IAS-IHPST Workshop: Boundaries and Levels of Biological Organization (1-2 July 2014)IAS-IHPST Workshop: Boundaries and Levels of Biological Organization (1-2 July 2014)IAS-IHPST Workshop: Boundaries and Levels of Biological Organization (1-2 July 2014)

       

IAS-IHPST WORKSHOP

BOUNDARIES AND LEVELS OF BIOLOGICAL ORGANIZATION

 

The IAS-Research Centre for Life Mind and Society of the University of the Basque Country (EHU/UPV) in collaboration with the Institut d’Histoire et de Philosophie des Sciences et des Techniques (IHPST) of the University Paris 1 Panthéon Sorbonne École Normale Supérieure and CNRS will be hosting an international workshop in Philosophy of Biology.

The workshop will discuss the notion of biological organization from a systemic- perspective. In particular it will focus on its intrinsic hierarchical dimension, and on the role organization plays in the understanding of the transition from pre-biotic to minimal living systems and of more complex forms of biological, cognitive and ecological systems.

 

Dates: July 1-2 2014

Venue: Room B1 – Centro Carlos Santamaria, Universidad del Pais Vasco (EHU/UPV) Campus de Guipuzkoa

Webpage: http://ias-ihpst.ias-research.net/

For more detailed information please contact the organisers Leonardo Bich  and Maël Montevil.

No registration and no fees are needed for attending the workshop. Access is free to everybody in the academic community interested in the topics of the workshop. If you intend to come, please send an email to leonardo[dot]bich[at]ehu[dot]es so that we can facilitate your entrance into the building.

Download the program

Download the abstracts

 

PROGRAM

TUESDAY 1st of JULY  
10:00 – 10:15 Opening
Session 1  
10:15 – 11.15 Hierarchical thinking in organicist and systems biology

Jon Umerez

IAS/Universidad del País Vasco

11:15 – 11:40 Coffee break and collaboration proposals
11:40 – 12:40 Levels, orders and boundaries: a look into the architecture of biological organization

Matteo Mossio

IHPST/Paris 1 Panthéon Sorbonne

12:40 – 14:30 Lunch break
Session 2  
14:30 – 15:30 Protocellular autonomy: getting organized through the construction of open boundaries

Kepa Ruiz Mirazo

IAS/Universidad del País Vasco

15:30 – 15:40 Break
15:40 – 16:40 Heredity and organization

Gaëlle Pontarotti, with commentaries by Francesca Merlin

IHPST/Paris 1 Panthéon Sorbonne

WEDNESDAY 2nd of JULY

 

 
Session 3  
10:00 – 11:00 Teleology as a principle

Nicole Perret

ENS Paris

11:00 – 11:40 Coffee break and collaboration proposals
11:40 – 12:40 Failed intentions, or why adaptive behavior is not sufficient for cognition

Xabier Barandiaran

IAS/Universidad del País Vasco

12:40 – 14:30 Lunch Break
Session 4  
14:30 – 15: 30 On the origin of autonomy: from chemical to biological organisation

Alvaro Moreno

IAS /Universidad del Pais Vasco

15.30 – 15: 40 Break
15.40 – 16 :40 Gaïa: what was it about?

Sebastien Dutreuil

IHPST/Paris 1 Panthéon Sorbonne

16: 40 – 16:50 Closing remarks

 

“The coevolution theory of the origin of the genetic code and an its extension” – IAS-Research Talk by Massimo Di Giulio“The coevolution theory of the origin of the genetic code and an its extension” – IAS-Research Talk by Massimo Di Giulio“The coevolution theory of the origin of the genetic code and an its extension” – IAS-Research Talk by Massimo Di Giulio

Dr.Massimo Di Giulio (Laboratory for Molecular Evolution, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, Napoli, Italy) will be giving an IAS-Research Talk entitled “The coevolution theory of  the origin of the genetic code and an its extension” on Friday, June 28th 2013, at 11.30 at the Carlos Santamaria Building Room B14.

Abstract

Background: The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids. However, this theory does not seem to attribute a role to the biosynthetic relationships between the earliest amino acids that evolved along the pathways of energetic metabolism. As a result, the coevolution theory is unable to clearly define the very earliest phases of genetic code origin. In order to remove this difficulty, I here suggest an extension of the coevolution theory that attributes a crucial role to the first amino acids that evolved along these biosynthetic pathways and to their biosynthetic relationships, even when defined by the non-amino acid molecules that are their precursors.

