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2013
19 february 2013
 
2012
13 december 2012
14 november 2012, 4
pm
9 November 2012
27-28 february 2012
Presentation 
2011
1 - 2 December 2011
Presentation
30 November 2011
29 may - 2 June 2011
Flyer
6 january 2011, 3:30 pm
5 january 2011, 4:30
pm
5 january 2011, 10 am
« Antifragility; a novel view of finances
that may be used in modelling metabolism »
4 january 2011, 4 pm 
2010
Shanghai, october 20th, 2010
Basel, september 27th, 2010
Barcelona, september 6th, 2010
25-27 august 2010
Copenhagen, Denmark
Gif sur Yvette, july
8th, 2010
« From EEC genes to Maxwell’s demon’s genes »
 Presentation (0.369
Mb)
4-6 june 2010
Segovia, Spain
Station
Biologique de Roscoff, Roscoff, France
Belgian Society for Microbiology, Brussels, march 25th, 2010
Presentation (1.1
Mb) 
2009
AgroParisTech, Paris, november 12th, 2009
« Maxwell’s demon’s genes: Information of
the program and information of the machine »
Presentation (0.644
Mb)  podcast 
European
Science Foundation-Universitat de Barcelona Conference in
Biomedicine
ECSB
II: Design, programming and optimisation of biological
systems
Sant Feliu de Guixols, Spain, 29 March – 03 April 2009
« Maxwell's demon's genes: Towards a cell
factory or towards a living synthetic cell? »
Presentation (0.588
Mb)
Ethical questions posed by Synthetic Biology
European
Group on Ethics in Science and New Technologies
Bruxelles, Belgique, 17 February
2009
« Will we be able to construct a synthetic cell? »
Presentation (0.276
Mb)  
2008
European
Molecular Biology Laboratory
9th
EMBL/EMBO
Joint Conference
Systems and Synthetic -
Biology Scientific and Social Implications
EMBL, Heidelberg,Germany,
7 november 2008
« Life and perpetuation of life of a synthetic bacterium »
Presentation (0.424
Mb)
The University
of Hong Kong: Department
of Biochemistry 14 october 2008 / Department
of Mathematics 16 october 2008
[discussions at the Hong
Kong University of Science and Technology:
Synthetic Biology SB 4.0]
Living organisms as information
traps:
Natural
selection and immortality (0.380
Mb)
« In vivo, in vitro, in
silico: the future of biology, from genomes to synthetic cells »
Presentation (0.640
Mb)
Swiss
Institute of Bioinformatics
Tenth Anniversary of the SIB
NCCR Frontiers in Genetics lecture,
Bern, Switzerland, 24 september 2008
« In vivo, in vitro,
in silico: the future of biology, from genomes to synthetic
cells »
Presentation (0.588
Mb)
Systems
chemistry symposium
« Frustration: physico-chemical prerequisites
for the construction of a synthetic cell »
Presentation (1.1
Mb)
Abstract. To construct a synthetic cell
we need to understand the rules that
permit life. A central idea in modern biology is that in addition
to
the four entities making reality, matter, energy, space and time,
a fifth
one, information, plays a central role. As a consequence of this
central
importance of the management of information, the bacterial cell
is
organised as a Turing machine, where the machine, with its compartments
defining an inside and an outside and its metabolism, reads and
expresses the genetic program carried by the genome. This highly
abstract organisation is implemented using concrete objects and
dynamics,
and this is at the cost of repeated incompatibilities (frustration),
which need to be sorted out by appropriate «patches». After describing
the organisation of the genome into the paleome (sustaining and
propagating
life) and the cenome (permitting life in context), we describe
some chemical hurdles that the cell as to cope with, ending with
the
specific case of the methionine salvage pathway.
European Conference on Synthetic Biology ECSB07
Design, programming and optimisation of biological systems,
Sant Feliu de Guixols, Spain , 24-29 november 2007
« Will we be able to construct
a synthetic bacterium»
Presentation (1.3
Mb).
Presentation (864
kb) video
LQ video
HQ
 La
biologie synthétique présuppose que
la combinaison de briques de base (au niveau de l'ADN)
placées dans un génome artificiel introduit
dans une cellule réceptrice appropriée
suffira à produire une usine cellulaire capable de
se reproduire et d'effectuer des tâches prédéfinies.
