Rhodes
  Historically, much of fundamental physics has been concerned with discovering the fundamental particles of nature and the equations which describe their motions and interactions. It now appears that a different programme may be equally important: to discover the ways that nature allows, and prevents, information to be expressed and manipulated, rather than particles to move

Andrew STEANE

 

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Selected courses and lectures in english

Archives of the Unit “Genetic of Bacterial Genomes”

Archives of the HKU-Pasteur Research Centre, Hong Kong

Unfortunately we have to delete many links over time, as they are not maintained by the institutions that created them. We apologise for the inconvenience. This is a considerable drawback in the role of the WWW, which increases noise over time rather than preserve informational sites.

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Synthetic / Symplectic biology

Beilstein Bozen Symposium
Prien-Chiemsee, Germany

20 may 2014
« The logic of metabolism »
amabiotics

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Novo Nordisk Foundation Center for Biosustainability, Copenhagen, Denmark

25 march 2014
« An instance of paralogous metabolism: the cysteine salvage pathway »
amabiotics

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Working Seminar Stanislas Noria
Department of Mathematics
HKU, Hong Kong, China

3 december 2013, 2 pm
« Metabolism and the emergence of the first cells »
amabiotics microme

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Genome L ectures
Beijing Genome Institute, Shenzhen, China

2 december 2013, 4 30 pm
« Paralogous metabolism: a consequence of the logic of metabolism »
amabiotics microme

pyramid

Syn Bio Summer Course
ERASynBio
Synthetic Biology in action!
CSIC, Madrid

6 july 2013
« Top-down functional analysis identifies overlooked functions for the SB chassis »
amabioticsmicrome

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Institut de Physique Théorique
CEA / Saclay

19 february 2013
« Antifragility and tinkering in biology. Flexibility is an efficient epigenetic solution for risk management »
amabioticsmicrome

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International Workshop: Around viability boundaries
University Pierre et Marie Curie, Paris

13 december 2012
« Antifragility and risk management in biology » amabioticsmicrome

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The University of Hong Kong
Li Ka Shing Faculty of Medicine
Department of Biochemistry

14 november 2012, 4 pm
« Novel pathways in sulfur metabolism »

amabioticsmicrome

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Working Seminar in Conceptual Biology (Stanislas Noria)
Department of Mathematics
The University of Hong Kong
Hong Kong, SAR Hong Kong, China

9 November 2012
« Compartmentalisation of information in biology »
amabioticsmicrome

Internationale Vorlesungsreihe — Synthetische Biologie
Universität Bremen
24 october 2012
Bremen, Germany

« (Re)constructing life: we should not forget the chassis »
Presentation bageco11

amabioticsmicrome

  klee

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COST Workshop on Whitefly Metagenomics –Synthetic Biology & Symbiosis
Cavanilles Institute on Biodiversity and Evolutionary Biology
University of Valencia
Valencia , Spain

27-28 february 2012
« Functional Analysis for Synthetic Biology. Metabolic Frustration is Driving Compartmentalisation » amabioticsmicrome

Presentation bageco11

Frontiers in systems biology II
Baptist University
The Croucher Foundation
Hong Kong, SAR Hong Kong , China

1 - 2 December 2011
« Ageing vs senescence: the fate of the cell factory » amabioticsmicrome

Presentation bageco11

Working Seminar in Conceptual Biology (Stanislas Noria)
Department of Mathematics
The University of Hong Kong
Hong Kong, SAR Hong Kong , China

30 November 2011
« Update of antifragility: a concept used in banking that may be relevant to (synthetic) biology » amabioticsmicrome

Bageco11
Bacterial Genetics and Ecology
Kerkyra, Greece

29 may - 2 June 2011
« Antifragility: a concept used in banking that may be relevant to (synthetic) biology » amabioticsmicrome

Flyer bageco11

Beijing Genome Institute

bgi

Shenzhen

6 january 2011, 3:30 pm
« Functional analysis in genome sequence annotation » amabioticsmicrome

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Croucher Advanced Study Institute

Faculty of Medicine HKU

5 january 2011, 4:30 pm
« Synthetic biology and aging » amabioticsmicrome

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Hong Kong University of Science and Technology

hkust

Biochemistry and Cell Biology

5 january 2011, 10 am
« Antifragility; a novel view of finances that may be used in modelling metabolism » amabioticsmicrome

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The University of Hong Kong

Li Ka Shing Faculty of Medicine
Department of Biochemistry

4 january 2011, 4 pm hku
« Stability requirements for efficient metabolic engineering »amabioticsmicrome

