sabato 7 aprile 2012

THE UNIVERSAL ANCESTOR: Origin and sunset of the third myth

Post n.6 (English)

All organisms living or extinct on our planet, according to the theory of the universal ancestor, descend from a single ancestral living organism. In English it is called the “Last universal common ancestor” (LUCA). This would explain also an undeniable truth: life is unitary. According to many researchers, there exists very forceful proofs which would confirm this theory and hence the unitariness of life, these concern both prebiotic Chemistry and in particular Genetics.
But what are these proofs?
For what concerns prebiotic chemistry the proofs are essentially three:
1)  The amino acids formed by the prebiotic way were surely chiral. Of these exists a structure L (Left) and its specular image D (Right).

                                               Ala L                      Ala D

Now, in all living organisms, the amino acids which contribute to the formation of proteins all have the structure L.
Chiral are also Ribose and Deoxiribose, fundamental compounds of nucleic acids; except that in these cases all living organisms use the D form.
2)  In Miller’sexperiment, about 60 different amino acids were found, but in all living organisms those which make up the proteins are only 20.
3)  At the beginning of the 60’s the genetic code is decoded. In particular, the mRNA, Ribonucleic acid, is made up of repetitive groups ribose-phosphate. Such groups bind themselves one to another for all the length of the molecule, forming the lateral skeleton of the mRNA. At every ribose is linked a nucleobase which can be: Adenine (A), Cytosine (C), Guanine (G), Uracil(U). The order in which these four nucleobases are disposed along the chain, gives the information for the synthesis of the proteins. In particular, each group of 3 nucleobases (triplet) codifies an amino acid and such correspondence is called: genetic code. It has been discovered that all living organisms use the same genetic code, this is hence universal.
But when is the idea of the universal ancestor born? And, further on, do researchers all have the same idea of the universal ancestor?
While concluding “The origin of the species”(VI edition) Charles Darwin writes: «And yet, if I base myself on the principle of natural selection with a differentiation of the characters, it does not seem incredible to me that, from some of these inferior and intermediate forms, both animals and plants could have developed; and if we admit that, we must also admit, similarly, that all the organisms that lived on earth could have descended from a single primitive form. But this deduction is essentially based on an analogy; hence it is not very important if it is or not accepted. It is surely possible, as G. H. Lewes affirms, that at the first beginning of life, many different forms evolved; but if it is thus, we can deduce that only very few have left behind them modified descendants».
Now it is evident that, although he conceded a certain opening, Darwin’s original idea was that life had its origin in a distant past, through a unique and spontaneous event.
Around 1930 appear, as the work of Oparin and Haldane, the first theories on the origin of life known as: theory of the prebiotic broth. Concerning the universal ancestor Mario Ageno (Lezioni di Biofisica 3, 1984) reports: «[…] Haldane thinks that all the actual organisms descend from a single ancestor. This because in all actual organisms, the greater part, not to say the whole, of the substances have asymmetric molecules and are hence optically active: of the two optical isomers, only one always the same, is present in all the organisms. There is no reason for which an organism that contains all the organic substances in the isomeric form in opposition to the ordinary one should not be perfect vital. It follows that if life had had many independent origins, organisms of this type, containing molecules specularly symmetric like the actual one, would be found in nature. Given that on the other hand they are not found, it is probable that life was created from inorganic matter only one time and that all the actual organisms all have one only unique ancestor».
In 1970 was published “Il caso e la necessità” by Jaques Monod. At that period the genetic code had been deciphered and it was also discovered that all living organisms use the same code for the assemblage of proteins. Without excluding other hypotheses Monod affirms: «Now thanks to the universality itself of its structures, from the code, the biosphere reveals itself as the product of a unique event […]. If this is really unique, as perhaps was the appearance of life itself, this depends on the fact that, before it manifested itself, its possibilities were almost none». Up to the beginning of the 80’s, it was a common belief that the choice of homochirality of the amino acid, and of the nature of the genetic code were simultaneous with the appearance of life. This would prove that life had its origin only once with the appearance of a first and single entity: the universal ancestor.
