CONTRIBUTIONS TO THE ORIGINS OF LIFE

JACQUES NINIO

( included in the web site http://www.lps.ens.fr/~ ninio )

TOPICS DISCUSSED HERE:

- Biographical notes

- Origin of the genetic code

- Evolution of transfer RNA structure

- Prebiotic replication

- Catalysis by peptides

- RNA catalysis

- Criticism of Eigen's work

- Criticism of chemical predestination

TOPICS NOT DISCUSSED HERE

- Evolution of the genetic code (see the forthcoming molecular evolution section)

- The sequence space (see the forthcoming molecular evolution section)

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BIOGRAPHICAL NOTES

For a long time, the origin of life appeared to me as a frontier in biology, the one to which I wished most to contribute. In this domain I had sound ideas and many advanced projects, but achieved little, in comparison to some other domains, being handicapped by my extremely poor understanding of chemistry. Yet, I made a number of valid publications, from which I have nothing to retract. In the theoretical domain, I published ideas on the origin of the genetic code, and on the evolution of transfer RNA structure [1,2]. Similiar idea have been published later under other signatures. Experimentally, I did work on prebiotic replication with oligonuecleotides instead of monomers [3], and work on RNA catalysis with nucleotide analogs [4]. I was well accepted in the origins of life scientific community, and knew personally most of the people who were doing important work in the 1970's and the 1980's.

I started to speculate on the origin of the code while doing my thesis on transfer RNA structure. As recounted in the section on RNA structure, I had, during the Christmas 1965 vacations, a wrong illumination about stereochemical complementarity between amino acids and anticodons. The main argument was that big amino acids (such as tryptophan and methionin) had non-degenerate codons, and small ones such glycine or alanine had fourfold degenerate codons. This was taken as an indication that the big ones could interact with three nucleotides simultaneously, while small ones could make contact with only two nucleotides. From this view of stereochemical relationships subtending the genetic code, I adhered to the idea of a reversibility in primitive translation, i.e., in the possibility of also translating from proteins to nucleic acids, in contradiction with the Central Dogma. These ideas were received with well-deserved skepticism. and Jacques Monod was seriously consdering putting an end to my fellowship. I met at that time Mirko Beljansky, who was studying what he thought to be non-ribosomal synthesis of peptides (it turned out to be a terminal acylation of viral RNA). In December 1966, there was a Meeting of the Biophysical Society in London, in which Francis Crick launched his ideas on the origin of the code (see the account in Nature, volume 212, page 1397). I was in the audience. According to Luisa Hirshbein's recollections, she did everything to dissuade me from taking part in the debate. Nevertheless, I did ask a question, after Crick's talk, possibly on what he thought of reverse translation, and I remember that he answered without aggressivity. On the previous day (I think), I had paid a visit to Pelc and Welton, in London, who had published in Nature, models of stereochemical interactions between amino acids and codons. So, I was sinking into marginality.

In May 1967, as recounted in other sections, I had an intuition about codon-anticodon recognition, and from this, about recogntion processes in general, which ultimately led to some of my most lasting contributions to molecular biology. At once, I abandonned most of my interest in stereochemical interactions between amino acids and nucleic acids. I maintained though a prejudice in favour of reverse translation, which is reflected in a sentence, Section 8, page 73 of the "missing triplet hypothesiss" [1]. After the publications of my ideas on codon-anticodon recognition, I had a period of very intense thinking on the genetic code and its origin. At that time, I completely abandoned my ideas on reverse translation. I had realized that the reverse of the peptide synthesis reaction was not reverse translation, but the hydrolysis of the terminal amino acid, coupled to a backward motion of the peptide chain ! I was in fact starting to think in terms of the kinetics of polypeptide synthesis on the ribosome.

Having rejected the "lock-and-key" very static imagery, I no longer thought it important to understand why a particular amino acid corresponded to a particular codon. The "dictionary" aspect of the code was played down, and I started thinking how the code came into being as a dynamical process. I had a theoretical idea about how non-coded petide synthesis could evolve into coded petide synthesis (see Section on the origin of the genetic code below). I put these ideas in a manuscript, which was submitted to the nascent "Journal of Molecular Evolution". It was rejected with unfair, insulting reports. Later, I incorporated my scheme in a review on codon-recognition [2], then in my book on molecular evolution [3]. There is nothing there, that I might wish to retract.