 

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Exploratory Round Table Conference of 2010 - Synthetic Biology
Shanghai, october 20th, 2010
« Natural selection and Maxwell's demon » amabioticsmicrome

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TARPOL summer school on synthetic biology
Basel, september 27th, 2010
« Metabolic and spatial frustration as a constraint for synthetic biology »
tarpol amabioticsmicrome

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EMBO Meeting 2010
Barcelona, september 6th, 2010
« Metabolic frustration as a constraint for synthetic biology »
tarpol amabioticsmicrome

pyramid

International workshop on synthetic biology
Interfacing biology, technology and society
« Molecular traffic jams and the reproduction vs replication dilemma »
25-27 august 2010
Copenhagen, Denmark
tarpol amabioticsmicrome

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Piotr Slonimski: from mitochondria to genomes
Gif sur Yvette, july 8th, 2010
« From EEC genes to Maxwell’s demon’s genes »
pdf Presentation (0.369 Mb) tarpol amabioticsmicrome

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The US-EC task force in biotechnology research
Exploratory workshop: Toward standards in synthetic biology
Molecular traffic jams and emergence of metabolic and regulatory conflicts
4-6 june 2010
Segovia, Spain
tarpol amabioticsmicrome

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The Third Schmid Training Course
International training course
The body plan, an information trapped by Maxwell's demons
10-14 may 2010
Station Biologique de Roscoff, Roscoff, France tarpol amabioticsmicrome

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Interfacing Systems Biology and Synthetic Biology
Belgian Society for Microbiology, Brussels, march 25th, 2010
« Maxwell’s demon’s genes »
pdf Presentation (1.1 Mb) tarpol amabioticssymB

 

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When evolution evolves
AgroParisTech, Paris, november 12th, 2009
« Maxwell’s demon’s genes: Information of the program and information of the machine »
pdf Presentation (0.644 Mb) video podcast tarpol probactys amabiotics

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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? »
pdf Presentation (0.588 Mb)
tarpol

pyramid

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? »
pdf Presentation (0.276 Mb)
biosapiens probactys e  tarpol

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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 »
pdf Presentation (0.424 Mb)
tarpol

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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:
pdf Natural selection and immortality
(0.380 Mb)
« In vivo, in vitro, in silico: the future of biology, from genomes to synthetic cells »
pdf Presentation (0.640 Mb) tarpol

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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 »
pdf Presentation (0.588 Mb) tarpol

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Beilstein Institut

Systems chemistry symposium
« Frustration: physico-chemical prerequisites for the construction of a synthetic cell »
pdf Presentation (1.1 Mb) biosapiens
probactys

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.

dna

ESF Programme on frontiers of functional genomics

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»
pdf Presentation (1.3 Mb).

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Synthetic Biology 3.0 Conference
Swiss Federal Institute of Technology (ETH), Zürich, Switzerland , 24-26 june 2007
« Can we design de novo a bacterial genome »

pdf Presentation (864 kb)
video video LQ video video HQ

fr-flagLa 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.  

en-flagSynthetic 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.

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6th Annual International Symposium, Systems Biology and the Environment
The Institute for Systems Biology, Seattle, USA , 22-23 april 2007

« Archives or palimpsests? Bacterial genomes unveil a scenario for the origin of life »
pdf Presentation (1.3 Mb)

dna

40 years Spetsai Summer School Anniversary Workshop on Molecular and Cell Biology at Spetsai: Past, Present and Future — A Forty Years's Anniversary,
Spetses, Greece, 1-5 september 2006

« From symplectic biology to synthetic biology: Universals in microbial genomes »
pdf Lecture (1.4 Mb)

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Taipei, Taiwan , 22 february 2006

« Symplectic biology: Lessons from microbial genomes »

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In-Silico Analysis of Proteins. Celebrating the 20th Anniversary of Swiss-Prot
Fortaleza, Brazil , 30 July - 4 August 2006

« Symplectic biology: lessons from microbes »     video  Video.
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European Union / US Department of Energy Synthetic Biology Workshop
Airlie House, Warrington, Virginia, USA, 24-25 april 2006

« Symplectic biology: Universals in microbial genomes »
pdf Presentation (1.4 Mb)

Although the expression Synthetic Biology (SB) has been present in the scientific and technical literature as early as in 1904, only in more recent times is has come to being an umbrella concept to cover the whole of research developed at the interface between Molecular Biology and sensu stricto Engineering.  Synthetic Biology is becoming an increasingly inclusive concept, which [i] encompasses new theoretical frameworks that address biological systems with the conceptual tools and the descriptive language of Engineering,  [ii] addresses old questions and challenges with fresh approaches inspired in electric circuitry and mechanical manufacturing and [iii] pursues the creation of new materials with á la carte properties based on the rational combination of standardized biological parts decoupled from their natural context. In fact, standarization and detailed description of minimal biological parts and their interfaces, to the degree of reliability of the components of modern electronic circuits is one of the trademarks of the whole field.

