all session sheetsoutstanding puzzles of evolutionary biology and a challenging case study of...
TRANSCRIPT
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Location The conference will be held at the Cité Internationale Universitaire de Paris (CIUP). The Cité Universitaire was created in the pacifist context of the 1920s to support exchanges among students of the whole world. It is located on a wooded park in the south of the French capital and represents the largest student housing and facilities in the Paris region (5,600 beds). The grounds of the Cité Universitaire accommodate 40 residences, doubling as an outdoor exhibit of architecture. The eclecticism of the buildings expresses the diversity of the countries that contributed to their construction. Residences evoke the architecture of their country of origin (e.g., English colleges), others originate from the international modern movement (decorative arts, Le Corbusier). Address: 17, boulevard Jourdan, 75014 Paris
Access within Paris
• Suburban train (called “RER”, line B): “Cité Universitaire” station
• Metro (ligne 4): “Porte d’Orléans” station, then Tramway (line T3)
• Tramway (line T3): “Cité Universitaire” station
• Bus (line 21): “Cité Universitaire-Gazan” station
• Bus (line 88): “Jourdan-Montsouris” station
• Car: From the Paris beltway (called “Boulevard Périphérique”), take the “Porte d’Orléans” or “Porte de Gentilly” exits, then follow the signs to the nearby “Charlety” parking garage.
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Conference Rooms
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Salon Gulbenkian
Monday, August 8
Program Time
AAALE - Alife Approaches to Artificial Language Evolution AAALE discusses operational experiments in cultural artificial language evolution with embodied agents (primarily humanoid robots). Such experiments have recently reached a new level of maturity thanks to significant progress in humanoid robotics, the availability of language technologies supporting constantly evolving grammars and embodied cognitive semantics, and new insights into semiotic dynamics and cultural evolution from a complex systems point of view. The topic of language evolution has been part of Alife and SAB conferences from the very beginning, simply because language evolution is one of the most outstanding puzzles of evolutionary biology and a challenging case study of cultural evolution. Moreover, performing experiments with robots in grounded
language evolution poses enormous challenges for Alife approaches to robotics. This is the first workshop ever that focuses specifically on Alife approaches to Artificial Language Evolution.
9:00-13:00
Open coffee break 10:00-12:00
[Lobby]
9:00 - Registration 9:15 - Introduction (Luc Steels - VUB AI-Lab, University of Brussels / Sony CSL Paris) Morning Session I: Concept and Lexicon Formation 10.00 - Coordination of meaning within different embodiments through linguistic interactions. Joachim de Greeff (University of Plymouth) 10:30 - From now to not-now: an evolutionary plausible model of the human ability to process time. Damien Munch and Jean-Louis Desalles (Telecom Paris Tech) Morning Session II: Grammar Formation 11:15 - Naming A Structured World: A Cultural Route to Duality of Patterning.
Francesca Tria (ISI Foundation, Torino) 11:45 - Evolutionary Simulations on the Emergence of Grammatical Agreement Katrien Beuls (VUB AI-Lab, University of Brussels) 12:15 - The Emergence of Case Marking Systems Remi van Trijp (Sony CSL Paris)
13:00-14:30 [Halls]
Lunch Break
14:30-18:30
Open coffee break 15:30-17:30
[Lobby]
Afternoon Session I: Action Language and Space 14:30 - How language and space scaffold sensorimotor cognition
Anthony Morse (University of Plymouth) 15:00 - Acoustic Packaging – Towards Bottom-Up Action and Language Learning in Tutoring Situations
Lars Schillingman (University of Bielefeld) 15:30 - The Evolution of Grounded Spatial Language
Michael Spranger (Sony CSL Paris)
Afternoon Session II: Robot Platforms and Language Research 16:30 - Short presentations followed by parallel demonstrations and/or videos
Manfred Hild (Myon - Humboldt University Berlin) Michael Spranger (Sony Humanoid Robot - Sony CSL Paris) Matthieu Lapeyre and Pierre Rouanet (HRI and Acroban - INRIA Bordeaux) Tony Belpaeme (iCub - University of Plymouth) Lars Schillingman (Nao/iCub - University of Bielefeld) Nicolas Boudot (Nao - Aldebaran Robotics Paris) Jean-Christophe Baillie (Jazz - Gostai Robotics Paris)
18:00 - Concluding panel (Chair: Manfred Hild)
Luc Steels Tony Belpaeme
Salon du Cambodge (morning) and Salle Nathan (afternoon)
Monday, August 8
Program Time
BioChemIT – 1st COBRA Workshop on Biological and Chemical Information Technologies BioChemIT will provide a forum to present and discuss the latest advances of Bio/Chem IT research. This workshop will foster interaction, exchange, and communication between Bio/Chem IT research groups and projects. It will contribute to building a scientific community, providing input for a future strategy and vision of Bio/Chem IT. Topics: biological/chemical information technologies; molecular and chemical computing; protocells and synthetic cells; molecular robots; integration of information processing with (bio-)chemical production; nano-bio-info interface; cellular engineering, artificial neurons, and programmable information chemistry; unconventional computing substrates, synthetic biology.
[Cam]
9:00-13:00
Open coffee break 10:00-12:00
[Lobby]
9:00 – Welcome.
9:15 – Invited lecture – Stepanek Frantisek: Challenges and opportunities in the engineering of chemical robots.
10:15 – Chu: Noise-speed-code trade-offs in gene computers.
10:45 – Goni-Moreno/Amos: Design of a genetic branch predictor.
11:30 – Corsi et al.: BZ oscillations inside lipid-enclosed droplets.
12:00 – Holley et al.: Computational explorations in BZ mediated geometric vesicle transcriptions.
12:30 – Lui et al.: Towards an in silico and in vivo Turing Test for Chells.
13:00-14:30 [Halls]
Lunch Break
[Nath]
14:30-18:30
Open coffee break 15:30-17:30
[Lobby]
14:30 – Invited lecture – Serge Kernbach.
15:30 – King et al.: Towards on-chip on-demand microfluidic production and manipulation of droplets for chemical computing.
16:00 – Tangen: On the external programming of a self-referential evolving micro-controller system.
16:45 – Chaplin et al.: Implementing conventional logic unconventionally: photochromic molecules as registers and logic gates.