Cette vue suppose qu'une cellule vivante se comporte
comme une machine de Turing qui ferait des machines
de Turing. Elle suppose qu'une structure spécifique
de l'ensemble données+programme peut être
physiquement séparée de la machine
et que le programme peut être exprimé en
un réplicateur et un constructeur qui contienne
une image de la machine à construire. Nous
montrons que les bactéries nous fournissent
un schéma de la cellule synthétique
si on la débarrasse d'appendices et de tympans
inutiles. En bref, un ensemble de gènes persistants
(appelé le paléome, pour rappeler que sa fonction
provient d'un scénario particulier de l'origine
de la vie) définit les programmes du réplicateur
et du constructeur, avec l'adjonction de gènes
requis pour la maintenance et la réparation.
Quelques règles d'organisation suggèrent
qu'il existe bien une image de la cellule associée à certains
gènes du paléome. Cependant le programme
génétique n'est pas un texte écrit
dans un monde abstrait. Il est porté par une
molécule particulière, l'ADN, qui est
contrainte par les lois de la physique des polymères
et de la chimie. Un génome type occuperait
un volume de rayon dix fois supérieur à celui
de la cellule. Pouvons-nous découvrir les
règles de l'organisation de l'ADN? L'analyse
des mots « flous » montre que c'est possible.
Nous montrons alors que nous devons prendre en compte
ces contraintes, associées à celles
de la transcription et de la traduction. Pour finir,
nous mettons en évidence quelques règles
de la vie en contexte, exactement ce qu'il nous faut
prendre en compte pour créer une usine cellulaire,
où
un ensemble de gènes (formant le cénome)
permet l'occupation d'une niche spécifique.
|
|
 Synthetic
biology postulates that combining biological nuts
and bolts (at the level of DNA) and placing the corresponding
artificial genome in an appropriate recipient cell
will result in a cell factory sufficient for its
own reproduction, as well as its ability to perform
designed tasks. This view assumes that a living cell
behaves as a Turing machine constructing Turing machines.
It supposes that a specific structure of data+program
can be physically separated from the machine and
that the program can be expressed into a replicator
and a constructor that harbours an image of the machine
it will construct. We show that bacteria might provide
us with a blueprint of the synthetic cell, when we
strip it from unnecessary appendages, spandrels and
the like. Briefly, a set of persistent genes (named
the paleome, to remind us that its function evolved
from a particular scenario of the origin of life)
define the replicator and the constructor programs,
with the important addition of genes required for
maintenance and repair. Some rules of organization
will be described suggesting that there may indeed
be some kind of image of the cell associated to some
of the genes making the paleome. However, the genetic
program is not a text written in an abstract world.
It is imbedded in a special molecule, DNA, that is
constrained both by rules of chemistry and rules
of polymer physics. A typical genome would spontaneously
occupy a volume with a radius ten times larger than
the radius of the cell. Can we uncover constraints
of DNA organization? A first analysis of flexible
words in genomes suggests that it is so indeed. We
suggest that much reflection is needed to approach
the way an artificial cell would be created, with
particular emphasis on the organization of transcription
and translation. Finally we give a few rules pertaining
to developing life in context — exactly what would
be the purpose of designing a cell factory, where
particular sets of genes allow the cell to occupy
a specific niche.
|
Presentation (1.3
Mb)
Lecture (1.4 Mb)
Taipei, Taiwan , 22 february 2006
« Symplectic
biology: Lessons from microbial genomes »
In-Silico Analysis of Proteins. Celebrating the
20th Anniversary of Swiss-Prot
Fortaleza, Brazil , 30 July - 4 August 2006
Video.
European Union / US Department of Energy Synthetic
Biology Workshop
Warrington, Virginia, USA, 24-25 april 2006
« Symplectic
biology: Universals in microbial genomes »
Presentation (1.4
Mb)
European Bioinformatics Institute
Hinxton,
UK, 4 July 2005
Presentation (2.6
Mb)
First EuroScience
Open Forum (ESOF2004)
25-28 August 2004
Stockholm City Conference Centre in Stockholm, Sweden
« The cell
as a living computer»
Stockholm_04 (3.0
Mb)
Summary
1 Summary
2
« Is the computer
metaphor relevant to describe living organisms?
Functional stabilization and epigenesis »
Presentation (1.74
Mb)
Video
Newcastle-upon-Tyne, 25 january 2006
Related publications:
A Danchin
The Delphic boat or what the genomic texts tell us
Bioinformatics (1998) 14: 383  
A Danchin
From protein sequence to function
Curr Opin Struct Biol (1999) 9: 363-367
Related publication:
A
Danchin, A Hénaut
The map of the cell is in the chromosome
Curr Opin Genet Dev (1997) 7: 852-854
8th European
Congress on Biotechnology
70th Event of the European Federation of the Biotechnology,
17- 21 August 1997,
Budapest, Hungary
« Biotechnology
and genomes »
Summary
of the presentation
25-28 September 1996
Final EU Conference of the « Yeast Genome Sequencing
Network »
Trieste, Italy.