Results: It is re-observed that the first amino acids to evolve along these biosynthetic pathways are predominantly those codified by codons of the type GNN, and this observation is found to be statistically significant. Furthermore, the close biosynthetic relationships between the sibling amino acids Ala-Ser, Ser-Gly, Asp-Glu, and Ala-Val are not random in the genetic code table and reinforce the hypothesis that the biosynthetic relationships between these six amino acids played a crucial role in defining the very earliest phases of genetic code origin.

Conclusion: All this leads to the hypothesis that there existed a code, GNS, reflecting the biosynthetic relationships between these six amino acids which, as it defines the very earliest phases of genetic code origin, removes the main difficulty of the coevolution theory. Furthermore, it is here discussed how this code might have naturally led to the code codifying only for the domains of the codons of precursor amino acids, as predicted by the coevolution theory. Finally, the hypothesis here suggested also removes other problems of the coevolution theory, such as the existence for certain pairs of amino acids with an unclear biosynthetic relationship between the precursor and product amino acids and the collocation of Ala between the amino acids Val and Leu belonging to the pyruvate biosynthetic family, which the coevolution theory considered as belonging to different biosyntheses.

On the origin of the tRNA molecule – IAS-Research Talk by Massimo Di GiulioOn the origin of the tRNA molecule – IAS-Research Talk by Massimo Di GiulioOn the origin of the tRNA molecule – IAS-Research Talk by Massimo Di Giulio

Dr.Massimo Di Giulio (Laboratory for Molecular Evolution, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, Napoli, Italy) will be giving an IAS-Research Talk entitled “On the rigin of the tRNA molecule” on Tuesday, June 11th 2013, at 11.30 at the Carlos Santamaria Building Room B14.

Abstract

A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure [Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199–214]. A non-monophyletic origin of this molecule has also been theorized [Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403–414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5’ and 3’ halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5’ and 3’ halves. Nature 433, 537–541]. It is shown that these tRNA genes codifying for the 5’ and 3’ halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5’ and 3’ halves, proves a non-monophyletic origin for tRNA genes — as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed.

Dr.Massimo Di Giulio (Laboratory for Molecular Evolution, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, Napoli, Italy) will be giving an IAS-Research Talk entitled “On the rigin of the tRNA Molecule” on Tuesday, June 11th 2013, at 11.30 at the Carlos Santamaria Building Room B14.

Abstract

A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure [Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199–214]. A non-monophyletic origin of this molecule has also been theorized [Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403–414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5’ and 3’ halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5’ and 3’ halves. Nature 433, 537–541]. It is shown that these tRNA genes codifying for the 5’ and 3’ halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5’ and 3’ halves, proves a non-monophyletic origin for tRNA genes — as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed.

Dr.Massimo Di Giulio (Laboratory for Molecular Evolution, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, Napoli, Italy) will be giving an IAS-Research Talk entitled “On the rigin of the tRNA Molecule” on Tuesday, June 11th 2013, at 11.30 at the Carlos Santamaria Building Room B14.

Abstract

A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure [Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199–214]. A non-monophyletic origin of this molecule has also been theorized [Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403–414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5’ and 3’ halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5’ and 3’ halves. Nature 433, 537–541]. It is shown that these tRNA genes codifying for the 5’ and 3’ halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5’ and 3’ halves, proves a non-monophyletic origin for tRNA genes — as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed.

“Synthetic Modeling of Life and Cognition: Open Questions” (SMLC 2013) – 12-14.09.2013, Bergamo, Italy “Synthetic Modeling of Life and Cognition: Open Questions” (SMLC 2013) – 12-14.09.2013, Bergamo, Italy“Synthetic Modeling of Life and Cognition: Open Questions” (SMLC 2013) – 12-14.09.2013, Bergamo, Italy

Call for Papers

Workshop “Synthetic Modeling of Life and Cognition: Open Questions” (SMLC 2013)

12-14th September 2013, University of Bergamo, Italy

Organizers:
Luisa Damiano (University of Bergamo)
Vincent C. Müller (Anatolia College/ACT & University of Oxford)

Website: http://www.pt-ai.org/smlc/2013

In recent decades researchers in various scientific domains have been working intensely on procedures directed to exploring life and cognition in a “synthetic” way, i.e. through modeling in artificial systems. Research on biological and cognitive processes is thus been increasingly based on implementations in “software” (simulations), “hardware” (robots) and “wetware” (chemical systems) used as scientific models of the processes in question. This scientific development is often seen as the emergence of a new general methodology, a “synthetic methodology”, slated to become a dominant force in science. This synthetic methodology poses a challenge for both science itself and the philosophy of science: to define the possibilities, the limits, and the ways of the synthetic modeling of life and cognition, and its relevance for biological, behavioral, cognitive, and social sciences.