17:15 – McCaskill: Spatially interfaced Chem-IT: towards electronic chemical cells.
17:45 – Rasmussen: ICT and chembio-based replication.
18:15 – COBRA discussion sesión.
18:30 – Close.
Peter Dittrich Martyn Amos
Salon David-Weill
Monday, August 8
Program Time
CoSMoS – 4th Workshop on Complex Systems Modelling and Simulation CoSMoS 2011 will be the fourth in a series of workshops that provide a forum for research examining all aspects of the modelling and simulation of complex systems. This year, we will place a special focus on how complex systems simulations can begin to approach the scale of real-world complex systems. We will accept both full papers (for oral presentation) and abstracts (for poster presentation), which will
be peer-reviewed. We will also have at least one invited speaker, and a panel discussion to close the workshop. As for the previous 3 workshops in the series, accepted papers and abstracts will appear in proceedings published by Luniver Press. Contributing authors and the first 40 attendees will receive a copy of the proceedings free of charge.
9:00-13:00
Open coffee break 10:00-12:00
[Lobby]
09:00 - Workshop arrival 09:15 - Welcome address 09:30 - Andrews et al: CoSMoS process, models and metamodels 10:10 - Evora et al: Agent-based modelling of electrical load at household level 11:20 - McEwan et al: A computational technique to scale mathematical models towards
complex heterogeneous systems 12:00 - Dirk Helbing, Keynote Address: Living Earth Simulator
13:00-14:30 [Halls]
Lunch Break
14:30-18:30
Open coffee break 15:30-17:30
[Lobby]
14:30 - Poster Session:
Mancy et al: Multiscale pairwise approximations for ecological modeling Alden et al: Developing an in silico tool to explore the mechanisms behind mucosal
lymphoid tissue formation Eleftherakis et al: Harnessing emergent properties in artificial distributed networks: an
experimental framework Clayton et al: Simulating cellular automata using Go
15:30 - Guest et al: Plotting a catchy tune: tracing sound meme evolution through visualisation 16:40 - Joint presentation:
Droop et al: Multiple model simulation: modeling cell division and differentiation in the prostate
Polack et al: Simulation validation: exploring the suitability of a simulation of cell division and differentiation in the prostate
17:40 - Panel Discussion
Paul Andrews Susan Stepney Peter Welch Carl Ritson
Salon de l’Argentine
Monday, August 8
Program Time
WAAT - Workshop on Artificial Autonomy: 20 years of practice of autonomous systems Autonomy is a system’s capacity to produce, sustain and regulate itself and its relationship with the environment it co-determines. WAAT will evaluate 20 years of practice of autonomous systems, from the first ECAL (1991) until today, and review the state of the art, future challenges and research milestones. The notions of autonomy, autopoiesis, emergence, enaction, etc., have played a central role in Artificial Life but have also experienced a relative displacement as the field has made progress in more specific and specialized research fields (from network topology to ant intelligence, from evolutionary robotics
to multicellular development). We believe that increasingly specialized trends in Alife should also be compensated with renewed attempts for integrative approaches. In this sense, reviewing and recovering the visionary and pioneering notion of autonomy 20 years later provides a challenging opportunity to re-assemble Artificial Life back into the organism-centered, emergent, holistic yet mathematically and conceptually mature notion of autonomy.
9:00-13:00
Open coffee break 10:00-12:00
[Lobby]
09:00-09:05 Opening remarks by the organizers (Tom Froese, Matthew Egbert, and Xabier Barandiaran)
09:05-09:30 Xabier Barandiaran: “Introduction to the practice of autonomous systems”
09:30-10:15 Paul Bourgine: “Reflections on Varela, ECAL, and artificial autonomy”
10:15-11:00 Ben Shirt-Ediss, Ricard Solé, Fabio Mavelli, and Kepa Ruiz-Mirazo: “On the chemical relevance of compartment ‘self-production’”
11:00-11:30 Coffee break
11:30-12:00 Theije Visser, Rineke Verbrugge, and Tjeerd Andringa: “Affective agents bridge the gap between life and mind”
12:00-12:45 Nathaniel Virgo: “Metabolism and Behaviour in Simple Dissipative Structures”
12:45-13:00 General Discussion
13:00-14:30 [Halls]
Lunch Break
14:30-18:30
Open coffee break 15:30-17:30
[Lobby]
14:30-15:00 Marzena Maria Bihun, Georg Martius, and J. Michael Herrmann: “Closing the Loop: From Self-Organization of Behaviour to Minimal Agency and Back”
15:00-15:30 Norihiro Maruyama, Geoff Nitschke, and Takashi Ikegami [presented by Ikegami]: “A Dynamic Soundscape”
15:30-16:00 Alberto Montebelli: “Ecological autonomy: the case of a robotic model of biological cognition”
16:00-16:30 Coffee break
16:30-17:00 Tom Froese, Takashi Ikegami: “A quantum theory of biological autonomy at the macro-level”
17:00-17:45 Maël Montévil, and Matteo Mossio: “The idea of closure in autonomous systems”
17:45-18:25 General Discussion / Panel discussion
18:25-18:30 Closing Remarks by the organizers (Tom Froese, Matthew Egbert, and Xabier Barandiaran)
Tom Froese Matthew Egbert Xabier Barandiaran
Salle Satsuma
Monday, August 8 morning
Program Time
ACCS Tutorial – Artificial Chemical Computing Systems The theme of the ACCS tutorial, Artificial Chemistry (AChem), is a research approach that implements Alife systems by taking inspiration from bio-chemical systems. In a typical AChem study, we model the behavior of biological molecules, but unlike MD (molecular dynamics) or systems biology, we minimize the computational cost by dramatically simplifying the model, and try to make self-organizing phenomena happen in a computer. Self-organization is one of the most distinctive features of bio-molecular systems, and with this AChem’s approach, we can take one of the most promising pathways towards the design of computational systems with emergent characteristics. The first half of this tutorial summarizes the
fundamental methodology for the AChem design. After prerequisite conditions for a typical AChem system are presented, the chemical reaction’s rate constants are formulated under the gas and liquid phases. In the latter half of the lecture, we we take three representative AChem systems, CGA, NAC, and ATN, and see how chemical approach makes those systems rich from the computational point of view.