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European Bioinformatics Institute
Hinxton, UK, 4 July 2005

« For a symplectic biology: is there a link between the architecture of the cell and that of the genome? »

pdf Presentation (2.6 Mb)

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Science and today's vision of the World
Istituto Veneto di Scienze, Lettere ed Arti
11-13 March 2005, Palazzo Franchetti, Venezia, Italy

« Is the computer metaphor relevant to describe living organisms?
Functional stabilization and epigenesis
»

pdf Presentation (1.74 Mb)

cube

First EuroScience Open Forum (ESOF2004)
25-28 August 2004
Stockholm City Conference Centre in Stockholm, Sweden

« The cell as a living computer»

pdf Stockholm_04 (3.0 Mb)

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8th Altenberg Workshop in Theoretical Biology
11-14 July 2002
Biological Information Beyond Metaphor
Organized by Werner Callebaut and Sahotra Sarkar
Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria

« Living Turing Machines »

pdf Summary 1 pdf Summary 2

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Biotechnology, Genomics

In-Silico Analysis of Proteins. Celebrating the 20th Anniversary of Swiss-Prot
Fortaleza, Brazil , 30 July - 4 August 2006

« Coping with cold and aging: lessons from the genome of Pseudoalteromonas haloplanktis »
    video   Video

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Newcastle-upon-Tyne, 25 january 2006

« Coping with cold and aging: Lessons from the genome of the versatile Antarctica bacteria Pseudoalteromonas haloplanktis TAC125 »

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Hong Kong Baptist University, Lectures in Physics
16 October 2001, Hong Kong, China

« The map of the cell is in the chromosome »

Related publications:

A Danchin
The Delphic boat or what the genomic texts tell us
Bioinformatics (1998) 14: 383
pubmed  bioinfo

A Danchin
From protein sequence to function
Curr Opin Struct Biol (1999) 9: 363-367
pubmed pdf

cube

Rikkyo International Workshop: Functional Genomics of Bacillus subtilis
Tachikawa Memorial Hall, Rikkyo Univrsity, January 26 - 27, 2001, Tokyo, Japan

« Elements of sulfur metabolism in bacteria »

cube

Mining bacterial genomes
National Research Council, April 16-17, 1999, Roma, Italy

« The map of the cell is in the chromosome »

Related publication:

A Danchin, A Hénaut
The map of the cell is in the chromosome
Curr Opin Genet Dev (1997) 7: 852-854 pubmed

cube

Eighth Workshop on Genome Informatics (GIW '97),
University of Tokyo, 12- 13 December 1997, Tokyo, Japan

« The map of the cell is in the chromosome »

8th European Congress on Biotechnology
70th Event of the European Federation of the Biotechnology,
17- 21 August 1997, Budapest, Hungary

« Biotechnology and genomes »

pdf Summary of the presentation

cube

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 pubmed

cube

Integrative Approaches to Molecular Biology
Cuernavaca, Mexico, 1996

« On genomes and cosmologies »

cube

10 -14 September 1992

First Escherichia coli genome meeting - Madison, USA

« 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 pubmed pubmed

A Danchin
A brief history of genome research and bioinformatics in France
Bioinformatics (2000) 16: 65-75 pubmed bioinfo

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Conceptual biology (merged with Symplectic Biology after 2009)

12-15 november 2007
What are the theoretical tools most useful for understanding biological systems?
Quels sont les outils théoriques les plus utiles pour comprendre les systèmes biologiques ?
Institut des Hautes Études Scientifiques (IHES), Bures-sur-Yvette, France

« The constructor and the replicator: prerequisites for the construction of a synthetic cell »

pdf Presentation (1.8 Mb)

pyramid

How complex is functional genomics?
Sixth Bologna Winter School, 13-19 February 2005, Bologna, Italy

« Exploration of neighborhoods for inductive reasoning »

pdf Summary (2,7 MB)

Related publications:

