OUTREACH AND TEACHING
Andrew STEANE
Selected courses and lectures in english
Archives of the Unit “Genetic of Bacterial Genomes”
Archives of the HKU-Pasteur Research Centre Ltd, Hong Kong
Many links are deleted over time, because they are not maintained by the institutions that created them. This is a major drawback in the role of the WWW, which increases noise rather than preserving information-rich sites.
Epistemology / History of Sciences
2023
 |
Synthetic / Symplectic biology / Genomics
2021
18 June 2021 (videoconference) 10 am (Paris
time)
2020
30 September 2020 (videoconference) 4 pm
(Hong Kong time)
23 April 2020 (videoconference)
10 January 2020, 11:45 am
2019
4 November 2019, 2:30 pm
Vendredi 15 Février 2019, 14h15-16h (séminaire
de travail Stanislas Noria)
Vendredi 15 Février 2019, 14h15-16h (séminaire
de travail Stanislas Noria)
2018
23 November 2018, 4:00 pm
22 November 2018, 2 pm
5 June 2018, 9:15 am
14 May 2018, 2:15 pm
21 February 2018, 10:15 am
22 January 2018, 8:00 pm
2017
6 November 2017, 11:00 am
3 November 2017, 4 pm
15 March 2017, 4:00 pm
2 February 2017, 5:00 pm
16 January 2017, 10:00 am
2016
9 December 2016, 3:00 pm
17 November 2016, 3:00 pm
18 November 2016, 2:30 pm
21 November 2016, 10 am
5 October 2016, 3 pm
<
2015
4 December 2015, 4:20 pm
<
30 November 2015, 3:30 pm
Synthetic biology in action
STS
forum
Kyoto, Japan
4-6 October 2015
9 March 2015
2014
20 May 2014
25 March 2014
2013
3 December 2013, 2 pm
2 December 2013, 4 30 pm
6 July 2013
19 February 2013
2012
13 December 2012
9 November 2012
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24 October 2012 |
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 |
27-28 february 2012
2011
1 - 2 December 2011
30 November 2011
29 may - 2 June 2011
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
« Natural selection and Maxwell's demon »
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)
The US-EC task force in biotechnology research
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)
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)
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
« 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.
2007
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)
 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. |
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Presentation (1.3 Mb)
2006
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
European Union / US Department of Energy
Synthetic Biology Workshop
Airlie House, Warrington, Virginia, USA, 24-25 April 2006
« Symplectic biology: Universals in microbial genomes »
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.
2002-2005
11-13 March 2005, Palazzo Franchetti, Venezia, Italy
« Is the computer metaphor relevant to describe living organisms?
Functional stabilization and epigenesis »
First EuroScience Open Forum (ESOF 2004)
25-28 August 2004
Stockholm City Conference Centre in Stockholm, Sweden
« The cell as a living computer»
Newcastle-upon-Tyne, 25 january 2006
Hong Kong Exhibition Centre, Wan Chai, SAR Hong Kong, december 2001
Related publications:
A Danchin
The Delphic boat or what the genomic texts tell
us
Bioinformatics (1998) 14: 383 doi:
10.1093/bioinformatics/14.5.383
A Danchin
From protein sequence to function
Curr Opin Struct Biol (1999) 9: 363-367
National Research Council
April 16-17, 1999, Roma, Italy
Related publication:
A Danchin, A
Hénaut
The map of the cell is in the chromosome
Curr Opin Genet Dev (1997) 7: 852-854 doi:
10.1016/s0959-437x(97)80051-2
17- 21 August 1997, Budapest, Hungary
25-28 September 1996
Final EU Conference of the « Yeast Genome Sequencing Network »
Trieste, Italy.
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 »
Presentation of the cell as a Turing machine
A Danchin
On genomes and cosmologies
In: "Integrative Approaches to Molecular Biology" (J Collado-Vides, B Magasanik and TF Smith eds), The MIT Press (1996) pp 91-111
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 doi:10.1128/mr.57.3.623-654.1993A Danchin
A brief history of genome research and bioinformatics in France
Bioinformatics (2000) 16: 65-75 doi: 10.1093/bioinformatics/16.1.65
Conceptual biology (merged with Symplectic Biology after 2009)
12-15 November 2007
Presentation (1.8 Mb)
« Exploration of neighborhoods for inductive reasoning »
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
This 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 doi: 10.1093/nar/23.17.3554A Danchin
mRNA turnover and DNA synthesis: a lesson from bacterial genome comparisons Mol Microbiol (1996) 20: 895-897 doi: 10.1111/j.1365-2958.1996.tb02527.x
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 doi: 10.1093/dnares/4.1.9
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: 8-11A 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 doi: 10.1186/1471-2180-4-9
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? »
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
Slide (1995) of an unlimited list of relevant neighborhoods to be combined to construct an inductive approach to biological functions25-28 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 doi:10.1111/j.1574-6976.1998.tb00368.x
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.
Anthropology, Epistemology, Ethics
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)
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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. |
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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 »
« What is life? »
22 february 2003
« Should we tell the truth? »
24 february 2003
« Controlling Information Technologies in Biological Sciences »
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
»
Presentation
Related publications:
A Danchin
Homeotopic transformation and the origin of translation
Progress in Biophysics and Molecular Biology (1989) 54: 81-86
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
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