9:00-13:00
Open coffee break 10:00-12:00
[Lobby]
Tentative Contents
• Solution space and biological evolution • Classical and recent AChem models • Chemical reaction velocity theory • Topological analysis and spatial models • Chemical Genetic Algorithms (CGA) • Network Artificial Chemistry (NAC) • Algorithmically Transitive Network (ATN)
Hideaki Suzuki Hiroki Sayama
Salle Nathan
Monday, August 8 morning
Program Time
SynBioCCC – Workshop on the Design, Simulation, Construction and Testing of Synthetic Gene Regulatory Networks for Computation, Control and Communications SynBioCCC will be the first workshop on synthetic biology in ECAL, and it aims at providing a forum for electrical and computer science/engineering researchers, who wish to be introduced to, or present their own work in, synthetic biology. This year, we will place a special focus on the three C’s (Computing, Control & Communications). Topics: Evolutionary & automated design of gene
regulatory networks (GRNs); Modeling & simulation of GRNs; Novel GRN designs for computing, control & communication; Results of implemented GRNs (in wet labs); New paradigms of computing using DNA/RNA, genes and cells.
9:00-13:00
Open coffee break 10:00-12:00
[Lobby]
09:00 - Tutorial
N. Kharma, Synthetic Biology: From Genes to Gene Regulatory Networks
10:00 - Invited Talk
F. Romero, Infobiotics workbench, a computational framework for multicellular synthetic biology models
11:30 - Presentation 1
D. Sanassy, Improving Computational Efficiency in Stochastic Simulation Algorithms for Systems and Synthetic Biology
12:00 - Presentation 2
M. Joachimczak, Evolving gene regulatory networks for control of artificial cells: signal processing, chemotaxis, multicellular development
Presentation 3 by Jake Beal, “TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering” will be exceptionally held on Friday, August 12 at 17:00 in Salle Satsuma.
Nawwaf Kharma Taras Kowaliw
Salle Satsuma
Monday, August 8 afternoon
Program Time
RUTSAC Tutorial – Research Using The Stringmol Artificial Chemistry As in an RNA World, a molecule in the Stringmol Artificial Chemistry can be both genomic and enzymic, facilitating rich interactions between the genome and the phenotype. The hands-on RUTSAC tutorial will equip attendees with the knowledge and experience necessary to set up experiments with the Stringmol Artificial Chemistry. The Stringmol system will be introduced in four stages, corresponding to four interactive tasks. Workshop attendees will participate in these tasks by running the Stringmol code and designing
their own molecules via an interactive website: 1) Bootstrap design: attendees will explore molecule-molecule interactions using the web-based demonstration tool. 2) Molecular diversity in a container: moving from a single molecule design to setting up and running a simulation of a container full of molecules. 3) Container war: observing the mechanisms of container takeovers through mutation and evolution. 4) Fight to the death: finally, the attendees will pit their replicator designs against each other, to see whose molecules will win in the fight to the death for resources!
14:30-18:30
Open coffee break 15:30-17:30
[Lobby]
S. Hickinbotham Ed Clark Adam Nellis
Salle Nathan Salon du Cambodge
Monday, August 8 afternoon
Program Time
SIM-A – System Immunology Models of Autopoesis Artificial life ultimately is the attempt to define the basic characteristics of living systems and emulate them in novel computational and physical means. In the past, the field has been greatly influenced by thinking in the fields of computational neuroscience and molecular evolution. We suggest that the immune system and computational immunology may be better starting points in the attempt to define the core concepts of living systems. Immune dynamics are by nature multiscale, ranging from the molecular through the cellular to the systemic. As such they embody the multicellular cooperativity of second order autopoetic machines, in which local unicellular interactions without specific control lead to
emergent cooperation and individual multicellular integrity. SIM-A is intended to bring together experimentalists and computational immunologists with an emphasis on what would be the best way to create a common language between the different models that have been created over the past years and insure that experimentalists are a driving force of this computational effort.
14:30-18:30
Open coffee break 15:30-17:30
[Lobby]
2:30 – 3:00 pm Hugues Bersini Varela's legacy: From linear to circular causality 3:00 – 3:30 pm Uri Hershberg What do we mean when we say cognitive? Two and a half
steps in the development of a cognitive paradigm to describe immunity
3:30 – 3:40 pm Short break 3:40 – 4:10 pm Véronique Thomas-Vaslin Modeling T lymphocyte population dynamics in mice and
during aging 4:10 – 4:40 pm Sol Efroni Reactive animation in T cell simulation 4:40 – 4:50 pm Short break 4:50 – 5:20 pm David Harel On sensual whiskers 5:20 – 5:50 pm Irun Cohen International lecture 5:50 – 6:00 pm Short break 6:00 – 6:30 pm Moderated panel discussion
Uri Hershberg Sol Efroni
Auditorium Adenauer
Tuesday, August 9 Morning
Program
Time
8:40-9:00 Introduction with René Doursat, Hugues Bersini, Paul Bourgine
9:00-10:00
Keynote 1: James D. Murray Universities of Princeton, Oxford and Washington On the Growth of Brain Tumours Enhancing imaging techniques, highlighting limitations of current imaging, quantifying therapy efficacy and estimating patient life expectancy. The prognosis for patients with high grade brain tumours (gliomas) is grim and the various treatment protocols such as surgery, radiation and chemotherapy cannot effect a cure. I shall
describe, without any technical details, a simple but very practical model which uses patient data and brain scans to quantify the spatio-temporal growth of such brain tumours. Analysis of the model shows how difficult it is to decide on the tumour volume to be treated and shows why such treatments have so little success. The model simulations can estimate life expectancy for individual patients and show how it is possible to use the patient’s past record to predict the efficacy of possible treatments. Recent patient data indicates that calculating such an index of treatment efficacy is indeed a realistic aim. With the increasing discussion about cell phone use and a possible increase in brain tumours, I shall describe how to obtain an estimate for when a brain tumour started following detection.
