Protometabolic pathways: exploring the chemical roots of systems biology [2018-2022]
Identity in Interaction: ontological and normative aspects of biological, cognitive and social individuality [2014-2019]
Autonomy and levels of organization
Extending sensorimotor contigencies to cognition
Towards an embodied science of intersubjectivity
Interaction dynamics and autonomy in social cognition
Autonomy in philosophy of biology and bioethics
Explaining biological organization: between mechanism and autonomy
The concept of autonomy in biomedical research and bioethics
Retecog: Red temática en ciencias cognitivas
Protometabolic pathways: exploring the chemical roots of systems biology
European Research Project — ITN (Marie Curie Innovative Training Network)
Understanding how prebiotic chemistry gave rise to life as we know it represents one of the greatest enduring mysteries. The complete absence of a historical record requires the collaboration of scientists from different disciplines with access to advanced tools in order to make any meaningful progress. Here, we plan to exploit this tremendous challenge to train a new generation of scientists to think big, but also to work methodically and logically alongside colleagues from academia and industry. Eight Early-Stage Researchers (ESRs) will be recruited to work in laboratories with expertise in systems chemistry, synthetic biology, microfluidics, and science philosophy to develop together a reconstituted protometabolism within compartments consisting of coacervates, vesicles, coacervate containing vesicles, and compartments etched into microfluidic chips. The underlying protometabolism will be composed of triose glycolysis and a reverse citric acid cycle and will be regulated by (metallo)peptide catalysts. Importantly, the protometabolism will support the maintenance of the compartment that houses the protocell. The ESRs that primarily focus on the construction of compartments that mimic protocellular structures will gain firsthand experience in how their formulations could be exploited as drug delivery vehicles through secondments at partner organizations. Similarly, the ESRs that develop (metallo)peptide catalysts will apply their newfound skills to the development of drug molecules through a secondment at a company that specializes in metallodrug formulations. Ultimately, by becoming experts in elucidating the chemical underpinnings of all known living cells, the ESRs will be extremely well positioned to enter a wide variety of research fields from synthetic biology to medicinal chemistry in either industry or academia.
Academic partners and PIs (PhD supervisors)
Sheref Mansy (CIBIO, University of Trento — Italy)
Dora Tang (Max Planck Institute, Dresden — Germany)
Mathew Powner (University College London — United Kingdom)
Peter Walde (ETH-Zürich — Switzerland)
Kepa Ruiz-Mirazo (University of the Basque Country — Spain)
Other (non-academic) partners
Elvesys Microfluidics (France), Cherry Biotech (France), MetalloFarm (USA),Nanovex Biotechnologies (Spain), Eureka Science Museum (Spain).
A call for PhD candidates will open soon! (end of 2018 — beginning of 2019)
Identity in Interaction: ontological and normative aspects of biological, cognitive and social individuality [MINECO 2014-2019]
This research Project intends to review the concepts of identity and individuality through a methodology that combines the descriptive approach of methodological naturalism with the normative evaluation of the epistemic and practical consequences. The aim is to question the essentialist framework starting from a detailed study of how entities in the biological, cognitive and social domain are generated and transformed. This project continues the previous work of the group, by expanding our line of research, which highlights biological organization, the sciences of complexity, the enactive approach in cognitive science and autonomy and the narrative perspective in bioethics. On the one hand, the task is to develop a descriptive and naturalist account of the ontological dimension, and on the other, to enable a normative evaluation of the adaptive, cognitive, ethical, ecological and educational consequences of the naturalized concepts.
The received concepts of identity and individuality have been criticised for not questioning the individualistic and particulate assumptions permeating research on living beings and their mental and social capacities. Naturalist descriptions of the organization of relevant entities make evident that there are two important challenges to the received concepts: 1) the massive interconnectivity makes it very difficult to establish which are the “primitive” entities or the starting point; 2) the heterogeneity of constituents shows that the conjunction of entities forms complex organizations instead of collections or populations of homogeneous elements.
We anticipate that new models and accounts are required for cases such as: metabolic interactions originating the first cells, lateral genetic transference, the formation of multicellular organisms, participatory sensemaking, social interaction as a source of the autonomy of patients (in the case of somatic disease, discapacity or mental disorder), technologically mediated interactions in social networks.
Thus, we will study more specifically the following examples of integrated heterogeneity in organized entities (via interaction): models of origin of life with different primitives (molecules, connected protometabolisms or sets of protocellular systems), the role of integrative mechanisms in evolution (for example, symbiosis), levels of organization in different evolutionary transitions, the multiplicity of social and embodied aspects of subjective identity, the role of narrative identity for generating autonomy with others.
The normative side of the project, linked to the naturalist one, aims to study how social, ethical, educative, ecological etc. values influence conceptualizations of individuality as well as to consider the normative consequences stemming from it.
In sum, we present an ambitious project, which is completely coherent with previous work of the group, and in accordance to the competences of the research team.