The workshop “Synthetic Modeling of Life and Cognition: Open Questions” will tackle this challenge by creating a strongly interdisciplinary forum that can formulate and address these fundamental questions. The workshop brings together pioneers of the synthetic exploration of life and cognition from different scientific domains (computer science, synthetic biology, cognitive, developmental, social robotics…), and invites them to discuss with philosophers and other specialists studying this emerging form of scientific investigation.

Invited speakers

  • Minoru Asada, Osaka University, Japan
  • Angelo Cangelosi, University of Plymouth, UK
  • Luciano Fadiga, University of Ferrara, Italy
  • Stuart Kauffman, University of Calgary, Canada
  • Pier Luigi Luisi, University of Rome Three, Italy
  • Giorgio Metta, Italian Institute of Technology, Italy
  • Giulio Sandini, Italian Institute of Technology, Italy
  • Ricard Solé, Pompeu Fabra University, Spain

Call for Papers

The SMLC 2013 workshop adopts an “Open Questions” format. – This means that the SMLC 2013 call for papers contains a list of questions on the synthetic modeling of life and cognition formulated by members of the Program Committee and other selected specialists on the basis of their expertise and in accordance with the topics of the workshop.

Deadline: 30.06.2013

Complete Call for Papers: http://www.pt-ai.org/smlc/2013/calls

 

Call for Papers

Workshop “Synthetic Modeling of Life and Cognition: Open Questions” (SMLC 2013)

12-14th September 2013, University of Bergamo, Italy

Organizers:

Luisa Damiano (University of Bergamo)

Vincent C. Müller (Anatolia College/ACT & University of Oxford)

WEBSITE: HTTP://WWW.PT-AI.ORG/SMLC/2013

In recent decades researchers in various scientific domains have been working intensely on procedures directed to exploring life and cognition in a “synthetic” way, i.e. through modeling in artificial systems. Research on biological and cognitive processes is thus been increasingly based on implementations in “software” (simulations), “hardware” (robots) and “wetware” (chemical systems) used as scientific models of the processes in question. This scientific development is often seen as the emergence of a new general methodology, a “synthetic methodology”, slated to become a dominant force in science. This synthetic methodology poses a challenge for both science itself and the philosophy of science: to define the possibilities, the limits, and the ways of the synthetic modeling of life and cognition, and its relevance for biological, behavioral, cognitive, and social sciences.

The workshop “Synthetic Modeling of Life and Cognition: Open Questions” will tackle this challenge by creating a strongly interdisciplinary forum that can formulate and address these fundamental questions. The workshop brings together pioneers of the synthetic exploration of life and cognition from different scientific domains (computer science, synthetic biology, cognitive, developmental, social robotics…), and invites them to discuss with philosophers and other specialists studying this emerging form of scientific investigation.

Invited speakers

  • Minoru Asada, Osaka University, Japan
  • Angelo Cangelosi, University of Plymouth, UK
  • Luciano Fadiga, University of Ferrara, Italy
  • Stuart Kauffman, University of Calgary, Canada
  • Pier Luigi Luisi, University of Rome Three, Italy
  • Giorgio Metta, Italian Institute of Technology, Italy
  • Giulio Sandini, Italian Institute of Technology, Italy
  • Ricard Solé, Pompeu Fabra University, Spain

Sponsors

  • Università degli studi di Bergamo, Italy
  • Research Center for Ars Vivendi at Ritsumeikan University, Kyoto, Japan
  • EUCog, European Network for the Advancement of Artificial Cognitive Systems, Interaction and Robotics

 

Call for Papers

The SMLC 2013 workshop adopts an “Open Questions” format. – This means that the SMLC 2013 call for papers contains a list of questions on the synthetic modeling of life and cognition formulated by members of the Program Committee and other selected specialists on the basis of their expertise and in accordance with the topics of the workshop.

