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Infos / Organisation Meeting |
 French Version
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Reférences Bibliographiques / References |
Infos Séquençages / Sequencing info |
Contact Participants / Reach Attendies |
Crédits / Credits |
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For the first
time, scientists coming from different perspectives have gathered
themselves together to reflect on the nature of the last common ancestor
of all beings living today. The Treille Foundation has enabled the
organization of a colloquium on this theme going beyond the usual
framework for scientific conferences. While numerous participants
presented several papers, some among them improvised. Very quickly, the
atmosphere of conviviality appropriate to "Les Treilles" gave rise among
all the members of our little group (many of whom had never met before) a
sentiment of belonging to one community, at the dawn of a new scientific
adventure. Within a field (the first step of life on earth) where the
confrontation of ideas (and now and then of personalities) could be
enlivened, the luminous atmosphere of Provence permitted the discussion of
even the more contradictory hypotheses in complete serenity.
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The first
objective of the colloquium was to assemble the researchers
appearing to come from different scientific 'tribes'. Each tribe has its
own rites, in particular the large conferences organized at regular
intervals, its journals of predilection and of great reputation. The
members of these different clans rarely mix , and only some of the more
audacious sometimes are accepted in two or three different tribes. At "Les
Treilles", at least five from among these were represented: those
researchers obsessed by the problem of the origin of life, the
large international meeting on which will be held at Orleans, that of
the archaeo-microbiologists, specialists of the third group of living
beings on earth, the archaebacteria or archea, that of the
'thermophilists' , who study microbial life at very high temperature ( up
to 110 °C) , that of the molecular evolutionists, who try to retrieve the
genealogy of all living beings (the universal tree) by comparing the
sequences of their macromolecules, and finally the genomicists, a new
tribe in formation, the aim of which is the exhaustive analysis of
genomes, rendered possible thanks to large programs of systematic
sequencing of DNA.
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Some
participants appear in none of the tribes mentioned, they have been chosen
by reason of their competence recognized in a domain the importance of
which appears crucial to confront the problem of the last common ancestor.
Some were confronted for the first time with the great questions posed by
the evolution of life, and they were not any less enthusiastic.
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Most of the researchers present were experimentalists, they
have behind them a long tradition of prudence, rigor, going sometime to
the point of opposition to all too speculative ideas. In particular,
reductionism of molecular biology and the division which has been created
since fifty years ago between the 'pure and hard' biochemists and the
evolutionists are major obstacles in a field where the imagination plays a
determining role. From this point of view, Christian
De Duve had played an irreplaceable role in the course of these
days. A Nobel prize winner, doyen of our colloquium, and recognized for
his work in cell biology, he has proved to have a fertile imagination,
playing a particularly active role in our discussions. Our hopes are that
the seminar at Treilles will be the foundation of a new theme of wholly
separate research: research on LUCA (the Last
Universal Common Ancestor)
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LUCA was baptised at Treilles, yet we don't
know if this name imposed itself, but it was not unanimous between us.
Other terms have been proposed over the years: the name progenote, put forward in 1977 by Carl Woese (the creator of the concept of
archaebacteria) had its hour of glory, but it seems on the decline. The
notion of 'progenote' is in effect associated with the conception of a
particularly primitive ancestor, much more simple than actual cells, but
which does not correspond any more with the thought of many specialists.
The majority vision today is more that of a common ancestor resembling
either bacteria or archaea, and for some , that of a creature intermediate
between prokaryotes (cells without nuclei) and eukaryotes (cells with
nuclei).
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The term
cenancestor (from the Greek root cen. together) proposed
by Fitch in 1987, has the favour of
purists. For others, it presents the inconvenience of being
incomprehensible to ordinary mortals, and even to the ordinary among
biologists. The appelation 'Last Common Ancestor' is more and more used in
the literature. José Castresana, remarked
during our seminar that it is also too vague. The term 'last common
ancestor' could be used (and is in effect) for all groups of organisms.
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LUCA is a
compromise between LCA and LUA (last universal ancestor) proposed at this
colloquium by Christos Ouzounis. It could be
popular with the media, since 'from LUCA to
LUCY' encapsulates or replays the trajectory of the evolution of life. It
defines a sympathetic entity, one which seeded our planet- we are all its
descendants.s
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Why focus
our attention on this key personage in our history? Why a colloquium on
this theme today? For a long while research on the origins of life has
been uniquely devoted to understanding how the first molecules of life
appeared on our planet. Once they were present, the consequences went of
themselves( the rest followed). There was no place for LUCA in these researches. On the other hand, the
cellular and molecular biologists (with rare exceptions) did not want to
waste their time (very precious time) speculating on the ancient
unknowable, when the inexhaustible richness of model studies offered
themselves to them, those more real (in the form of proteins and nucleic
acids).
