthesis of an RNA molecule reproducing itself and this, evolving, had learnt to synthesize proteins.
Manfred Eigen is a sustainer of the RNA World, he excludes chance: «The genic patrimony that today one meets in living organisms could not have produced itself by chance as though throwing dice». (Gradini verso la vita, 1992), and he explains how this process could have made the first steps towards the origin of life. He goes from the idea that in the prebiotic world must have existed an ambiance in which were present a population of at least 1010 auto reproducing molecules of nucleic acid  also of small dimension, (100-300 nucleotides). These, through reproducing also in the presence of rudimental enzymes, have participated in a process of functional optimization, of selection, to the point of attaining dimensions such as to give origin to functional proteins. To sustain his ideas, Eigen develops a mathematical simulation of a process auto-catalytic (hypercycle).
But how were the first molecules capable of reproducing themselves have their origin?
Eigen tries to give an answer of a deterministic type: in the prebiotic world must have existed amino acids, ribose and deoxiribose, nucleobases. For the origin of amino acid, he indicates Miller’s experiment, whereas for the origin of the other compounds, he gives vague answers and insufficient, quoting also experiments in ambiance without water. For the molecular asymmetry, which one meets in all organisms, he does not give satisfactory answers if not to recall phenomena which have already been confirmed as without influence. He imagines, furthermore, that in the prebiotic broth would be present polypeptides of the type proteinoid of Fox with weak catalytic abilities and also stereospecific (hence privileging the dominion of chemical laws). Some of these must have been capable to synthesize molecules of RNA, even though, as they are rudimentary catalysts, the time requested for such synthesis must have been long. In the end the Ribozymes could have given a contribution of their own.
As already mentioned in preceding articles, also in the RNA World, all the big problems of prebiotic chemistry are left in silence.
And so one can only conclude that on the origin of life nothing is known. Chance though is not involved, or is it?
At the conclusion of the chapter were she treats the RNA World, (work already quoted) Iris Fly affirms: «In conclusion, more general comment is opportune. Traditionally the genetic conception was associated with the assumption that the synthesis, highly improbable, of a single sequence reproducing itself was sufficient to the origin of life. […] The role assigned to the contingent events in the actual scenes of the “RNA World” is still considerable. Kavanarioti for example speaks of processes of diversification, active inside the populations of the first catalysts which would have led “not by selection but by chance” to the emergence of better catalysts».
But what type of chance? One wants to simulate a throwing of dice, waiting in reality for a tornado?
Who made the effort of giving a more detailed explanation to the appearance of the first molecules reproducing itself is C. De Duve in a new essay (Alle origini della vita, 2008). The structure of the essay is very interesting. He discerns above all 7 peculiarities, but those which interest us are principally the 1st “deterministic necessity”: «According to these interpretations, things could not have gone differently, seeing the chemical-physical conditions which existed». And the 5th “frozen change”: «Here the singleness is given by the decision imposed by pure chance between two or more possibilities which are not the same any more once one has taken a decision, and has hence taken a way without return». Going from some of the actual knowledge on the biochemistry of life and analysing the data given by prebiotic chemistry, Christian De Duve tries a strong conjectural effort in the tentative to give a deterministic answer to the appearance of an RNA World, and afterwards to the origin of life.
He considers plausible, like Eigen, the presence, in the prebiotic broth, of sugars, nucleobases, phosphate and he poses the problem of the synthesis of the nucleotides: «These facts suggest the existence of an ancient cauldron in which sugar interacted with pyrophosphoric compounds and with nucleobases to produce a variety of the sugar-phosphate, nucleosides and derivatives more complex, among which the ATP and its homologous. The substances which ended making an important metabolic function, in particular for the synthesis of RNA, emerged for this mixture by selection, as I have already suggested. The identification of the conditions in which these reactions could have taken place with only the help of catalysts (multimers) at hand in the prebiotic era, pose one of the problem most difficult for future researches».
The problem of the separation of the functional nucleotides presents itself immediately: «The mixture could have contained other bases with appropriately complementary structures. If things were really so, was chance responsible for their refusal, or also a bidden factor? According to a recent theoretical study, the choice of the nucleobases could not have been purely accidental, but it could have been the result of a process of selection, influenced by the resistance to error».
And for Ribose: «The choice of ribose poses similar questions. The choice of this sugar rather than the others was fortuitous or due to some molecular property which advantaged the molecules containing ribose with respect to the others?».
And on the chirality: «The choice of chirality could have been as we have seen, the consequence of a frozen accident or, alternatively, of some physical tendency».
And on the synthesis of RNA: «If we think attentively on the problem, the possibility that the RNA is the product of a fortuitous chance, gifted with the capacity of reproducing itself can be refused because it poses requests absolutely implausible to chance, at the same time suffocating the research. Unless one wants to invoke the similarly suffocating hypothesis of the intelligent design, we have to resort to the opinion that the prebiotic conditions were such as to advantage the synthesis of the reproduction of the RNA molecules through simple chemical processes. At first sight, however, also this hypothesis seems to impose a too great effort on credibility».
Unfortunately, of these simple chemical processes there is no trace and that which remains is, in the end, only the effort on our credibility.
And hence one can only conclude that on the origin of life nothing is known. Chance though is not relevant, or perhaps it is?
The larger part of scientists is conscious that life could not have had its origin by chance, but its place has been taken by ideas most hypothetic, often not very credible, impossible to verify experimentally and also with too many frozen accidents.
But what remain? Or the intelligent design or chance.
Well, what now? Better pull up the blanket and cover oneself under the theory of Darwin.
And so chance, like the Phoenix, becomes a myth, for many scientists another fortress against the fundamentalism, and all are waiting for a tornado which can construct a Boeing.
                                                                                      Giovanni Occhipinti

Translated by Silvia Occhipinti: 20.09 2012
To know more:
Prebiotic chemistry and origin of life
ISBN  978-88-488-1152-1

Nessun commento:

Posta un commento