In the same years has its origin the theory of the “RNA World”. The theory, at the beginning, affirmed that life would have had its origin with the appearance of self-reproducing molecules which, through a process of evolution, would have given origin to the proteins and afterwards to the DNA. The theory concentrated above all on the origin of self-reproducing RNA molecules and put off for a second time the choice of the 20 amino acids and the origin of the genetic code. It could not though put off the problem of asymmetry, because the RNA contains the D Ribose. In the prebiotic world existed surely both D Ribose and L Ribose. When was this choice made? In such an ambience it is very difficult to imagine the formation of self-reproducing molecules of RNA containing only D Ribose. The opinion which has most credit is that the choice of the D Ribose was made by some physical agent or by chance, in the prebiotic phase, that is before the appearance of such macromolecules and hence, before the appearance of the universal ancestor. In other words, the choice of the molecular asymmetry is not simultaneous with the appearance of the LUCA. But then, it cannot be a demonstration that all living organisms derive from a single ancestral form; the LUCA could appear, not appear, or there could be more than one. However, the sustainers of this theory are convinced of the existence of the LUCA, but it is not understandable, through the “RNA World”, how and when its appearance happened.
And for what concerns genetics, what are the proofs of the universal ancestor?
 The DNA (deoxiribonucleic acid) is the molecule that contains genetic information.
 It is written in the DNA if an organism will be a human being, a tree, or a microorganism. It is made up of a phosphate group, a sugar deoxiribose and 4 nucleobases, as in the RNA, except that instead of uracil (U) it contains thymine (T) and it presents a double helix structure. In the DNA of all organisms, have been found tens of thousands of segments called genes. Every gene is made up of some hundreds of triplets of nucleobases. The genes of DNA are transcribed into RNA and translated into proteins. It is genes, or groups of genes, which establish the colour of the skin, the number of fingers in a hand, and so on. Every living organism always transmits its own genetic patrimony to its descendants and such a transmission is called vertical. Often in the descendants, the hereditary patrimony goes through mutations, that is a nucleobase is substituted by another nucleobase changing the sense of the triplet which now codifies for another amino acid. If such a substitution is neutral or if it gives to the new organism an advantage with respect to the other organisms, it is maintained and is transmitted to the descendant. If on the other hand the mutation is a disadvantage, it is probable that the organism dies and this evolution line extinguishes itself. The study of the disposition and of the number of nucleobases in the genes and of the amino acids in the proteins is called: DNA sequencing.
The comparative analysis then compares the DNA or the proteins of the various organisms and from this comparison one can go back to the universal ancestor. With the help of palaeontology one can often go back to the period in which this separation took place. Hence we know that man and chimpanzee have in common 99% of their DNA and that their ancestor must have lived about 5-6 millions of years ago; that Mammalia and reptiles had a common ancestor about 150 millions of years ago. In particular the genetic sequencing and that of the proteins, confirms at a molecular level Darwin’s theory of evolution. Because the genes transmit themselves from one organism to their own descendants establishing a tie of heredity, Darwin’s genealogical tree, which was concerned with superior organisms, can be extended back in time, also to microorganisms seeking for the common ancestor. It is a tree where all the branches converge into a trunk which hence represents the universal ancestor.
But what is meant here by universal ancestor?
In the debate on the thermophile as first organisms, Iris Fly (Origine della vita sulla terra, 2005) points out: «For this reason it is appropriate to underline that this conclusion is not referred to the first living organisms, but to the common ancestor of all the organisms which live today on the earth. This hypothetic organism – at the roots of the tree of evolution – must already have possessed a complex biochemical mechanism and it is believed that it was developed from the first living systems through a complex story of evolution». Hence: life has its origin and after  a long evolution process would have emerged a single organism which has given origin to all living organisms. But according to the preceding theories, the appearance of a unique ancestor and the origin of life coincided.
To resume, the ancestor of the first theories does not coincide with that of genetics and the sustainers of “RNA World” accept the LUCA but do not say how it originated.
But then, the universal ancestor is more a myth than a certitude.
However, on the beginning of the new millennium, the existence of a universal ancestor seems to be a confirmed theory, the problem seems to be resolved definitely: all living organisms or extinct organisms have had their origin from a unique universal ancestor and the phylogenetic tree is its representation.