« In
silico comparison of bacterial genomes »
P Glaser, F Kunst, M Arnaud,
M-P Coudart, W Gonzales, M-F Hullo, M Ionescu, B
Lubochinsky, L Marcelino, I Moszer, E Presecan, M
Santana, E Schneider, J Schweizer, A Vertes, G Rapoport,
A Danchin
Bacillus subtilis genome project: cloning and
sequencing of the 97 Kb region from 325o to
333o
Mol Microbiol (1993) 10: 371-384
Integrative Approaches to Molecular Biology
Cuernavaca, Mexico, 1996
« On genomes and cosmologies »
10 -14 September 1992
« Colibri:
a functional database for the Escherichia coli genome »
C
Médigue, A Viari, A Hénaut, A Danchin
Colibri: a functional data base for the Escherichia
coli genome
Microbiol Rev (1993) 57: 623-654 
A
Danchin
A brief history of genome research and bioinformatics
in France
Bioinformatics (2000) 16: 65-75
12-15
november 2007
Presentation (1.8
Mb)
« Exploration
of neighborhoods for inductive reasoning »
Summary (2,7
MB)
C
Médigue,
T Rouxel, P Vigier, A Hénaut, A Danchin
Evidence for horizontal gene transfer
in Escherichia coli speciation
J Mol Biol (1991) 222: 851-856
M
Borodovsky, JD McIninch, EV Koonin, KE Rudd, C Médigue,
A Danchin
Detection of new genes in a bacterial
genome using Markov models for three gene classes
Nucleic Acids Res (1995) 23: 3554-3562
A Danchin
mRNA turnover and DNA synthesis: a lesson
from bacterial genome comparisons Mol Microbiol (1996) 20: 895-897
A Danchin
Comparison between the Escherichia
coli and Bacillus subtilis genomes suggests that
a major function of polynucleotide phosphorylase is to synthesize
CDP
DNA Res (1997) 4: 9-18 
P
Nitschké,
P Guerdoux-Jamet, H Chiapello, G Faroux, C Hénaut,
A Hénaut, A Danchin
Indigo: a World-Wide-Web review of
genomes and gene functions
FEMS Microbiol Rev (1998) 22: 207-227
EPC Rocha, A Sekowska, A Danchin
Sulphur islands in the Escherichia
coli genome: markers of the cell's architecture?
FEBS Lett (2000) 476: 8-11
A
Sekowska, V Dénervaud,
H Ashida, K Michoud, D Haas, A Yokota, A Danchin
Bacterial variations on the methionine
salvage pathway
BMC Microbiol (2004) 4: 9 
The concept of neighborhood in
genomics was presented as a core in silico method during many
lectures from 1994 (at the EMBL in Heidelberg) to year 2000
(mostly in various places in the USA and in UK), illustrated
by the exploration of the enigmatic link between the gene mssA (cmk)
and gene rpsA in an operon conserved throughout bacterial
clades. The concept of neighborhood was first implemented in
the Entrez software at the NCBI.
3-5 June 2000
Uehara
Memorial Foundation Symposium
Genome Science: Towards a new paradigm?
Organized
by Hiroshi Yoshikawa, Naotake Ogasawara and Noriyuki
Sato, Tokyo, Japan
« Just
so genome stories: what does my neighbor tell me? »
Lecture
An illustration is the following excerpts:
15
- 17 May 1991
2-6
October 1994
« On
genomes and cosmologies: the Bacillus
subtilis example»
4 -12 November 1994
« Large
scale analysis of the E. coli genome »
C
Médigue, T Rouxel, P Vigier, A Hénaut,
A Danchin
Evidence for horizontal gene transfer
in Escherichia coli speciation
J Mol Biol (1991) 222: 851-856
The
concept of neighborhood, later to be the basis for a new
area of bioinformatics has
been proposed as a basis for inductive reasoning in genome
studies and illustrated in all the following lectures:
Slide (1995) of an
unlimited list of relevant neighborhoods to be combined
to construct an inductive approach to biological functions
25-28 June 1995
« New
insights from the study of B.