10:00-10:30
Coffee break & posters [Halls]
10:30-12:10
Track 1A: Evolution & Games Chair: Tom Lenaerts
E. Pestelacci, M. Tomassini & A. Antonioni Coordination games on small-worlds: Artificial agents vs. experiments
F.C. Santos, J.M. Pacheco & B. Skyrms Co-evolution of pre-play signaling and cooperation
J.M. Pacheco, F.C. Santos, M.O. Souza & B. Skyrms Evolutionary dynamics of collective action
P. Mariano & L. Correia Evolution of partner selection
Auditorium CFB
Tuesday, August 9 Morning
Program
Time
10:30-12:10
Track 1B: Autopoietic Systems Chair: Barry McMullin
J. Soto-Andrade, S. Jaramillo, C. Gutiérrez & J.C. Letelier Ouroboros avatars: A mathematical exploration of self-reference and metabolic closure
D.A. Contreras, U. Pereira, V.C. Hernandez, B. Reynaert & J.C. Letelier A loop conjecture for metabolic closure
A. Filisetti, A. Graudenzi, R. Serra, M. Villani, D. De Lucrezia & I. Poli The role of energy in a stochastic model of the emergence of autocatalytic sets
N. Nanas Autonomous learning in an information stream through autopoiesis
Auditorium Adenauer
Tuesday, August 9 Afternoon
Program
Time
13:40-15:20
Track 2A: Language Evolution Chair: Luc Steels
L. McCrohon & O. Witkowski Devil in the details: Analysis of a coevolutionary model of language evolution via relaxation of selection
J. Arranz, J. Noble & E. Silverman The origins of communication revisited
R. Uno, K. Suzuki & T. Ikegami An interactive wall game as an evolution of proto language
M. Spranger Recruitment, selection and alignment of spatial language strategies
15:20-15:50 Coffee break & posters [Halls]
15:50-16:20 Poster pitch 1
16:20-17:20
Keynote 2: Ricard Solé Universitat Pompeu Fabra, Barcelona Synthetic biocomputation: the possible and the actual Computation is defining trait of biological systems and a broad framework that captures the complex adaptive nature of molecules, cells and organisms. Computation is also at the core of the genotype-phenotype mapping, since it provides a natural framework to define function in a self-consistent way. The study of existing biological systems (from signalling cascades to ant colonies or brains) as well
as the evolution of synthetic in silico networks performing computations reveals a number of nontrivial patterns of organization, sometimes in clear conflict with standard view of engineering or optimization. In spite of our increasing knowledge, there is a lack of a theoretical framework where computation and its possible forms is integrated within a general picture. Synthetic biology provides a new avenue where engineered molecular circuits can be implemented to perform non-standard computations. Here we review recent advances in the domain of multicellular synthetic computing and suggest a potential morphospace of computational systems including both standard and non-standard approximations.
17:30-18:00 Poster pitch 2
Auditorium CFB
Tuesday, August 9 Afternoon
Program
Time
13:40-15:20
Track 2B: Selection Dynamics Chair: Richard Watson
J. Clune, D. Misevic, C. Ofria, R. Lenski, S. Elena & R. Sanjuan Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes
H. Williams, R. Boyle & T. Lenton Spatial structure creates community-level selection for nutrient recycling
S. Powers, C. Heys & R. Watson How to measure group selection in real-world populations
X. Wu & W. Banzhaf Evolutionary transition through a new multilevel selection model
Auditorium Adenauer
Wednesday, August 10 Morning
Program
Time
9:00-10:00
Keynote 3: David Harel Weizmann Institute of Science Can we Computerize an Elephant? The talk shows how techniques from computer science and software engineering can be applied beneficially to research in the life sciences. We discuss the idea of comprehensive and realistic modeling of biological systems, where we try to understand and analyze an entire system in detail, utilizing in the modeling effort all
that is known about it. I will address the motivation for such modeling and the philosophy underlying the techniques for carrying it out, as well as the crucial question of when such models are to be deemed valid, or complete. The examples will be from among the biological modeling efforts my group has been involved in: T cell development, lymph node behavior, organogenesis of the pancreas, and fate determination in the reproductive system of the C. elegans nematode worm. The ultimate long-term “grand challenge” is to produce an interactive, dynamic, computerized model of an entire multi-cellular organism, such as the C. elegans, which is complex, but well-defined in terms of anatomy and genetics.
10:00-10:30
Coffee break, posters & art [Halls]
10:30-12:10
Track 3A: Swarms Chair: Marco Tomassini
H. Hamann, T. Schmickl & K. Crailsheim Explaining emergent behavior in a swarm system based on an inversion of the fluctuation theorem
A. Stranieri, E. Ferrante, A.E. Turgut, V. Trianni, C. Pinciroli, M. Birattari & M. Dorigo Self-organized flocking with an heterogeneous mobile robot swarm
J.-M. Montanier, & N. Bredeche Surviving the tragedy of the commons: Emergence of altruism in a population of evolving autonomous agents
A. Rodriguez & J. Gomez Programs self-healing over a termites simulator based on language games and evolutionary computing
Auditorium CFB
Wednesday, August 10 Morning
Program
Time
10:30-12:10
Track 3B: Cellular & Biochemical Networks Chair: Christoph Flamm
B. McMullin & J. Decraene Evolution of self-maintaining cellular information processing networks
J. Payne & J. Moore Robustness, evolvability, and accessibility in the signal-integration space of gene regulatory circuits
S. Khor Why aren’t protein residue networks smaller worlds
Q. Pan, C. Darabos, A. Tyler, J. Moore & J. Payne The influence of whole genome duplication and subsequent diversification on environmental robustness and evolutionary innovation in gene regulatory networks
Auditorium Adenauer
Wednesday, August 10 Afternoon
Program Time
13:40-15:20
Track 4A: Towards Artificial Agency and Cognition Chair: Inman Harvey
G. Martius & J.M. Herrmann Tipping the scales: Guidance and intrinsically motivated behaviour
M. Egbert & X.E. Barandiaran Quantifying normative behaviour and precariousness in adaptive agency
A. Ghoneim, D. Essam and H. Abbass On computations and strategies for real and artificial systems
F. Mokom & Z. Kobti A cultural evolutionary model for artifact capabilities
15:20-15:50 Coffee break, posters & arts [Halls]
15:50-17:30
Track 5A: Agents: Mind, motion and evolution Chair: Mark Bedau
M. Schilling Learning by seeing: Associative learning of visual features through mental simulation of observed action
D. Misevic, C. Ofria & R.E. Lenski Digital sex: Causes and consequences
A. Watkins, J. Noble & C.P. Doncaster An agent-based model of jaguar movement through conservation corridors
N. Tomko, I. Harvey, A. Philippides & N. Virgo Many hands make light work: group evolution and the emergent division of labour
17:30-18:00 Coffee break, posters & arts [Halls]
18:00-20:00
Pioneers discussion
Mark Bedau Takashi Ikegami Barry McMullin Norman Packard Steen Rasmussen Luc Steels Susan Stepney
Back to the Origins of Alife