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The situation
has much changed today, precisely thanks to the progress of
molecular biology. One has become aware , in comparing the molecules of
life of all organisms (from bacteria to humans) that they display common
points, a fossilized record of their ancestral background. These are the
researches which have been conducive to the discovery of the presence on
earth of a group of prokaryotes, the archaea, as distant from the bacteria
as from the eukaryotes.
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In
comparing the fundamental mechanisms of life in the three Domains
(bacteria, archaea, and eukaryotes) it then becomes possible to define "
the smallest common denominator of the three": LUCA.
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There
remains a division between the biologists loving evolution, who
also reconcile themselves with first origins in going back to the past,
and the pioneers of researches on the origins of life, who try since the
founder experiment of Stanley
Miller in 1953 to start from point zero (the primitive soup or dawn
of stone) to advance towards the present. The time has come to gather
together all the tribes.
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Some questions debated at "Les Treilles"
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Is it possible to draw up an 'Identikit'
portrait of LUCA ?
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The
comparison of genes present in the three domains of life is one of
the favoured approaches for achieving knowledge of LUCA. This necessitates as a preliminary step the
complete inventory of genes present in each domain. This work will benefit
from the large number of genomes which will be completely sequenced in the
years to come. A certain number of these have already been completed. The
colloquium at Treillles is being held within three months after the
publication of the complete sequence of the genome of the yeast of the
bakery (baker's yeast) , Saccharomyces cerevisiae, and one month before
the publication in Science of the first genome of an archaea, Methanococcus
jannaschii. Odile Ozier-Kalogeropoulos
has therefore presented the results obtained with the complete analysis of
S. cerevisiae, while Nikos Kyrpides gave us a
hint in advance of those obtained in analysing the genome of
Methanococcus jannaschii.
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Christos Ouzounis
and Nikos Kyrpides have presented a first
preliminary work comparing between genomes for organisms belonging to all
three domains. This work should open on the inventory of proteins common
to the three domains, that is to say present similarities of sequence
which one could reasonably suppose to all be derived from the same common
ancestor (In technical terms, these proteins are said to be homologs).
These homologous proteins have a strong chance of having been present in
the LUCA.
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Right
now, the first results suggest a degree of complexity unexpected in
LUCA. That organism would without doubt have
already possessed many thousands of genes (and therefore of different
proteins). It seems that all the large systems which permit the
maintenance and expression of genetic material were already present, as
were also many metabolic capacities. José
Castresana contributed solid arguments to advance the iconoclastic
idea according to which the molecular mechanisms of oxygen respiration
were already present in LUCA, despite an
environment apparently impoverished in oxygen! Was oxygen already present
on our planet in localized niches, or alternatively did the mechanisms of
oxidative respiration have another function in the epoch of LUCA ?
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One
question which is more general remains to be posed: is the presence
of the same gene in the three domains at the present day always synonymous
with the presence in LUCA ? Was the transfer of
genes which distributed or could distribute throughout the living world an
invention which only appeared more lately in one of the three domains? In
particular, Jim Brown and Hervé Philippe have shown that many protein
phylogenies suggest the transfer of a very large number of genes
implicated in the metabolism of bacteria to the eukaryotes, without doubt
by the intermediation of mitochondria, cellular organelles which have
evoloved in the eukaryote cells starting from ancient endosymbiotic
bacteria.
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Communion around LUCA
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To understand the origin and
evolution of real genomes with the object of going back in time, it is
equally necessary to understand the mechanisms of their recent evolution.
The comparative analysis of genomes of organisms relative to the
evolutionary plan is very instructive from this point of view. Odile Ozier-Kalogeropoulos
has also compared a part of the genome of the yeast Kluyveromyces lactis
with that of S. cerevisiae, while Renaud de
Rosa has compared the genome of two bacteria, the coccibacillus
Escherichia coli , of which more than 60% of the sequence is known, and
the pathogen Haemophilus influenzae, of which the sequence has been
completely determined in the last year. These works put forward evidence
for very important differences in the rate of evolution of one gene
compared to another (and thus of one protein to another) , of phenomena of
rapid and massive loss (relative to evolution) of certain genes, and
finally a large number of proteins called paralogs, that is to say having
diverged by duplication since the time of a common ancestral gene.