subtilis in silico »
P
Nitschké, P Guerdoux-Jamet, H Chiapello, G Faroux,
C Hénaut, A Hénaut, A Danchin
Indigo: a World-Wide-Web review of genomes
and gene functions
FEMS Microbiol Rev (1998) 22: 207-227
5-8 October 1996
Hilton Head Island, Savannah, USA
« Small
genomes: sequencing, functional characterization and
comparative genomics »
23-27 October 1996
Seoul, South Korea
« Lessons
from in silico comparison of bacterial genomes »
27-30 October 1996
« Recent Advance in Genome Biology of Micro-organisms »
International
symposium, Kasuza DNA Research Institute, Japan
« Bacterial
genomes in silico »
25-28 January 1997
Small genomes: sequencing, functional characterization and
comparative genomics (TIGR Science Education Foundation,
inc.), Hilton Head, Savannah, USA.
« Lessons
from bacterial genomes comparison in silico »
6-9 April 1997
Integrating Genetic, Biochemical and
other Data in the Post-Genomics Era
The Banbury Center, Cold Spring Harbor Laboratory, USA
« The
concept of neighborhood for genome annotation »
24-27 June 1997
The Fifth International Conference on Intelligent Systems for Molecular Biology
(ISMB-97) Hakidiki, Greece.
« Bacterial
genomes in silico »
15 -19 July 1997
Lausanne, Switzerland.
Presentation
in English (772 kb)
Presentation (260
kb)
Conference (628
kb)
BioCampus Conference
« Public Perception of GMO », November
24, 2006, The Old University building, Copenhagen
« An avatar of domestication: GMOs »
Summary (428
kb) Questions
and Answers on the Danish TV (DR2)
| L'explosion
démographique a conduit à industrialiser
l'agriculture en accélérant le processus
de domestication. Les organismes génétiquement
modifiés représentent le dernier avatar
de ce processus. Les réactions du public à cet égard
sont bien compréhensibles car elles manifestent
simplement le désarroi devant les changements
extraordinaires subis par la Terre depuis une cinquantaire
d'années. Cependant la Nature elle-même
pourrait se venger des outrages que l'Homme lui fait
subir, car l'Artifice
ne peut subsister que dans un environnement très
protégé. Un raisonnement simple démontre
alors que les OGM animaux sont potentiellement bien
plus dangereux que les OGM végétaux et
de sérieux problèmes pourraient apparaître
de ce côté. |
|
Human
demographic explosion required industrialisation of
agriculture via acceleration of the process of domestication.
Genetically modified organisms are the latest avatar
of that process. Public reactions in this domain are
quite understandable as they show how people are disoriented
by the extraordinary changes suffered by the Earth
for the past fifty years. However Nature might come
back with a vengeance as Artifice
can only survive in a highly protected environment while
Nature is adapted to propagate in unpredictable environments.
Indeed, a straightforward line of reasoning shows that animal
GMOs can in principle become much more dangerous than
plant GMOs, and major problems could come from
that quarter. |
« Micro-organisms:
untapped genetic resources; The cell factories: what microbes
can bring to us »
Presentation (3.4
Mb)
EU_Report (2.8
Mb)
« What is life? »
22
february 2003
« Should we
tell the truth? »
24 february 2003
Presentation:
a word about GMOs
« Controlling
Information Technologies in Biological Sciences »
Summary
of the presentation
Related publications:
S Brunak, A Danchin, M Hattori, H Nakamura,
K Shinozaki, T Matise, D Preuss
Nucleotide sequence database policies
Science (2002) 298: 1333
Trani. Italy:
13-15 dec 1986
»
Related
publications:
 A
Danchin
Homeotopic transformation and the origin
of translation
Progress in Biophysics and Molecular Biology (1989) 54: 81-86
S
Lévy, A Danchin
Phylogeny of metabolic pathways: O-acetylserine
sulphydrylase A is homologous to the tryptophan synthase beta
subunit
Mol Microbiol (1988) 2: 777-783
 A
Danchin
Une Aurore de Pierres. Aux
origines de la vie
Le Seuil (1990), 276 pp
 A
Danchin
« Uma aurora de pedras. Nas origens da
vida » ,
Portuguese translation; Almedina, Coimbra 1992
 A
Danchin
Dai minerali alla vita
Prometeo (1996) 14: 16-21
A
Danchin
Des minéraux à
la vie: une alternative à la soupe prébiotique
In: Dictionnaire de l'ignorance, Aux frontières
de la Science (PUF) (1998) pp 196-212
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