In addition to an exceptional selection of keynote speakers, the ECAL 2011 organizing committee is also thrilled to announce a 2-hour panel discussion involving several internationally renown pioneers of Artificial Life. They will talk about the most impressive achievements of Alife in the past, since inception of the field, and point to what they think are the most promising research directions for the future. Moderator: Hugues Bersini
Auditorium CFB
Wednesday, August 10 Afternoon
Program
Time
13:40-15:20
Track 4B: Morphologies & Development 1 Chair: Peter Dittrich
L. Schramm & B. Sendhoff An animat’s cell doctrine
S. Cussat-Blanc, N. Bredeche, H. Luga, Y. Duthen & M. Schoenauer Artificial gene regulatory networks and spatial computation: A case study
T. Miyake & K. Tominaga Modeling cell division of B. subtilis using dynamic division of reaction spaces in a membrane artificial chemistry
T. Maekawa, O. Ueno, N. Kawai, E. Nishina, M. Honda & T. Oohashi Evolutionary acquisition of genetic program for death
15:20-15:50 Coffee break, posters & arts [Halls]
15:50-17:30
Track 5B: Biochemical Modeling Chair: John McCaskill
P. Kreyssig & P. Dittrich Reaction flow artificial chemistries
N. Virgo, C. Fernando, B. Bigge & P. Husbands The elongation catastrophe in physical self-replicators
T. Veloz, Bryan Reynaert, D. Rojas & P. Dittrich A decomposition theorem in chemical organizations
R. Plasson, K. Montagne, A. Padirac, T. Fujii & Y. Rondelez A DNA toolbox for engineering in vitro life-like behaviors
Auditorium Adenauer
Thursday, August 11 Morning
Program
Time
9:00-10:00
Keynote 4: Eric Wieschaus Princeton University 1995 Nobel Prize in Physiology The mechanics of shape change in the Drosophila embryo With the first three hours of development, the Drosophila embryo establishes a precise pattern of transcription factors that divides the blastoderm into groups of cells destined to form different organs and
tissues in the adult. . . . In my talk I will discuss the relationship between the initial transcription profiles and a novel pulsating reorganization of the Actin/Myosin cytoskeleton in the apical region of cells that will make the ventral furrow. We show that the resultant contractile pulses drive cell shape changes in the entire mesodermal primordium. The individual contractions appear to be unpolarized but they result in polarized wedge-like constrictions because global tension in the sheet is polarized along the AP axis. We analyze the force distributions in the mesodermal primordia using a combination of genetics and RNAi to lower adhesive strengths between cells, and laser dissections to locally disrupt the cytoskeleton.
10:00-10:30
Coffee break, posters & art [Halls]
10:30-12:10
Track 6A: Complexity Chair: Susan Stepney
I. Harvey Opening stable doors: Complexity and stability in nonlinear systems
P. Wills Life requires genetic representation and vice versa: Consequences for Alife
T. Froese, N. Virgo & T. Ikegami Life as a process of open-ended becoming: Analysis of a minimal model
M. Bedau, A. Buchanan, D. Chalmers, C. Cooper Francis, N. Packard & N. Pepper Evidence in the patent record for the evolution of technology using citation and PageRank statistics
Auditorium CFB
Thursday, August 11 Morning
Program
Time
10:30-12:10
Track 6B: Evolutionary Robotics Chair: Jordan Pollack
Y. Sato, H. Iizuka & T. Ikegami An experimental and computational approach to the dynamic body boundary problem
M. Lones, A. Tyrrell, S. Stepney & L. Caves Controlling legged robots with coupled artificial biochemical network
D. Knox & J. Rieffel Scalable co-evolution of soft robot properties and gaits
A. Nellis & S. Stepney Embodied copying for richer evolution
Auditorium Adenauer
Thursday, August 11 Afternoon
Program Time
13:40-15:20
Track 7A: Systems Biology Chair: Luis Rocha
R. Belavkin, A. Channon, E. Aston, J. Aston & C. Knight Theory and practice of optimal mutation rate control in Hamming spaces of DNA sequences
J. Fisher & J. Moore Distinguishing the effects of epistasis and pleiotropy using a variant of the NK model
C. Knibbe, D.P. Parsons & G. Beslon Parsimonious modeling of scaling laws in genomes and transcriptomes
P. Stano, P. Carrara, T. Souza & P.L. Luisi An update on the minimal cell project: From the physics of solute encapsulation to the experimental modeling of cell communities
15:20-15:50 Coffee break, posters & arts [Halls]
15:50-17:30
Track 8A: Morphologies & Development 2 Chair: René Doursat
A. Khuong, G. Theraulaz, C. Jost, A. Perna & J. Gautrais A computational model of ant nest morphogenesis
D. Cockburn & Z. Kobti WASPS: A weight-allocated social pressure system for the emergence of agent specialization
N. Bhalla, P. Bentley, P. Vize & C. Jacob Staging the self-assembly process using morphological information
J. Clune & H. Lipson Evolving three-dimensional objects with a generative encoding inspired by developmental biology
17:30-18:00 Coffee break, posters & arts [Halls]
Auditorium CFB
Thursday, August 11 Afternoon
Program
Time
13:40-15:20
Track 7B: Robot Control Chair: Jozef Kelemen
K. Nakamura, I. Suzuki, M. Yamamoto & M. Furukawa Virtual fluid environment on behavior ability for artificial creature
J.N. Pereira, P. Silva, P.U. Lima & A. Martinoli Formalizing institutions as executable Petri nets for distributed robotic systems
S. Oliveira, L. Nunes & A. Lyhne Christensen An experiment in mixing evolving and preprogrammed robots
E. Matsuda, J. Hubert & T. Ikegami A robotic approach to understand the role of vicarious trial-and-error in a T-maze task
15:20-15:50 Coffee break, posters & arts [Halls]
15:50-17:30
Track 8B: Robotics Chair: Takashi Ikegami
E. Hourdakis & P. Trahanias Computational modeling of online reaching
H. Moriguchi & H. Lipson Learning symbolic forward models for robotic motion planning and control
J. Yosinski, J. Clune, D. Hidalgo, S. Nguyen, J.C. Zagal & H. Lipson Evolving robot gaits in hardware: the HyperNEAT generative encoding vs. parameter optimization
P. Santana, R. Mendonça, L. Correia & J. Barata Swarms for robot vision: The case of adaptive visual trail detection and tracking
Auditorium Adenauer
Thursday, August 11 Evening Program
Time
18:00-19:00
Keynote 5: Jordan Pollack Brandeis University Prospects for machine embryogenesis In Nature, the embryogenesis process proceeds from a single fertilized cell through division, migration, specialization and apoptosis. Although a lot is known about development, we still have a long way to go from theories of pattern formation towards understanding the intelligence within an unsupervised manufacturing
process which robustly assembles complex biological forms. Our approach has been to co-evolve bodies and brains in simulation and then convert them into reality using commercial manufacturing technology. I will review several generations of robots which were automatically designed using co-evolutionary techniques. The goal has been the fully automated design and construction of artificial lifeforms. The first generation was based on genetic programming and a simulation of LEGO rod adhesion. The second generation used direct evolution on a iterative simulation of truss structures and used 3D printing for the output. A third generation was based on generative representations using L-systems.