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The rapid
evolution of the sequence of certain proteins renders difficult to
determine evidence in support of their relationship to one domain or to
another. This could be in part explained by the presence in the genomes
completely sequenced of many genes coding for proteins which have no
detectable homologs in the other two domains. In certain cases, it is
possible to find evidence for resemblance of one domain to the other at
the level of 3-dimensional protein structure. Chris
Sanders has presented a work of structural analysis which announces
the putting in place of a systematic strategy for identifying the very
large number of genes and functions possible in entire genome sequences.
The number of genes possessing homologs in the three domains (thus likely
to be present already in LUCA ) will also
become augmented in years to come.
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What root for the universal
tree
What can be made of genes which are present only in two
domains? Were they already present in LUCA and
in this case, have they been later (eventually) lost only in one of the
three domains, or have they really appeared in one branch common to the
two domains? the problem is complex; in effect certain genes are present
only in Bacteria or Archaebacteria, others in archaebacteria and
eukaryotes, others again in Bacteria and the eukaryotes.
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S. Miller & C. de Duve
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If one puts
aside the problem of sampling, it will be a priori easier to answer
the question posed if one knows the placement of the root of the universal
tree which connects the three Domains (between them). That is a question
which is very controversial. Many authors actually situate this root in
the Bacterial branch (the eukaryotes and archaebacteria are in this case
brother groups). Jim Brown has presented some
results along this line, based on some universal trees founded on proteins
having diverged since the time of duplication before the separation of the
three domains.
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Location of LUCA and Hyperthermophiles
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This result could explain the presence of numerous characters
of the "eukaryote" type within the archaea, as well as protein phylogenies
which associate archaea and eukaryotes. It exists along with other
phylogenies associating Archaea and Bacteria. Jim
Brown interprets those in terms of the transfer of genes from one
Domain to the other.
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The
validity of these results is however contested
by Patrick Forterre and Hervé Philippe, on the basis of studies on the
variability of the evolution of different positions of amino acids in the
same protein. According to them, there no longer remains exploitable
information permitting the rooting of trees based on sequences having
diverged so long ago. For Hervé Philippe,
aberrant trees between proteins of three domains (for example those which
do not permit finding division into three of the living world) are the
norm, and it is the "coherent" trees which demand to be explained. He
suggests that the appearance of "monophyletic" groups in a molecular tree
indicates an important switch in the structure/function of the molecule
studied.
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It is important to
note that the position of the root of the universal tree in the bacterial
branch favors the idea by which LUCA resembles
actual prokaryotes. Nevertheless, as long as the position of the root is
not known with certainty, the question remains open. In particular , if
the root is situated in the branch of the eukaryotes, LUCA could in fact resemble a cell of this type!
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The eukaryote/prokaryote transition (or
vice-versa?)
For Christian de Duve, LUCA very much resembles a real bacterium ( or
archaeon). He presents an original scenario which envisages the transition
of prokaryotes to eukaryotes in a quasi-solid milieu in which loss of the
bacterial wall is followed by the expansion of the cytoplasmic membrane to
permit phagocytosis. This expansion leads to the formation of
intracellular membrane networks characteristic of eukaryote cells.
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G. Ourisson & N. Glansdorff
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Other participants are in contrast in
favor of a LUCA in which the genome was more of
the eukaryote type. For Nicolas Glansdorff, the
operons appeared slowly. perhaps in a lineage common to archaea and to
bacteria. For Rudiger Cerff, the genome of
LUCA was fragmented into numerous chromosomes
the genes of which contained introns. Patrick
Forterre thinks that LUCA was neither
prokaryote nor a eukaryote , but an organism of intermediate type , the
descendants of which have opted for opposite adaptive strategies;
adaptation towards miniaturization and the maximum replication rate having
led to prokaryotes, while feeding on other organisms by predation led to
the birth of eukaryotes.
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For
many participants, LUCA was not an organism, but a collection of diverse
organisms exchanging their genes more or less without constraint. In this
respect was found debate of the same type as that concerning the problem
of the African Eve. Without doubt a population geneticist would have been
needed to relate to our reflections. We regretted the absence of Miroslav Radman, prevented at the last minute from
participating in our colloquium. His lab studies the mechanisms of
speciation at a molecular level, and it seems that certain of these are
common to both prokaryotes and eukaryotes, suggesting that the notions of
species and species barrier existed already during the epoch of LUCA ?
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Another
essential question remains to be posed- what decisive invention ,
appearing with LUCA, gave it such a
predominance over its competitors of the epoch that only its descendants
today populate our planet?
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Was LUCA a
hyperthermophile?