The SMLC 2013 workshop questions are cutting-edge open questions defining the agenda of the nascent  interdisciplinary community dedicated to support the reflected and cooperative development of the synthetic modeling of life and cognition.

We welcome abstracts presenting and critically supporting original approaches directed to tackle the issues defined by the questions, and able to stimulate discussions and the emergence of new research lines in the interdisciplinary community created by the workshop.

The list of the SMLC 2013 workshop open questions can be found below. The questions are divided in three groups on the basis of their contents, and each question has an ID number.

We invite specialists from all the different research fields involved in this highly interdisciplinary forum to submit abstracts. In particular we welcome researchers from biology, synthetic biology, computational biology, AL, cognitive sciences, sciences of complex systems, computer sciences, AI, cognitive robotics, developmental robotics, social robotics, philosophy of science, philosophy of mind, philosophy of biology, philosophy of cognitive science, epistemology.

The Program Committee will select the papers to be presented at the workshop as talks through a double-blind peer review process.

We are planning to publish proceedings of the conference with a reputed publisher.

Information on how to prepare your abstract(s):

Each abstract should be anonymised for blind review and should include:

– the ID number and the short version of the question you are addressing;

–  the title of your contribution;

–  a text of up to 1000 words (excl. references) in a PDF;

–  a short abstract of up to 150 words.

Deadline: 30.06.2013

Submission at: https://www.easychair.org/conferences/?conf=smlc2013

Latest Information at http://www.pt-ai.org/smlc/2013/paper-submission

For any further information, please do not hesitate to contact the organizers.

Thank you for contributing to this emergent research area!

SMLC 2013: Open Questions

This is the list of questions on the synthetic modeling of life and cognition, formulated by members of the Program Committee and other selected specialists on the basis of their expertise and in accordance with the topics of the workshop.

a) Synthetic exploration of life 

(1) What are the possibilities and the limits of the synthetic study of the origins of life?

(2) Aiming at a universal biology: what can be the contribution of the synthetic methodology?

(3) Does the synthetic modeling of life need teleology?

(4) How can we test for artificial life?

b) Synthetic exploration of cognition

(5) What can synthetic biology offer to the study of cognition?

(6) What is the role of embodiment in the synthetic exploration of cognition?

(7) How can one build an agent aware of its environment?

(8) How can we model conscious experience?

(9) The extended mind thesis: can it be explored synthetically?

c) Possibilities, limits, ways and impacts of the synthetic modeling of life and cognition:

(10) The “sciences of the artificial” and the “sciences of the natural”: How can we guarantee positive  interaction?

(11) What are the characteristics and roles of synthetic models?

(12) Do different forms of the synthetic modeling have different explanatory powers?

(13) Which levels of abstraction are appropriate in the synthetic modeling of life and cognition?

(14) What are the impacts of the synthetic methodology on the dichotomies ‘science/engineering’, and ‘artificial/natural’?

(15) The synthetic methodology: What are the environmental and social impacts?

 

Explanations of the open questions on

http://www.pt-ai.org/smlc/2013/open-questions

Call for Papers

Workshop “Synthetic Modeling of Life and Cognition: Open Questions” (SMLC 2013)

12-14th September 2013, University of Bergamo, Italy

Organizers:

Luisa Damiano (University of Bergamo)

Vincent C. Müller (Anatolia College/ACT & University of Oxford)

WEBSITE: HTTP://WWW.PT-AI.ORG/SMLC/2013

In recent decades researchers in various scientific domains have been working intensely on procedures directed to exploring life and cognition in a “synthetic” way, i.e. through modeling in artificial systems. Research on biological and cognitive processes is thus been increasingly based on implementations in “software” (simulations), “hardware” (robots) and “wetware” (chemical systems) used as scientific models of the processes in question. This scientific development is often seen as the emergence of a new general methodology, a “synthetic methodology”, slated to become a dominant force in science. This synthetic methodology poses a challenge for both science itself and the philosophy of science: to define the possibilities, the limits, and the ways of the synthetic modeling of life and cognition, and its relevance for biological, behavioral, cognitive, and social sciences.