19:00-20:00
Art Show: Louis Bec Institut Scientifique de Recherche Paranaturaliste Upokrinomenes: a fabulated epistemology Zoosystemician Louis Bec forces us to question the validity of each claim by reformulating and staging scientific discourse. His reasoning possesses all the marks of scientific assertiveness, combining scientific jargon with scholarly neologisms. Questioning life and our inability to understand it through traditional
investigative methods, he founded the field of Upokrinomenology. It is a theory of life using models based on computer science, robotics, video and other interactive devices, where irony holds a significant place. By putting scientific discourse into perspective, he challenges us to investigate, unravel and interpret the propositions that he makes. In this research, scientific discourse becomes poetic and Louis Bec becomes a storyteller. Founder of the Scientific Institute of Paranaturalistic Research, he invites us to discover a life we did not know existed, one that looms at the border between shapes, language and behavior [after C. Beaugrand & A. Charre, Reinventing the museum]. His presentation will be followed by a short film by Agnès Varda featuring Louis Bec.
20:00-20:30
Pre-Banquet Concert: François Pachet Sony Labs, Paris The Continuator Project: playing with virtual musicians François Pachet (guitar player) and Jeff Suzda (professional sax player) will perform a short Jazz concert with their band “Quintet of Two”. They comprise the two human musicians in the group, performing alongside three “software” musicians. The goal of this project is to play “standard” jazz using virtual instruments intimately controlled by the human players. The technologies employed,
developped at Sony CSL, involve Markov chains, constraint programming, signal processing, and a great degree of musical tuning. The performance is still exploratory, but we hope to convey a sense of the direction we are heading to: enhance musical expressivity through controllable machines.
Auditorium Adenauer
Friday, August 12 Morning
Program
Time
9:00-10:00
Keynote 6: Jacques Demongeot Université Joseph Fourier, Grenoble General architecture of a genetic regulation network: Applications to embryologic and immunologic control The general architecture of a genetic regulation network consists of strong connected components of its interaction graph, to which are attached three kinds of sub-structures. (1) A set of up-trees, issued from the sources of the interaction graph of the network, made
either of small RNAs or of genes repressors and/or inductors, self-expressed without any other genes controlling them. (2) A set of circuits in the core (in graph sense) of the strong connected components of the interaction graph. (3) A set of down-trees going to the sinks of the interaction graph, i.e., to genes controlled, but not controlling any other genes. The various state configurations it is possible to observe in the above sub-structures correspond to different dynamical behaviours. We show that these dynamics have in general a small number of attractors, corresponding to the functions of the tissue they represent in the Delbrück’s paradigm. Examples of such dynamics will be given in embryology (feather morphogenesis in chicken, gastrulation and wings morphogenesis in Drosophila) as well as in immunology (rearrangements of the genes of the TCRα receptors in mice)
10:00-10:30
Coffee break, posters & art [Halls]
10:30-12:10
Track 9A: Ecological Modeling Chair: Mario Giacobini
P. Gerlee & T. Lundh Urdar: An artificial ecology platform
R. Gras, A. Golestani, M. Hosseini Sedehi, M. Khater, Y. Majdabadi Farahani, M. Mashayekhi, S. Md Ibne, E. Salehi & R. Scott EcoSim: An individual-based platform for studying evolution
J. Clune, H. Goldsby, C. Ofria & R. Pennock Selective pressures for accurate altruism targeting: Evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory
J. Kim, J. Yun, J. Hong, H. Kwon & J. Chun Ecohydrologic and biogeochemical process networks in forest ecosystems in monsoon East Asia: Identification and interpretation
12:10-13:40 ECAL’13 bid
Auditorium CFB
Friday, August 12 Morning
Program
Time
10:30-12:10
Track 9B: Complex Networks Chair: Andrew Wuensche
E. zu Erbach-Schoenberg, C. McCabe & S. Bullock On the interaction of adaptive timescales on networks
J. Lizier, S. Pritam & M. Prokopenko Computational capabilities of small-world Boolean networks
A. Kolchinsky & L.M. Rocha Prediction and Modularity in Dynamical Systems
R. Watson, R. Mills & C. Buckley Transformations and multi-scale optimisation in biological adaptive networks
Salle Nathan
Friday, August 12 afternoon
Program Time
CS-Sports – Complex Systems in Sports The main topic of CS-Sports is the intersection between complex systems and sports, for instance the application of complex networks to the description and analysis of team sports, and its application to the prediction of team performance and outcome. The workshop is addressed to computer, social and sports scientists, interested in unraveling the dynamics and emergent patterns of games in team sports. A complex systems approach can also be applied to the evolution of robots playing sports such as Robosoccer. The format is preferably peer reviewed papers, but can also include poster sessions and panel discussions. In addition, the organizers may give an introductory talk to present the main topics and current state of the art in this scope; a round table may close the workshop with brainstorming on the topic of how to apply complex systems to sports analysis and prediction.