Certain authors think that life
appeared at very high temperature and that LUCA
itself was a hyperthermophile (an organism living between 80 and 110 °C).
However, Stanley Miller and Antonio Lazcano put us on guard against the danger of
extrapolating the supposed conditions of life of LUCA to that of the origins (of life). We have seen
in effect that LUCA was already a very
sophisticated organism, its appearance has therefore been preceded by a
long period of evolution. Stanley Miller
insists equally on the instability of numerous prebiotic compounds at very
high temperature. Stanley Miller and Patrick Forterre e out the stress on the
contradiction which exists between the idea of a primordial evolution
which be entirely produced at high temperature (of the origin of LUCA ) and the hypothesis of an RNA world, taking
into account the instability of this molecule at temperatures in the
neighbourhood of the boiling point of water. Piero
Cammarano nevertheless presents some new facts on the evolution of
elongation factors (which participate in protein synthesis) in favour of
the ancientness (antiquity) of hyperthermophilic bacteria. There again,
the viability of molecular phylogenetic analysis is at the centre of the
debate. Patrick Forterre remarked that the
results obtained with ribosomal RNA , which are generally interpreted in
favour of the antiquity of hyperthermophiles (their branches declare
themselves by a reduced length). could be tainted with error, given their
higher GC content, which has the effect of artificially reducing the rate
of evolution.
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Nicolas Glansdorff
thinks that the formation of operons could have been produced in response
to adaptation of prokaryotes to thermophilic conditions, whereas Purificacion Lopez-Garcia presented a new scenario
which envisages how an ancestral thermophile was modified in graduated
steps towards the bacteria and archaea. This scenario is based on the
study of enzymes which introduce supercoils into the DNA molecule (gyrase
and reverse gyrase) and on the hypothesis of a precise geometry of this
molecule necessary for its function. This geometry will have been
initially adapted to temperatures in the region of 50 to 70 °C: the gyrase
and reverse gyrase will have then appeared in order to permit he
adaptation of organisms to lower and higher temperatures respectively. In
effect, the action of these enzymes permits counteracting the effects of
changes of temperature on the DNA double helix (opening at high
temperature, compression at low temperature).
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Whether or not
hyperthermophiles were near LUCA, their
study is a particularly fascinating field of research. Franck Robb presented some experiments which
contribute evidence on the mechanisms permitting proteins of
hyperthermophilic archaea to function at temperatures in the neighbourhood
of the boiling point of water. One of the strategies utilized is the
formation of a network of ionic interactions at the surface of the
protein. He furthermore presented the first results showing that the
hyperthermophilic archaebacteria are particularly resistant to ionizing
radiation. These organisms should possess DNA repair mechanisms of
extremely good efficiency.
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The age of LUCA.
Some
months before holding our colloquium, an article published in the
American review Science rejuvenated LUCA. It
would have been two billion years old, not 3.5 or 4 as one thought
previously according to examination of microfossils found in some
sedimentary rocks of this epoch which are still detectable. Hervé Philippe has subjected the facts of this work
to a thorough critical analysis from which he deduces (sets forth) that
the date advanced of 2 billion years rests on facts of very bad quality.
The protein phylogenetic trees used gave for the most part aberrant
results and the calibration of the molecular clock is itself in question.
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M. Fontecave & O. Ozier-Kalogeropoulos
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Could we go back in time, beyond the epoch
where LUCA lived?
The complexity of LUCA suggests that a long period (at least in terms
of evolutionary changes) preceded its emergence. The first steps of life
on our planet had been the appearance and assembly of the molecular
constituents of life until the appearance of he first cells. The genome of
these first cells was without doubt constituted by molecules of RNA and
not DNA. In contrast to DNA, RNA could in effect play at the time the role
of enzyme and of genetic material. Stanley
Miller and Christian de Duve think that
the appearance of RNA was itself a late event , in effect, this molecule
does not seem to be able to be synthesized by simple methods of prebiotic
chemistry. RNA would have therefore been preceded by molecules the exact
nature of which we will never know.
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If until
LUCA the
first cells were RNA based , the road ought to have been very long, always
in terms of evolutionary changes. Patrick
Forterre suggested dividing this evolution into several periods:
the two ages of the RNA world (before and after the invention by RNA of a
genuine system for synthesis of proteins) and the first age of the DNA
world (from the first DNA cell until the emergence of LUCA. . How to obtain information about these
different stages? According to him; the RNA virus and certain DNA viruses
could be the descendants of cellular organisms having lived before LUCA. They would only have survived the domination of
the latter as parasites of its descendants. The study of the molecular
biology of viruses could contribute information on the stages of evolution
before LUCA.
