IAS-Research Talk by Marc Artiga (Universitat de València): “Do Bacteria Really Talk to Each Other?”

Do Bacteria Really Talk to Each Other?

Marc Artiga (Universitat de València)

Tuesday January 14 at  at 11:30 (Centro Carlos Santamaria, B14)


In the last two decades, there has been a growing interest in bacteria and other microorganisms. This research has provided interested insights into the nature of life (Parke, 2013), cooperation (Lyon, 2007), individuality (Clarke, 2016), species (Franklin, 2007) and other issues in philosophy of science (O’Malley, 2014). In this talk, I will focus on the capacity of some bacteria to produce molecules that are usually classified as ‘signals’ and I would like to defend two claims. First of all, I will argue that in this context expressions such as ‘signalling’ should be taken at face value and that certain interactions between bacteria actually qualify as genuine forms of communication. The second goal is to use this case study to revise our general theories of signalling. In particular, I will argue that there are some aspects of bacterial signalling that do not fit the standard model; some features that usually included in the definition of communication are probably not necessary (e.g. response flexibility) and others that are not included are crucial (e.g. being a minimal cause). Finally, I will discuss the relationship between my proposal and other accounts, such as the ‘influence’ approach and the Organizational Approach to Biological Communication (Frick, Bich and Moreno, 2019).

IAS-Research Seminar by Arantza Etxeberria (UPV/EHU): “Revisiting the “organism/environment interaction” category”

Revisiting the “organism/environment interaction” category

Arantza Etxeberria (UPV/EHU)

Tuesday 12 November 2019 at 11:30  (Centro Carlos Santamaria, B14)


The “organism/environment interaction” has been an important category in biomedical sciences since the end of the 19th century. It brings forward the view of the organism as an autonomous biological entity, with an internally controlled and regulated physiology, interacting with an environment providing opportunities and viability constraints for its living activities. It is often remarked that organisms can transform or construct these environments according to their needs (dialectical views of development and evolution; niche construction; technologies), or that they need to accommodate their lives and norms to restricted environments in case of disease. This presentation will introduce work in progress intending to examine and discuss the current scientific role of this category in biomedicine. On the grounds of some conceptual and empirical challenges, proposals tending to privilege deeper interconnectivities will be considered. This research is integrated within the Inter-identity Project (Mineco FFI2014-52173-P Research Project on Identities in interaction).

International Workshop: Conceptual Issues on ‘Life, Mind and Society’ in Dialogue with Alvaro Moreno

Date: 19-20 November 2018

Location: Faculty of Education, Philosophy and Anthropology (Salón de Grados) [Ibaeta Campus, Donostia-San Sebastián, Basque Country, Spain]

Keynote Speakers: William Bechtel (University of California San Diego), James Griesemer (University of California, Davis), Alicia Juarrero (University of Miami), Alvaro Moreno (UPV/EHU), Ana Soto (University of Tufts).

Full Program (pdf)


IAS-Research Talk by Nathaniel Barrett (University of Navarra): “The contrasts of feeling: Toward an integrated theory of affect and consciousness”

Date and time: November 27, Tuesday, 11:30 a.m.

Location: Carlos Santamaría Building, Room B14.

Speaker: Nathaniel Barrett (“Mind-Brain Group,” Institute for Culture and Society, University of Navarra)

Title: The contrasts of feeling: Toward an integrated theory of affect and consciousness


What is affect and how does it relate to other qualities of experience? Affect presents special challenges to explanation that are well known to investigators of pleasure and pain but normally do not enter into philosophical and scientific discussions of consciousness. In this paper I present an attempt to integrate affect and consciousness into a single theory based on the idea that affect is not a specially discriminated quality of experience but rather a function of the way the “feeling self” expands and contracts in relation to the qualities of feeling (Arnold 1960; Frederickson 1995). The key term for the elaboration of this thesis is contrast. Drawing from theories of the nonlinear dynamics of perceptual categorization (e.g. Freeman 1999; Spivey 2007) I propose that perceptual experience is constituted by complex contrasts specified by sensorimotor dynamics within a continually evolving, high-dimensional “contrast space” (cf. the “quality space” in Clark 1993; 2000). For this approach, affect pertains to “implicit” higher-order contrasts that obtain between successive contrast spaces of perceptual dynamics. That is, the affective tone of a perceptual feeling is not determined by perceptual qualities themselves but rather by the way in which these qualities are specified within an evolving contrast space that “expands” and “contracts.” I further suggest that the evolving contrast space of experience can be thought of as a dynamically constituted “feeling self.”


IAS-Research Talk by Denis Walsh (University of Toronto) “Summoning and Sedimentation: Concepts for an agent-centred evolutionary biology”

Date and time: December 11, Tuesday, 11:30 a.m.

Location: Carlos Santamaría Building, Room B14.

Speaker: Denis Walsh (University of Toronto)

Title: Summoning and Sedimentation: Concepts for an agent-centred evolutionary biology


I attempt to motivate an agent-centred ‘contact’ theory of evolution. I draw on debates in the philosophy of mind to illustrate a distinction between ‘foundationalist theories’ and ‘contact theories’. Traditional approaches to thought, perception, knowledge, linguistic meaning, are foundationalist. They start with the separation of an ‘inner’ mental realm from an outer realm, and posit mental ‘givens’ as the foundational elements. Foundationalist theories of the mind have well-known structural problems. Two, in particular, appear to be insuperable: (i) underdetermination (skepticism), and (ii) the missing agent. I argue that gene-centred evolutionary theory is also a foundationalist theory. It too suffers from the same problems. One prominent solution in the philosophy of mind is to adopt a wholly different kind of theory, a contact theory of the agent. I argue that a contact theory can have the same salutary consequences for the understanding of evolution as it does for mental phenomena.

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





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



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



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

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.


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 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.


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

Call for Papers

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

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

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