13:30-17:30
Open coffee break 14:30-16:30
[Lobby]
13:30 - Introduction to the workshop, by Carlos Cotta
13:45 - Presentation of the We-Sport social network, by Marco Ivaldi and Luca Ferreri
14:30 - Break
15:00 - Basketball scoring in NBA games: a example of complexity, by Yves De Saá Guerra, Juan Manuel Martín González, Samuel Sarmiento Montesdeoca, David Rodríguez Ruiz, Nieves Arjonilla López and Juan Manuel García Manso
15:30 - Onset of coherent attitude layers in a population of sports, by Robert Hristovski, Natàlia Balagué, Josep Juaneda and Pablo Vazquez.
16:00 - Selecting Attributes for Sport Forecasting using Formal Concept Analysis, by Gonzalo A. Aranda-Corral, Joaquín Borrego-Díaz and Juan Galán-Páez
16:30 - The physical condition from the perspective of complexity: Application of a physical activity program for Alzheimer's disease, by Yves De Saá Guerra, Juan Manuel Martín González, Samuel Sarmiento Montesdeoca, David Rodríguez Ruiz and Dario Rodriguez
17:00 – FIFA World Cup 2010: A Network Analysis of the Champion Team Play, by Carlos Cotta, Antonio Mora, Celilia Merelo-Molina and Juan J. Merelo
J. Merelo Guervós A. Mora García C. Cotta Porras
Salle Satsuma
Friday, August 12 afternoon
Program Time
DDLab – Exploring Discrete Dynamics with DDLab: From Cellular Automata to Random Networks Discrete dynamical networks (DDN), which include cellular automata (CA) and random Boolean networks (RBN), are at the very core of complexity and emergent self-organisation, and provided the inspiration for the founding ideas of Artificial Life, notably by Chris Langton. Discrete Dynamics Lab (DDLab) is an open-source interactive graphics software able to explore a huge diversity of behaviour, space-time patterns, and basins of attraction representing the convergent flow in state-space. The latest version of DDLab is documented in the book Exploring Discrete Dynamics, which has just been published. The workshop will include a tutorial to demonstrate DDLab and try out your own experiments (please bring your laptop), and an opportunity for a 10mn presentation of your work involving
DDLab. Selected papers will be published in a special issue of the Journal of Cellular Automata (JCA). See www.ddlab.org for the compiled software, source code, and documentation.
13:30-17:00
Open coffee break 14:30-16:30
[Lobby]
13:30 – 14:30 tutorial/demo showing how to use DDLab and its range of functions,
referring to "Exploring Discrete Dynamics" – the DDlab manual, and including the following topics:
– starting DDLab – CA, RBN, DDN and hybrid networks – – value range – network size – neighborhood – – network geometry – wiring – rules and rulemix – – network architecture – network graph – – initial state – space-time patterns, 1d/2d/3d – – basins of attraction and subtrees (running backward) – learning – – presentation options – measures, parameters and data – filing – – attractor jump graph – chain rules and encryption – – classifying CA rule space – vector PostScript graphics – – source code and algorithms – 14:30 – 15:00 questions, discussions, wish-lists 15:00 – 15:30 coffee break 15:30 – 17:00 short presentations, discussions, and hands on experiments with
personal laptops or with the overhead projector laptop
17:00-17:30
SynBioCCC - Workshop on the Design, Simulation, Construction and Testing of Synthetic Gene Regulatory Networks for Computation, Control and Communications
17:00 – Presentation 3 Jake Beal, TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering
Andy Wuensche Andy Adamatzky G. Juárez Martínez
Salon du Cambodge
Friday, August 12 afternoon
Program Time
iBioMath – First International Workshop on Integral Biomathics Are we nearly there yet? (This is a common question asked by small children in the back of the car.) Are the definitions of what is life (Schrödinger, Varela), life itself (Rosen) and more than life itself (Louie) convergent? Did we really expect a discovery such as the arsenic-incorporated Mono lake bacteria to start redefining our concept of life? Are not life forms inevitable in the evolution of the Universe? Where is the boundary between the machine and the organism? Is there such a boundary at all? Are our theories of living
and cognitive systems strong enough? Does our underlying understanding of computation and cognition, of the difference between living, non-living and synthetic systems, of sensing and action suffice for building systems that really can mimic living systems, for building systems that really can cope with the vagaries of real environments, of real sensors, and real actuators that don’t always behave quite as model systems do. Or is there a theoretical (or even not so theoretical) underlying area that is still missing? These are some of the basic questions posed by the emerging discipline of Integral Biomathics we wish to address in iBioMath’11.
13:30-17:30
Open coffee break 14:30-16:30
[Lobby]
13:30 – 13:50: Plamen L. Simeonov (JSRC, Berlin) On Integral Biomathics and the INBIOSA project 13:50 – 14:10: Andrée C. Ehresmann (Université de Picardie Jules Verne, Amiens) A dynamic model for emergence and self-organization in multi-scale
systems 14:10 – 14:30: Tatsuya Nomura (Ryukoku University, Shiga) Category Theoretical Formalization of Autopoiesis from Perspective of
Distinction between Organization and Structure 14:30 – 14.45: Coffee Break 14:45 – 15:05: Ron Cottam, Willy Ranson & Roger Vounckx Trans-temporal Cancerous Life 5.05 – 15:25: Anya Yermakova (Oxford University) Process-based agents 15:25 – 15:45: Coffee break 15.45:16:00: Plamen L. Simeonov Introduction to the discussion 16:00 – 17.30: DISCUSSION
Plamen Simeonov Andrée Ehresmann Leslie Smith
Salon de l’Argentine
Friday, August 12 afternoon
Program Time
INCUP – Information Coding in Unconventional Computing Substrates A conventional computing medium is a cleverly prepared semiconductor structure, where two different potential levels represent the logical TRUE and FALSE states. As it is well known, this approach is highly successful and modern society cannot exist without silicon-based computers. An unconventional computer, whether physical, chemical or a living substrate, solves problems in a natural way, i.e. as the result of the time evolution that proceeds according to the laws of physics. Information coding is the translation of system
state into a string belonging to a formal language. We know many types of computing medium like self-assembling nano-particles, chemical far-from-equilibrium systems, interacting microfluids or living organisms. The application of a photosensitive Belousov-Zhabotinsky reaction for direct image processing is a beautiful example. INCUP aims to bring together physicists, mathematicians, chemists, biologists and engineers to discuss what the optimal representation of information for unconventional computing could be.