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An
event essential for all this evolution had
been the invention of DNA. Today the synthesis of DNA depends on a key
enzyme, ribonucleotide reductase (RNR), which makes the precursors of RNA
(reduction of ribose of RNA by elimination of oxygen to give a
deoxyribose). Marc Fontecave has made the point
of our knowledge on the 3 classes of RNR known at present and on their
distribution in the living world. He presented the characterization by his
team of the first RNR of archaebacteria, in collaboration with Franck Robb. This work has permitted the
demonstration for the first time that the three classes of RNR derive from
the same ancestral enzyme. Marc Fontecave and
Franck Robb have taken advantage of their
common presence at Treilles to write up an article reporting this
discovery. The existence of an RNR homologue in the three domains of life
strengthens the idea according to which the genome of LUCA was already composed of DNA.
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To
establish the 'identikit'-portrait of predecessors of LUCA, Antonio Lazcano has
proposed using the paralog proteins the origin of which (by gene
duplication) is before the cell of LUCA. Arturo Becerro presented an example in a
work-in-progress of this strategy in the study of the evolution of genes
implicated in certain metabolic pathways. Another example of comparative
analysis of metabolic pathways in the three domains was presented by Nicolas Glansdorff. Again, the problem is that of
distinguishing duplications which may have occurred before or after LUCA , only the first can be permitted in
reconstituting the history of genes before LUCA. Bernard Labedan and
Renaud de Rosa have shown in effect that recent
duplications are numerous within the bacteria and Odile Ozier-Kalogeropoulos has reported results of
the same type in yeast.
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P. Lopez Garcia, B. Labedan & R. deRosa
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Bernard Labedan
summarized work in collaboration with Monica
Riley on the protein families of E. coli which suggested
that many ancestral proteins had already been formed from large modules
the shape and function of which were close to that of genuine proteins. To
rediscover the most ancient homologies, we must without doubt make an
analysis of proteins in modular terms and perform structural analysis of
the type proposed by Chris Sander.. The problem
will then be to distinguish between homology (shared structural heritage
from a common ancestor) and analogy (shared structure acquired by
convergent evolution). As a matter of fact, everyone agreed on the
necessity of combining genomic studies (comparison of sequences) and
structural facts which could be more informative on the level of
functions, for the purpose of analysing evolution of he latter, which are
the true targets of natural selection.
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Finally the question poses itself: is
it possible to extrapolate from present-day metabolism to ancestral
metabolism? Guy Ourisson has presented an
attempt of this genre in the case of cellular membranes which he considers
as ought to have formed (themselves) very early, perhaps before all other
processes. He has shown how the very wide variety of amphiphilic membranes
of the present day , often uncovered from sediments in the form of their
"molecular fossils", form an evolutionary series. By retrograde analysis,
it can be deduced that the first membranes were probably formed by
phosphates of polyprenyl, which he has obtained by abiotic reactions- and
therefore probably prebiotic.
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From his
perspective, Christian de
Duve pointed out that present day metabolism up to protometabolism
preceded the RNA world (the world of thioesters which he popularised in
his book "Blueprints of a Cell". He pitted himself against the
absolutist idea of a world of omnipotent RNA. According to him, all
present enzymes have not been preceded by the corresponding ribozyme, and
he would imagine a world of peptide catalysts which were efficacious and
very early diversified. Stanley Miller, who has
made the point on the present state of research in the field of origins of
life in his introductory discussion, proposed in conclusion a true
programme of experimental research for connections between prebiotic and
contemporary metabolism and advanced many new avenues.
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P. Cammarano, P. Lopez Garcia, A. Lazecano & A. Becerra
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In
conclusion, Christian de
Duve emphasized the quality and intensity of the discussions. In
appearance, each had defended his point of view on the hotly debated
questions, but it was evident that the arguments brought to bear by one
and another will contribute to the enrichment in the months to come of
many reflections, reposing of questions , or deepening (profound study) of
diverse hypotheses. The majority are going away only to meet again for the
editing of a series of articles to appear in a special number of the
international review "Journal of Molecular Evolution" dedicated to this
meeting. In the opinion of many participants, it is one of the best
scientific meetings at which they have had the occasion to participate
(the setting of Treilles very much contributed to this appreciation), and
we all hope to renew this experience in the years to come.
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Several papers coming out of this exciting workshop (including new
collaboration initiated at "Les Treilles" ) have been published recently
in a special issue of "Journal of Molecular Evolution" Vol 49, Oct
1999. |