To everyone his ancestor. All meet at the trunk of the tree being connected with Darwin’s original idea and the universal ancestor becomes the third myth.
But the universal ancestor did really exist?
Everything seemed fairly clear when, half way through the 90’s were discovered, in the world of bacteria and among mono cellular eukaryotes the lateral transmission also called horizontal transmission: genes do not transmit only from one organism to its descendants, but also from cells which do not present any link of hereditary type.
This discovery was a bomb: the genealogical tree, based on vertical transfers, that is on the descendance and the parental link, loses suddenly its trunk. If the genealogic tree is still valid for the superior organisms, when one descends to the bacterial level, the construction of a phylogenetic tree becomes very complicated and the concept of universal ancestor disappears. At a bacterial level, therefore, it is not always clear if a given gene belongs to the evolution line of such an organism, or if it has been transmitted by other bacteria belonging to different evolution lines. This renders confused the concept itself of LUCA as is admitted also by C. De Duve in his last book (Alle origine della vita, 2008) and continues: «C. R. Woese, one of the protagonists of this discovery affirms: “The ancestor cannot be identified as a single line of organisms. It was a common aggregation but very flexible of primitive cells which evolved as a unity, and which in the end attained a phase in which it broke into various distinct communities”».
In the same essay is published the figure of the genealogical tree by W. F. Doolittle, another protagonist of this discovery.

The trunk becomes a reticular structure, and even if many researchers do not yet accept this new vision, it has all the same given a hard blow to the theory of the universal ancestor. To sustain the universal ancestor would remain only the three problems not resolved of prebiotic chemistry and that is: molecular asymmetry, the choice of the 20 natural amino acids, and the nature of the genetic code.
According to the theory of Bernal, the argyles had a fundamental role in the origin of life. On the basis of this theory, a study on the interaction between the double electric strata and the amino acids has been carried out at the Magistri Cumacini at Como and published in “Prebiotic chemistry and the origin of life”. The experimental data on the interaction between diaphragms of quartz and amino acids, the discovery that colloidal silica rotates the plane of polarized light and probably presents a single left helicoidal structure, indicate that life had, probably, its origin on firm land. These data indicate that probably the colloidal silica kept on firm land the amino acids L whereas the D amino acids was transported by the waters and rivers into the primitive ocean where it was destroyed. On firm land the choice of the natural amino acids also took place. Probable is the existence of a direct physic-chemical system of recognition and complementarity between triplets of nucleobases and amino acids. This could clarify the interdependence between nucleic acid and proteins, and a primitive mechanism of synthesis of the proteins. These experimental indications postulate deterministic solutions to the three problems of prebiotic chemistry, and they suggest that life, on our planet, has had many origins, all almost the same, because the physic-chemical conditions were similar.
But if the universal ancestor disappears, what does the unity of life depend on.?
For that which concerns prebiotic chemistry, it was the physic-chemical conditions of our planet to create the bases of unity of life.
For what concerns its evolution, it is probable that as life had different origins, similar cells in a certain ambiance, gave origin to a population. In the different environments the various populations developed their own metabolic ways. The unity of life could hence depend on lateral transmission, that is on the genetic exchanges between microorganisms without parental link, because this has permitted and permits the sharing of metabolic processes. Without lateral transmission every organism would have continued to develop each one its own metabolic processes, life would not have been a unique process and it would have evolved with difficulty.
As a conclusion to this article, I would like to quote an extract of an article by James L. Van Etten on the place to be assigned to the virus on the tree of life, (Virus giganti ,Le Scienze, dicembre 2011): «Didier Roult of the Unité de Recherche Maladies Infecteuses et Tropical Emergentes from Marsiglia, entered with strength into the debate with a strong denial: “There does not exist a tree of life”. The actual organisms are chimeras ,”made up of sequence of different origin which render obsolete the theory of the tree of life”. The tree imagined by Darwin is pertinent in the genomic era only if it is constructed gene by gene, to be used to deduce the evolutive story of the gene, not of the form of life».
We do not know what will be the effect of this strong denial on the tree of life. But we know that on its trunk, the myth of the universal ancestor goes towards its sunset, dragging with it the other two myths, that is the paradigm which for almost a century has dominated the origin of life.
                                                                                                             Giovanni Occhipinti

 Translated by Silvia Occhipinti: 28.11 2012
To know more:
Prebiotic chemistry and origin of life
ISBN  978-88-488-1152-1


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