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
pubmed pdf

frCette conférence rappelait l'article qui montre, pour la première fois, que dans le génome de la bactérie la mieux connue, Escherichia coli, un sixième des gènes provient d'ailleurs. Ce résultat, qui démontre l'importance considérable du transfert génétique latéral chez les bactéries, montre aussi que la fidélité de la réplication n'est pas le caractère premier des espèces, mais que les gènes de correction des erreurs se propagent par transfert horizontal.

  ukThis article showed, for the first time, that in the genome of the best known bacteria, Escherichia coli, one sixth of the genes comes from outside. This result, that emphasizes the importance of lateral gene transfer in bacteria, also shows that replication accuracy is not a prime character of wild type species, but that genes coding for error proof-reading are propagated by horizontal transfer.

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
pubmed

A Danchin
mRNA turnover and DNA synthesis: a lesson from bacterial genome comparisons Mol Microbiol (1996) 20: 895-897 pubmed

frCet article résume une série d'exposés (1994-1996) où l'idée de l'exploration des voisinages génomiques, bibliographiques et métaboliques est illustrée par la mise en évidence un rôle spécifique de la dégradation de l'ARN dans la synthèse de novo de l'ADN  

ukThis article summarizes a series of presentations (1994-1996) where the exploration of neighborhoods in the genome, in the literature and in metabolic pathways is illustrated by the discovery of a coupling in bacteria between mRNA degradation and DNA de novo synthesis

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 pubmed DNARes 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 pubmed pdf

frCet article illustre popular le concept de voisinage permet de faire des inférences efficaces. Il décrit la base de données Indigo où le voisinage des gènes d'organismes modèles peut être exploré   ukThis article illustrates how the concept of neighborhood allows investigators to perform inductive reasoning. It describes the Indigo database where gene neighborhoods can be explored

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 pubmed pdf

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 pubmed BMC

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? »

pdf Lecture

An illustration is the following excerpts:

15 - 17 May 1991
Genome analysis research in the EC, Elounda, Crete, Greece

« Databases for bacterial genomes »

frCette conférence, peu connue en raison de la domination européenne d'alors, marquait la première grande découverte de la génomique: dans le chromosome III de la levure, et dans près de 100 kb du génome de Bacillus subtilis on remarquait une bonne moitié de gènes totalement inconnus. Piotr Slonimski les nomme alors les EEC genes (comme l'acronyme de l'Union Européenne de ce temps) pour elusive, esoteric, conspicuous genes. La construction de bases de données relationnelles introduit le concept de voisinage dans l'analyse des génomes   ukThis conference is little known as it marked a clear European domination in genomics, back in 1991. There the first major discovery of genomics was presented: in yeast chromosome III as well as in a contiguous segment of almost 100 kb of Bacillus subtilis one found some half of the genes of totally unknown structure and function. Piotr Slonimski coins the name EEC genes (as the acronym of European Union at that early time) for elusive, esoteric, conspicuous genes. The construction of relational microbial genome databases introduces the concept of neighborhood in genome analysis

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2-6 October 1994
Twentieth EMBO Annual Symposium 1994
« Genomes and Chromosomes », Heidelberg, Germany

« On genomes and cosmologies: the Bacillus subtilis example»

4 -12 November 1994
Third International Escherichia coli Genome Meeting - Woods Hole MA, USA

« 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
pubmed pdf
frCet article montrait, pour la première fois, que dans le génome de la bactérie la mieux connue, Escherichia coli, un sixième des gènes provient d'ailleurs. Ce résultat, qui démontre l'importance considérable du transfert génétique latéral chez les bactéries, montre aussi que la fidélité de la réplication n'est pas le caractère premier des espèces, mais que les gènes de correction des erreurs se propagent par transfert horizontal   ukThis article showed, for the first time, that in the genome of the best known bacteria, Escherichia coli, one sixth of the genes comes from outside. This result, that emphasizes the importance of lateral gene transfer in bacteria, also shows that replication accuracy is not a prime character of wild type species, but that genes coding for error proof-reading are propagated by horizontal transfer

The concept of neighborhood, later to be the basis for a new area of bioinformatics pdf  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 pdf

25-28 June 1995
Eighth Bacillus subtilis international conference, Standord, Ca, USA

« 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 pubmed pdf

frCet article illustre popular le concept de voisinage permet de faire des inférences efficaces. Il décrit la base de données Indigo où le voisinage des gènes d'organismes modèles peut être exploré   ukThis article illustrates how the concept of neighborhood allows investigators to perform inductive reasoning. It describes the Indigo database where gene neighborhoods can be explored

5-8 October 1996
Eighth International Genome Sequencing and Analysis Conference

Hilton Head Island, Savannah, USA

« Small genomes: sequencing, functional characterization and comparative genomics »

23-27 October 1996

Genome Symposium

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

9th International Conference on Bacilli

Lausanne, Switzerland.