In the summer 1971, I had in my hands a preprint of Manfred Eigen's hoax "Self-organization of matter and the evolution of biological macromolecules". I studied it carefully, ad saw that it was scientifically vacuous. (See section below on the criticism of Eigen's work). In June 72, I gave a (critical) bibliographical seminar at the Pasteur Instiute on this work.

In October 71, I joined the laboratory of François Chapeville at Institut de Biologie Moléculaire, Jussieu, Paris, in which I attempted to initiate biochemical work on transfer RNA. I was also involved in writing the review on codon-anticodon recognition for "Progress in Nucleic Acid Research". I included there my ideas on the evolution of transfer RNA 3d structure. I do not know when exactly I got this idea. In any event, I consider that the idea is still valid [2, 3] (see section below on the evolution of tRNA 3d structure).

It is apparent, from my records, that I was following many threads at the same time. I was aware of the early results on prebiotic replication. In June 71, I attended a prestigious conference "From Theoretical Physics to Biology" in Versailles (see the section on RNA structure). There, I met Leslie Orgel, he invited me for a post-doctoral period at The Salk Institute, and I prepared myself for the event. In my report to the CNRS, I read this detail which I had forgotten: it was envisioned that I would work on the possibiliites of recognition of amino acids by oligonucleotides: which is the simplest nucleic acid structure capable of recognizing an amino acid? (i.e., tRNA ancestors).

I also devised an epistemological criterium for judging the validity of some proposals on the origin of life, which I called "l'axiome du choix permis" (the allowed choice axiom - see the section on "criticism of biochemical predestination").

Nevertheless, I was also interested in the non-enzymatic replication experiments. Most internucleotide linkages that were obtained at that time were of the 2'-5' type instead of the biological 3'-5' type or, even worse they were often of the 5'-5' type, which did not allow an extension of the chain beyond the dinucleotide level. I thought that the problem would be solved by using nucleotide oligomers as polymerizing units, instead of using nucleotide monomers. I wrote a little note, based upon model-building with space-filling components, explaining why in a universe of nucleic acids containg both RNAs with 2'-5' bonds, and RNAs with 3'-5' bonds, the latter should replicate more faithfully. The argument was astute, but with an unjustified hidden assumption. The reviewer pointed out this flaw, and I did not insist because, in any event I had the hope of settling the problem experimentally in the near future.

I also spent two months in Alan Michelson's laboratory , perhaps in 1972, during which I acquired some experience with oligonucleotides. In particular, I did experiments on oligomer condensation with carbodiimide.

In September 1972, I joined Orgel's laboratory at the Salk Institute in La Jolla (Southern California). I immigrated with my wife, two children, and a baby-sitter from Brittany. I came alone first,and was hosted by Daniel Blangy. Within a few days I got a car; A gorgeous 1951 pink Cadillac, acquired from Rolf Lohrmann at the symbollic price of 75 dollars, and I rented a superb house in Del Mar, with two levels, two bathrooms and a big terrace right on the beach. At high tide, the waves were breaking on the terrace. We were coming from France with low salaries, and this represented an almost unbelievable increase in living standards. Very luckily, it was the case that the currency exchange rate between French Francs and US dollars was at that time extremely favourable to the French Francs. I had also a modest complement from the Salk Institute. But essentially we were living on the French salaries.

This was an exceptional period in my life. In Orgel's laboratory, I was pursuing two lines of research in parallel. One was the prebiotic replication of nucleic acids, in which I linked oligomers instead of monomers (see section on prebiotic replication below). The other was all that turned around the accuracy of molecular processes. I worked very hard, experimentally on the first subject, and had daily discussions with Orgel on the second subject (see forthcoming section on the accuracy of molecular processes). By March 74, I had made several theoretical breakthroughs on accuracy, and had also nearly completed a massive work on prebiotic replication, which I completed during a subsequent period of two months at the Salk Institute (August 25th - October 25th, 1975). There was a pluridisciplinar library at the Salk Institute, and I gained there contact with many important books on disciplines outside molecular biology (d'Arcy Thompson, Karl von Frisch, Bela Julesz). I also had the occasion to meet many important people who visited the Salk, or just gave a seminar.