The workshop “Synthetic Modeling of Life and Cognition: Open Questions” will tackle this challenge by creating a strongly interdisciplinary forum that can formulate and address these fundamental questions. The workshop brings together pioneers of the synthetic exploration of life and cognition from different scientific domains (computer science, synthetic biology, cognitive, developmental, social robotics…), and invites them to discuss with philosophers and other specialists studying this emerging form of scientific investigation.

Invited speakers

  • Minoru Asada, Osaka University, Japan
  • Angelo Cangelosi, University of Plymouth, UK
  • Luciano Fadiga, University of Ferrara, Italy
  • Stuart Kauffman, University of Calgary, Canada
  • Pier Luigi Luisi, University of Rome Three, Italy
  • Giorgio Metta, Italian Institute of Technology, Italy
  • Giulio Sandini, Italian Institute of Technology, Italy
  • Ricard Solé, Pompeu Fabra University, Spain

Sponsors

  • Università degli studi di Bergamo, Italy
  • Research Center for Ars Vivendi at Ritsumeikan University, Kyoto, Japan
  • EUCog, European Network for the Advancement of Artificial Cognitive Systems, Interaction and Robotics

 

Call for Papers

The SMLC 2013 workshop adopts an “Open Questions” format. – This means that the SMLC 2013 call for papers contains a list of questions on the synthetic modeling of life and cognition formulated by members of the Program Committee and other selected specialists on the basis of their expertise and in accordance with the topics of the workshop.

The SMLC 2013 workshop questions are cutting-edge open questions defining the agenda of the nascent  interdisciplinary community dedicated to support the reflected and cooperative development of the synthetic modeling of life and cognition.

We welcome abstracts presenting and critically supporting original approaches directed to tackle the issues defined by the questions, and able to stimulate discussions and the emergence of new research lines in the interdisciplinary community created by the workshop.

The list of the SMLC 2013 workshop open questions can be found below. The questions are divided in three groups on the basis of their contents, and each question has an ID number.

We invite specialists from all the different research fields involved in this highly interdisciplinary forum to submit abstracts. In particular we welcome researchers from biology, synthetic biology, computational biology, AL, cognitive sciences, sciences of complex systems, computer sciences, AI, cognitive robotics, developmental robotics, social robotics, philosophy of science, philosophy of mind, philosophy of biology, philosophy of cognitive science, epistemology.

The Program Committee will select the papers to be presented at the workshop as talks through a double-blind peer review process.

We are planning to publish proceedings of the conference with a reputed publisher.

Information on how to prepare your abstract(s):

Each abstract should be anonymised for blind review and should include:

– the ID number and the short version of the question you are addressing;

–  the title of your contribution;

–  a text of up to 1000 words (excl. references) in a PDF;

–  a short abstract of up to 150 words.

Deadline: 30.06.2013

Submission at: https://www.easychair.org/conferences/?conf=smlc2013

Latest Information at http://www.pt-ai.org/smlc/2013/paper-submission

For any further information, please do not hesitate to contact the organizers.

Thank you for contributing to this emergent research area!

SMLC 2013: Open Questions

This is the list of questions on the synthetic modeling of life and cognition, formulated by members of the Program Committee and other selected specialists on the basis of their expertise and in accordance with the topics of the workshop.

a) Synthetic exploration of life 

(1) What are the possibilities and the limits of the synthetic study of the origins of life?

(2) Aiming at a universal biology: what can be the contribution of the synthetic methodology?

(3) Does the synthetic modeling of life need teleology?

(4) How can we test for artificial life?

b) Synthetic exploration of cognition

(5) What can synthetic biology offer to the study of cognition?

(6) What is the role of embodiment in the synthetic exploration of cognition?

(7) How can one build an agent aware of its environment?

(8) How can we model conscious experience?

(9) The extended mind thesis: can it be explored synthetically?

c) Possibilities, limits, ways and impacts of the synthetic modeling of life and cognition:

(10) The “sciences of the artificial” and the “sciences of the natural”: How can we guarantee positive  interaction?

(11) What are the characteristics and roles of synthetic models?

(12) Do different forms of the synthetic modeling have different explanatory powers?

(13) Which levels of abstraction are appropriate in the synthetic modeling of life and cognition?

(14) What are the impacts of the synthetic methodology on the dichotomies ‘science/engineering’, and ‘artificial/natural’?

(15) The synthetic methodology: What are the environmental and social impacts?

 

Explanations of the open questions on

http://www.pt-ai.org/smlc/2013/open-questions