13:30-17:30
Open coffee break 14:30-16:30
[Lobby]
13.40 Peter Dittrich, Friedrich Schiller University Jena TBA 14.10 Ivan Erofeev, Moscow Institute of Physics and Technology Digital photo-control of the network of live excitable cells joint work with N. Magome and K. Agladze, Institute for Integrated Cell-Material Sciences, Kyoto University 14.40 Julian Holley, University of the West of England Pathways to learning and adaptation in networks of BZ encapsulated vesicles 15.10 Coffee break and posters 15.40 Gerd Gruenert, Friedrich Schiller University Jena Architectural properties of bioreactor embedded chemical droplet computers 16.00 Jan Szymanski, Institute of Physical Chemistry, Polish Academy of Sciences Chemical pulses in biomimetric droplets 16.20 Konrad Gizynski, Institute of Physical Chemistry, Polish Academy of Sciences Optical control of BZ droplet dynamics 16.30 Jerzy Gorecki, Institute of Physical Chemistry, Polish Academy of Sciences Computer modeling of interacting BZ droplets joint work with Joanna Natalia Gorecka, Institute of Physics, Polish Academy of Sciences 17.00 Open discussion
Jerzy Gorecki Andy Adamatzky
Salon David-Weill
Friday, August 12 afternoon
Program Time
MASmms – Workshop on Multi-Agent Systems in Biology at meso or macroscopic scales Multi-agent modeling concerns the study and conception of systems composed of autonomous entities (the agents) in interaction with each other or with their environment. Multi-Agent Systems (MAS) have the capability to simulate complex phenomena and allow to design their distributed solutions by a collectivity of agents. Many domains in computer science, distributed artificial intelligence, software engineering; but also physics, mathematics and, obviously, biology are concerned by multi-agent modeling at the cellular and subcellular level. MASmms aims at organizing interactions among the members of the recently emerging MAS community that works on biological problems at meso or macroscopic scales using in silico experiments. Another aim of this workshop will be to meet European researchers involved in similar topics.
13:30-17:30
Open coffee break 14:30-16:30
[Lobby]
13h30 Opening talk B. Laforge (LPNHE – UPMC) 13h45 Massive multiagent system for multicellular system using multicore
programming P. Ballet (LISyC – UBO) 14h30 Confronting a spatially explicit population model with biased random
walk to agroecosystems complexity N. Parisey (INRA – le Rheu) 15h15 Coffee Break 15h45 Exploration of Synaptic Functional Connectivity in Human Central
Nervous System using Self-Organizing Agents O. Gurcan, O .Dikenelli, C. Bernon, P. Glize and K.S. Turker (Ege University, IRIT and Koc University) 16h15 A Shape-Based Grained Multi-Agent Model to Simulate Electron
Transfer F. Vallee and M. Beurton-Aimar (LaBRI - UBdx) 16h45 GPU implementation of multi-agent system Discussion from experiences of participants – several existing applications
and frameworks in OpenCL will be presented
Pascal Ballet M. Beurton-Aimar Guillaume Hutzler Bertrand Laforge
Salon Gulbenkian
Friday, August 12 afternoon
Program Time
MEW – 3rd Morphogenetic Engineering Workshop On the one hand, phenomena of spontaneous pattern formation are generally random and repetitive, whereas, on the other hand, complicated heterogeneous architectures are the product of human design. Biological organisms are rather unique examples of natural systems that are both self-organized and architectured. Can we export their precise self-formation capabilities to technological systems? To address this issue, MEW 2011 proposes a new field of research called “Morphogenetic Engineering”, which explores the artificial design and implementation of autonomous systems capable of developing complex, heterogeneous morphologies. Particular emphasis is set on the programmability and controllability of self-organization, properties
that are often underappreciated in complex systems science—while, conversely, the benefits of self-organization are often underappreciated in engineering methodologies.
13:30-17:30
Open coffee break 14:30-16:30
[Lobby]
13:30–13:40 - Foreword from the organizers: Rene Doursat — Complex Systems Institute,
Ecole polytechnique, Paris — and Hiroki Sayama — Binghamton University SUNY Morphogenesis in engineering models 13:40–14:10 - Keynote: Jacob Beal — BBN Technologies and CSAIL, MIT, Cambridge
Morphogenesis as a reference architecture for engineered systems (J. Beal, A. Mozeika, J. Lowell & K. Usbeck)
14:10–14:40 - Speaker 2: Wenguo Liu — Bristol Robotics Lab (BRL), University of the West of
England (UWE), Bristol Autonomous docking in a self-assembly robotics system (W. Liu & A.F.T. Winfield)
14:40–15:10 - Speaker 3: Ada Diaconescu — Telecom ParisTech, Paris
Self-growing software from architectural blueprints (A. Diaconescu, B. Debbabi & P. Lalanda)
Models and engineering of morphogenesis 15:30–16:00 - Speaker 4: Borys Wrobel — Institute of Oceanology, Polish Academy of
Sciences, Poznan Robustness to damage in artificial 3-D multicellular development (M. Joachimczak & B. Wrobel)
16:00–16:30 - Speaker 5: Jae Kyun Shin — School of Mechanical Engineering, Yeungnam University, South Korea One-rule firing cellular automata as a bottom-up pattern design system (J.K. Shin)
16:30–17:00 - Speaker 6: Sebastien Mazac — IRIT, Universite de Toulouse L-System driven Morphogenesis (S. Mazac, S. Cussat-Blanc & Y. Duthen)
17:00–17:10 - Speaker 7: Sylvain Cussat-Blanc — IRIT, Universite de Toulouse
An open-source generic rendering tool for developmental models (S. Tournois, S. Cussat-Blanc, J. Pascalie, H. Luga & Yves Duthen)
17:10–17:40 - Panel discussion
René Doursat Hiroki Sayama