In November 73, Leslie Orgel organized an informal meeting with top scientists such as Richard Feynmann, Alexander Rich, Murray Goodman, Stanley Miller, Don Glaser, , etc. Manfred Eigen was also invited. Orgel wished to discuss the possibility of developping an advanced experimental strategy for in vitro selection of peptides with a given catalytic activity. There would be a combinatorial synthesis of peptides, and a mechanism to amplify the synthesis of the peptides having the desired catalytic activity. The meeting is mentioned in my book ([3], Princeton edition, page 88. I added:

"Half-way between the sifting method inspired by biochemistry and genetics which I propose, and the peptide-selection machine which Orgel envisaged, are various semi-selective methods. For example, a means of obtaining a peptide catalyst capable of acting on DNA would be to prepare a mixture of peptides, and filter them through a resin containing DNA which would retain peptides having affinity for it. After this selection, the peptides could be subjected to a sifting procedure to detect either destabilizing cutting peptides, or stabilizing ones. I consider that selective methods for producing peptides at will with a given activity will eventually be of more benefit in medical applications than the production of authentic enzymes by transplantation of genes".

Upon my return in France, in Chapeville's laboratory, I made several attempts to develop an experimental activity on the origins of life. My strategy, more modest than Orgel's was to prepare random peptide mixtures, and make a screening for the peptides having the highest catalytic activity (see section below on peptide catalysis). Françoise Bernardi started to work on this theme, had preliminary encouraging results, but we had difficulties identifying the most active peptides.

In March 1976, I wrote a letter to John Kendrew, then director of the European Molecular Biology Laboratory, in which I proposed to launch a team of about six individuals (three researchers, three technicians) on experimental molecular evolution. More specifically, I proposed the theme of the "search for peptides with catalytic activity by selective methods". Before consulting the Advisory Committee, Kendrew wrote "I had always had the impression that your own interests were primarily in doing theoretical work, and only secondarily in experimental work. Was I wrong ? And if we came to the conclusion that a group on the scale you suggest could not be fitted into the laboratory, would you also be interested in a smaller operation with a more theoretical slant, or even a completely theoretical one ?". To this, I answered in a two-pages letter, to which I would not change a line to-day. The project was not retained by the Advisory Committee. Kendrew wrote that "everybody thought it a most interesting and worthwhile one, and we had some comments from Francis Crick in the same direction". However, the committee doubted whether the proposed work "would interact much with the work of other groups already planned".

So, this line of work came to an end. I started many things, and in 1978, I found myself at the head of a small team named "biochimie de l'évolution". Two researchers were doing experimental work on DNA polymerase kinetics (see forthcoming section on the enzymology of DNA and RNA polymerases), a technician was doing computer work on the prediction of RNA secondary structures (see section on bio-informatics), and there was a young student, Philippe Marlière who had both an interest in bio-informatics, and an interest in the origins of life. He had a solid background in chemistry, and started a project of his own, on analogs of nucleic acids, with simpler backbones. Mots of the work was done in external laboratories, having better competence in chemistry. Marlière first constructed models of nucleic acids with a peptidic backbone. He saw that "some simple polymers to which nucleotide bases where hooked, could well form good helices when the repeating backbone unit contained an even number of atom links" (as reported in [3], Princeton edition, page 62). I do not remember precisely what he did after that (he moved to the Pasteur Institute).

I maintained a theoretical interest for the subject, which is reflected in my book, which I started to write in 1977 [3]. After the discovery of RNA catalysis in living cells, I considered making with RNA what I hat attempted to do with peptides: look for catalytic activities in randomly synthesized RNAs. I took in my group a laboratory technician to initiate the work (June 1982), and made, in this choice, on of the biggest mistakes in my scientific carreer. Although we had at that time, good competence in all the molecular biology techniques we needed, there was always something wrong in his experiments. Ultimately, I had the revelation that he was, probably, a drug addict. Fortunately, he left in October 84 for a laboratory on the Mediterranean coast. In the mean time he had not produced a single valid experiment.