« Bacillus subtilis in silico »

17- 21 August 1997
8th European Congress on Biotechnology
70th Event of the European Federation of the Biotechnology
Budapest, Hungary

« The concept of neighborhood in genome exploration »

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Anthropology, Epistemology, Ethics

Transcultura International Meeting, Order and Disorder
Chinese Academy of Social Sciences, Beijing, China , 5-7 march 2007

« Survivre dans un avenir imprévisible : quelques conséquences malheureuses de la génération de la diversité, et la Civilisation comme remède »

pdf Presentation in English (772 kb)

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EAGLES Food Workshop, Huyagang HNA Resort Hotel, Hangzhou, China , 4-5 december 2006
« New trends in the epidemiology of emerging diseases »
pdf Presentation (260 kb)

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Les Rencontres du Palais Thott, Ambassade de France, Kongens Nytorv, November 23, 2006
« Nature and Artifice: a reflection on domestication and GMOs »

pdf Conference (628 kb)

BioCampus Conference « Public Perception of GMO », November 24, 2006, The Old University building, Copenhagen
« An avatar of domestication: GMOs » pdf Summary (428 kb)       Questions and Answers on the Danish TV (DR2)

fr-flag 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.   en-flagHuman 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.

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The knowledge-based bio-economy ,Transforming life sciences knowledge into new, sustainable, eco-efficient and competitive products
European commission, Brussels, Belgium, 15-16 September 2005

« Micro-organisms: untapped genetic resources; The cell factories: what microbes can bring to us »

pdf Presentation (3.4 Mb)

pdf EU_Report (2.8 Mb)

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Dialogues for the progress of Mankind
22-24 February 2003
Fondation Charles Léopold Meyer pour le Progrès de l'Homme
Peking University, Beijing

« What is life? »

22 february 2003

« Should we tell the truth? »

24 february 2003

pdf Presentation: a word about GMOs

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7th Western Pacific Congress on Chemotherapy and Infectious Diseases
WPCCID, 11-14 December 2000
Hong Kong, China

« Controlling Information Technologies in Biological Sciences »

pdf 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
pdf

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Symposium "J Monod and molecular biology, Yesterday and Today"
From enzyme adaptation to natural philosophy: heritage from J Monod
Trani. Italy: 13-15 dec 1986

« Order and Necessity »

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Centre Royaumont pour une Science de l'Homme

Le débat Chomsky-Piaget 1975
Commentaire sur le concept de phénocopie

MIT Endicott House: neural origins of language 1974

 

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    1995 L'année Pasteur

From spontaneous generation to molecular evolution, february 1995
100th Anniversary of Louis Pasteur death, by the Institut Pasteur, the Oswaldo Cruz Foundation and UNESCO
Rio de Janeiro, Brazil
« Homeotopic transformation and the origin of translation »
 
Presentation pdf

Related publications: UKUS A Danchin
Homeotopic transformation and the origin of translation
Progress in Biophysics and Molecular Biology (1989) 54: 81-86
pubmed

frIl est amusant de constater qu'à l'Institute for Scientific Information, le titre de cet article a été changé et a confondu «homeotopic» avec «homeotropic» en altérant significativement le sens   ukIt is revealing to note that the title of this article has been misspelled at the Institute for Scientific Information, modifying «homeotopic» into «homeotropic», changing the meaning of the concept
UKUS 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
pubmed pdf
frCet article démontre pour la première fois la parenté entre la biosynthèse du tryptophane et celle de la cystéine (codés par la même case du tableau du code génétique). Il conforte l'idée de l'existence de transformations homéotopiques à l'origine de la vie   ukThis paper shows for the first time the common origin in tryptophane and cysteine biosynthesis (coded by the same box in the genetic code table). It substantiates the idea of homeotopic transformations at the origin of life
fr A Danchin
Une Aurore de Pierres. Aux origines de la vie
Le Seuil (1990), 276 pp

pt A Danchin
« Uma aurora de pedras. Nas origens da vida » , Portuguese translation; Almedina, Coimbra 1992

it A Danchin
Dai minerali alla vita
Prometeo (1996) 14: 16-21

fr 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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