In 1983, I think, Marie-Christine Maurel, then a college teacher, came to my laboratory, saying that she was very interested in the origins of life, and was prepared to all sacrifices to work on the subject. I asked her to acquire first some laboratory practice, and she spent two years preparing a diploma in Alain Favre's laboratory. Then she started working in my lab on catalysis by RNA molecules. We transposed to RNA the strategy which Françoise Bernardi had applied to peptides around 1975. Nothing worked as well as one of the controls -pure adenine. I then remembered a result by Orgel on "prebiotic adenosine", and worked out the implications. So, we published in 1987 one of the earliest papers ever published on artificial RNA catalysis (see section on RNA catalysis below). Subsequently, she worked mostly on her own. I considered that I did not have enough merit in her production to put my name on her articles.

In 1988 I became more and more involved in cognitive sciences, and at the end of 1991, I resigned from my position of leader of the "biochimie de l'évolution" group. I joined the physicists at Ecole Normale Supérieure. In 2000, I started writing an updated version of my book on evolution [3], and completed a first draft. On this occasion I sharpened a number of ideas, in the light of the last 20 years of progress, and these can be turned into publishable articles. But I have too many other projects running in parallel.

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ORIGIN OF THE GENETIC CODE

My ideas on the origin of the code emerged from a gedanken experiment of "evolutionary regression". I was wondering how a primitive bacterium, in which proteins were synthesized at a low accuracy level could escape from the error-catastrophe. I thought that part of the answer was in the possibility that primitive bacteria used much shorter proteins than they use to-day. From there, I started thinking about an evolutionary path from non-coded peptide synthesis to coded translation. Here is the theory, reproduced from [2], Princeton edition, page 86. I have rewritten here each sentence as a separate paragraph.

"I am supposing that we have primitive synthesis, catalysed by a crystal or whatever, of a defined dipeptide, for example methionine-tyrosine.

"Later, this synthesis becomes complicated by one step; a tripeptide is formed: methionine-tyrosine-valine, the bond between the second and third amino acids being facilitated by the presence of an oligonucleotide, let us say AGCG.

"There is no coding relationship, just a coupling between two events: binding of a cofactor AGCG and addition of valine to the dipeptide methionine-tyrosine.

"At a third stage a tetrapeptide methionine-tyrosine-valine-histidine, or the same with glutamine as the fourth amino acid, is synthesized.

"As for the tripeptide, synthesis would depend on the presence of an oligonucleotide, the nature of which would determine which of the two tetrapeptides were made.

"We still have no genetic code, but peptide synthesis with 'options' on the fourth position.

"We now see the distance which separates this synthesis from one using a code: the system with options has to become repetitive so that, from the fifth amino acid on for example, the same regular process is reiterated allowing the next amino acids to be put into place.

"Later, the regular iteration can be made to start right from the beginning of the chain.

"To sum up, what is fundamental in the genetic code, from my point of view, is not linear correspondence between a messenger RNA and a protein but the existence of an 'elongation cycle'; a reiterative process which causes the (n)th amino acid and the (n+1)th to be added on in exactly the same manner."

For reasons unknown to me, it seems that this hypothesis on the origin of genetic code has never been quoted, and not even plagiarized. Yet, I think that what I did, which was to de-emphasize the code as a linear correspondence, and reinterpret it as an iterative process is still worth serious consideration.

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THE EVOLUTION OF TRANSFER RNA 3d STRUCTURE.

Here again, I quote the two paragraphs in [3], Princeton edition, pages 86-87 in which the hypothesis is given (see also Figure 16, page 88 in [3], and Figure 5, page 326 in [2]).

"We can imagine a primitive tRNA made of two pieces; a short oligonucleotide to which an amino acid is attached non-specifically and a hairpin - that is, the end of a nucleic chain folded on itself and forming a loop in its middle:

(short figure provided, not reproduced here)

"We know that quite often a nucleic acid double helix can be associated with a supplementary filament which come to lie in the wide groove of the double helix, forming a three filament structure.

"The primitive tRNA would have been formed from the association of the hairpin with the oligomer carrying the amino acid, energy for the interaction being derived principally from formation of the triple helix between nucleic chains.

"The amino acid, attached to the oligomer, would come into contact with the loop, which would influence its position in space for various reasons (attractions due to opposite charges, repulsions, steric hindrance).

"This primitive tRNA, without an anticodon, combines a general principle of attraction without specificity (between nucleotide chains) with a principle of specific positioning not requiring attraction (interaction between the amino acid and the loop).

"From here, it was possible to conceive successive enlargements of the molecule, according to the order of events shown in Fig. 16."

The last sentence may appear very elliptical here, but there lies some of the strength of the proposal. The triple helix configuration is in fact at the core of tRNA 3d structure (the DiHU stem + the extra loop), a field in which I was particularly competent (see the Section on RNA structure). The model was developped before the elucidation of tRNA 3d structure, and it remains essentialy unchanged with the modern structure.

Similar proposals were made later by several other authors, in prestigious journals, without giving credit to my earlier work.

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PREBIOTIC REPLICATION

Soon after my arrival in Leslie Orgel's laboratory, it was decided that I would work on non-enzymatic replication of nucleic acids, by condensing oligonucleotides on a polymer matrix, instead of condensing monomers. The idea that oligonucleotide ligation was the primitive form of replication was natural to me. Prior to my work, most prebiotic replication experiments had been done with monomers, using homopolymeric templates (Poly(A), Poly(U), Poly(C)). Some success had been achieved in linking purine residues (GMP and AMP) opposite the complementary templates. However, the incorporation of pyrimidines was problematic. UMP could be incorporated, but in a triple helix configuration. I expected that U could be incorporated as part of an oligonucleotide, in a double helix configuration. There was also the problem that very little 3'-5' bonds were formed in the prebiotic replication experiments with monomers. I expected that if oligonucleotides were used instead of monomers, the geometric constraints at the site of condensation might be different, and might favour the 3'-5' bond.

Orgel was, on the other hand, mostly concerned with the search for the perfect condensing agent. At that time, he had developped with Rolf Lohrmann a strategy of derivatization of the nucleotide units, in which an imidazol group was hooked onto the 5' phosphate of the nucleotide, and they were studying a still more powerful derivatization, with methyl-imidazol. The preparation of these active monomers required a large number of horrifying procedures in organic chemistry, in which the compounds were dissolved in anhydrous organic solvents.

For my work on oligomer condensation, I needed to prepare a number of different oligomers and polymers, and I did it using some molecular biology techniques, such as enzyme purification and radioactive labelling of a terminal phosphorus. There was no expertise for this in the lab, except at the beginning, thanks to the presence of a German post-doc, Christoph Biebricher. I went through all the molecular biology preparations honorably (some of my oligomer preparations were even used, subsequently, by Hiroaki Sawai in the same lab). Then, I had to derivatize all the oligomers, using the established organic chemistry procedures. Then I had to combine oligomers and polymers, and study many condensation reactions. Then I had to analyze the products of the reactions. The work was a massive one, and on several occasions, I stayed in the lab until midnight. On the whole, the results were quite good, and in the direction of my expectations.

They are summarized as follows [4]:

"We have studied a number of condensation reactions involving ImpU, ImpT, ImpC, ImpA, ImpG, ImpUpG and ImpCpA as activated nucleotide donors and a variety of homo- and hetero-polynucleotides as templates. We did not obtain any evidence of a template effect with ImpU and ImpT, but observed some condensations of ImpC with GpG on appropriate templates. ImpA and ImpG take part in a number of more or less efficient template-directed reactions, as do ImpUpG and ImpCpA.

"Our results suggest that, on the primitive Earth, pyrimidine nucleotides could most easily have been incorporated into polymers as constituents of short oligomers, which contained one or more purine nucleotide. The linkage of the product depends strongly on the nature of the substrates; the percentage of the natural 3'-5' linkage was, in some cases, less than 10% and, in others, as high as 70%. Wobble-pairing was often very effective in promoting condensations, suggesting that transition mutations would have been very frequent in prebiotic polunucleotide replication".

I feel that this article stands very honourably in the line of Orgel's production. It was published in 1978, three years after the work was fully completed. It seems that Orgel felt very insecure with my results that showed, in many cases, a high proportion of 3'-5' linkages, but he became progressively convinced, from further experiments performed in his laboratory.

There is a printing mistake in this paper, which was made by the publisher after receiving the corrected proofs. In many cases, I had done experiments and controls in which the incubation times were identical. In [4], Table 1, page 96 all incubation durations of 32, 33 or 36 days are in fact durations of 2, 3 or 6 days respectively. I thought that Leslie would request a correction, but he did not, and I left things as they were, expecting that the readers would correct by themselves (which they did not).

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CATALYSIS BY PEPTIDES.

The project was described as follows in my 1974 report to the CNRS:

"Il s'agit (idéalement) de déterminer pour chaque niveau de complexité des peptides (ceux de longueur cinq; de longueur dix etc.) les activités catalytiques qui peuvent se manifester, en conjonction ou non avec des ions métalliques: quels facteurs d'augmentation de vitesse peuvent être obtenus, avec quelles spécifictés. Ceci, non pas par construction de peptides modèles, mais par des techniques sélectives, en recherchant une activité dans un mélange de peptides, de la même manière qu'on identifie et qu'on isole une activité enzymatique dans un extrait cellulaire brut. (---).

"Pratiquement, dans la première phase, exploratoire que nous avons entamée, les peptides sont obtenus par digestion de protéines de séquence connue et les activités catalytiques seront celles classiquement examinées dans l'étude des systèmes modèles".

The experimental work was performed entirely by Françoise Bernardi. After some unsuccessfull attempts with peptides generated by protein hydrolysis, the peptides were prepared from several separate amino acid mixtures. Each mixture was formed by random condensation of 2 or 3 different amino acids, chosen among the 20 canonical amino acids of the genetic code. The petide mixtures were spotted on chromatographic paper, and partially separated by paper chromatography. They were revealed, I think, by the ninhydrin reaction. The tested catalytic activity was the hydrolysis of para-nitrophenyl-acetate, a colourless reagent, well known in studies of artificial catalysis, which turned brown when it was hydrolyzed.

Very rapîdly, we saw that petide mixtures containg serine, histidine and methionine gave the best results. One of the fractions, eluted from paper chromtagraphy, was (slightly) more active, per mole of amino acid, than the most active model peptide studied so far. However, we were not able to purify this activity, or learn more about it. This type of difficulty was one of the main reasons for abandonning this line of work.

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RNA CATALYSIS

When it became clear, from the work of Tom Cech, Sidney Altman and co-workers that some RNA catalysts were used in living cells, I thought of transposing to RNA the strategy I had initiated with peptides.

Marie-Christine Maurel did all the experimental work. She used the same model-reaction (the hydrolysis of para-nitrophenyl acetate), and studied the catalytic activity, in this reaction, of ribosomal RNA or transfer RNA fragments. The results were negative. Then she used random polynucleotides of various nucleotide composition, and the results were again negative. As a matter of fact, the most active compound was the control, pure adenine! I then remembered a few things I had learnt in Orgel's laboratory, and put them together (i) imidazole is a powerful catalyst. It is the active principle in histidine, which is often found in the catalytic centres of proteins (ii) adenine is composed of a 5-membered and a six-membered ring. The 5-membered ring has the imidazole structure. (iii) in standard RNA structures, the imidazole activity of adenine is masked, because it is through the imidazole group that adenine is linked to ribose (iv) however, in prebiotic condensations of adenine with ribose, the ribose is hooked to the N6 of adenine, leaving the imidazole group free. From this, one could expect that the "prebiotic" adenosine (i.e., N6-ribosyl adenine) could be a good catalyst. It turned out to be half as good as histidine [5]. At the end of the note describing the work we wrote:

"It is difficult however to conceive a precise prebiotic replication of polymers containing four canonical nucelotides and, in addition, mofified nucleotides with good catalytic potential. One might envisage instead the existence of two classes of compounds. On one side, there would be regular nucleic acids, of the size of tRNA molecules, providing some kind of scaffold. On the other, there would be small oligonucleotides with a nucleotide catalyst at their end. The oligonucleotides would base-pair to the scaffold. If two or three such oligonucleotides become fixed, they might form the equivalent of the catalytic site of an enzyme". To-day I would be tempted to make an alternative suggestion: That there were replicable RNA sequences, catalytically inactive in their standard form, but active when, by mistake, some active nucleotide analog was incorporated at some specific position.

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CRITICISM OF EIGEN's WORK

Eigen has launched what looks like a theory of prebiotic replication of nucleic acids. It is in reality a work on the population genetics of bacteria: autonomous organisms which self-replicate accurately and occasionally mutate. The property he attributes to "RNA species" are just those of bacterial sub-populations. This work is, in my opinion, one of the biggest scientific mystifications of the twentieth century. What is tragic there, is that so many uninformed scientists have lost so much time refining Eigen's calculations, with the sincere belief that they would contribute to the origins of life. This is discussed in [5], Princeton ediiton, page 56, in which I wrote:

"Recently some physicists attempted a take-over bid of the study of evolution, assuming that, with their superior science of differential equations, they would be able to reveal the essential truths of the phenomena. What came out of this was the application of mathematical treatments to the simplest test case of population genetics: bacterial competition in the chemostat. Or rather, after having changed the words, these physicists described competition between DNA molecules in the prebiotic soup, attributing to the molecules the same reproductive properties as to bacteria".

See also [5], Princeton ediiton, pages 89-91, in relation to the origin of the code.

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CRITICISM OF CHEMICAL PREDESTINATION

In theories of the origins of life, one often encounters "why" questions of the kind: "why nucleic acids use the 4 canonical nucleotides" or "why the proteins use this set of 20 amino acids" or "why particular codons correspond to particular amino acids" ?

There are answers such as:

- the canonical nucleotides, or the canonical amino acids were those obtained most easily under prebiotic conditions

- the canonical nucleotides, or the canonical nucleotides are used because they are the best suited for their functions.

What I felt was that both answers could not be correct simultaneously, that it would be too much of a coincidence if the products generated most abundantly at one step in evolution were exactly the most suited products for the next step.

So, I thought one could use quantitative arguments to remove the "overdeterminacies" in the theories. I wrote an article on this, and sent it to François Jacob, with the hope he would submit it to PNAS. But he said that there would be problems with such philosophical articles. This line of thinking is somewhat reflected in [3], Princeton edition, bottom of page 77.

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MISCELLANEOUS

I wrote several reviews in which the evolution or the origin of the code was discussed ([6] _ [12]) and several book reviews on evolution or the origins of life [13].

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REFERENCES

MAIN ARTICLES

(1983) Genetic Takeover and the mineral origins of life (Cairns-Smith). FEBS Letters 154, 219-220.

(1983) Molecular theory of evolution (B.-O. Küppers). Biochimie 65 N° 8-9, XVII.

(1985) Seven clues to the origin of life (A.G. Cairns-Smith). Nature 318, 119-120.

(1987) The semantic theory of evolution (M. Barbieri). FEBS Letters 222, 220.

(1990) a vie plus têtue que les étoiles (F. Trémollières) Alliage 6, 115.

(1991) Une aurore de pierres. Aux origines de la vie (A. Danchin) Pour la Science 167. 106.

(1980) The origin of life. A warm little pond. (C.E. Folsome) FEBS Letters 112, 116-117.

(1980) The evolution of adaptation by natural selection. (J.M. Smith and R.E. Holliday, eds). FEBS Letters 120, 306.

(1981) The hypercycle. (M. Eigen and P. Schuster) Biochimie 63, N°6, pp. XXIV-XXV.

(1981) The origins of life and evolution. (H.O. Halvorson and K.E. van Holde, Eds). FEBS Letters 136, 186.

(1982) Evolution now. A century after Darwin (J.M. Smith, ed.) FEBS Letters 150, 263.

(1983) The physicochemical factors of biological evolution (S.E. Shnol). Biochimie 65 N°3, XI-XII.