KEYWORDS: Autonomy, biological organization, group identity, enaction, ethics comittee, evolutionary transition, heterogeneity, interactions
Autonomy and levels of organization
This project aims at searching into and solving several conceptual problems that arise when the idea of levels of organization is tried to make compatible with a theoretical perspective based on the concept of autonomy, as applied to the fields of biology, cognitive science and bioethics. In other words, we propose to expand in this direction some of our previously explored lines of work with the central goal of studying the role of this notion of levels of organization in the constitution of a minimal autonomous organization (in the transition from pre-biotic self-organizing phenomena to unicellular organisms), as well as in the evolution towards more complex forms of autonomy (multi-cellular organisms, cognitive and social systems), contrasting our analysis through specific models and applications. Especial emphasis will be put on the relationship that this problem holds with the articulation of explanations in terms of underlying material mechanisms. In particular, the investigation attempts to determine whether the notion of levels of organization is already implicit in the idea of mechanism, as this is usually employed in biology and cognitive sciences, and to what extent a re-elaboration of this concept of mechanism from a non-reductionist perspective is actually required, so as to fit naturally within the framework of a general theory of autonomous systems.
Extending sensorimotor contigencies to cognition
While the majority of current robot architectures is based on a “perception-then-action” control strategy, the eSMCs project adopts a theoretical perspective that turns this classical view upside-down and emphasizes the constitutive role of action for perception. The key concept our project is based on is that of sensorimotor contingencies, that is, law-like relations between actions and associated changes in sensory input. We will advance this concept further and suggest that actions not only play a key role for perception, but also in developing more complex cognitive capabilities. We suggest that extended sensorimotor contingencies (eSMCs) may be exploited for the definition of object concepts and action plans and that their mastery can lead to goal-oriented behaviour. The project pursues the following objectives: We will employ this approach to establish computational models that are suitable as controllers for autonomous robots; we will implement these eSMCs-based models on robotic platforms with different sensor-actuator equipment; we will investigate learning and adaptivity of eSMCs in artificial systems, focussing on sensorimotor interactions, object recognition and action planning; we will investigate and validate the concept of eSMCs in natural cognitive systems, by carrying out behavioural and neurophysiological studies on healthy human subjects; finally, we will test predictions derived from this concept in patients with movement dysfunctions, where ensuing changes in perceptual and cognitive processing will be tested. A set of benchmarks and task scenarios will be developed serving as demonstrators for the enhanced performance of artificial systems based on the eSMCs approach. Moreover, the usefulness of the approach for the development of applications in augmenting human behaviour will be demonstrated.
TESIS: Towards an embodied science of intersubjectivity
TESIS —Towards an Embodied Science of InterSubjectivity — is an integrated Marie-Curie ITN programme to investigate the foundations of human sociality. It brings together the complementary expertise of 13 European research institutes, clinical centres and private enterprises that span the biomedical sciences and the humanities. Thus, TESIS provides critical mass in the fields of philosophy, cognitive neuroscience, developmental psychology, psychiatry and societal outreach.
The network will advance our understanding of human intersubjectivity based on the following research and training objectives:
(1) To investigate the neural underpinnings of affective exchange with others, of shared action spaces and joint object relations, endorsing a novel interactive embodied neuroscience;
(2) To investigate the development of social skills in infants in the context of the awareness of others during interaction, yielding an interactive concept of embodied social cognition;
(3) To investigate the inter-subjective factors affecting psychopathologies, especially schizophrenia, autism and somatoform disorders and to draw implications for treatment;
(4) To investigate in toddlers and young children the understanding of toys, objects and cultural artefacts and the links between materiality and sociality;
(5) To investigate cultural interactive patterns and shared practices such as group learning, playing, teamwork, distributed cognition, creating applied knowledge for education, management, and organizational development.
By integrating state of the art and novel approaches to studying interactive situations, TESIS will significantly extend the individualistic and static paradigm still dominant in social cognition research. The major breakthrough to be expected from TESIS is a comprehensive framework for embodied inter-subjectivity applicable in the biomedical sciences, the humanities, and society in general, showing how we become human by embodied interaction with others from the beginning.
Local members: Ezequiel Di Paolo: Training Manager, Miriam Kyselo: Postdoctoral Fellow, Hanne De Jaegher: Associated Research Fellow
More information: tesisnetwork.wordpress.com
Interaction dynamics and autonomy in social cognition
FP7-PEOPLE-2009-IEF, 253883 Social cognition is concerned with how cognitive agents understand and navigate the social world. Most social cognition research today whether in cognitive science, psychology or neuroscience focuses only on the individual mechanisms needed to figure out others mental states. But this view over-emphasises the individual and gives social dynamics no more than a contextual role. However, there is an alternative: the process of interaction itself may be crucial to social cognition. To articulate this alternative, we need 1. to know whether the interaction process can enable or even constitute social cognition, 2. to know how individuals change through interaction, 3. to re-assess the function of individual mechanisms in the context of interaction. This project proposes an original theoretical framework with direct relevance for empirical work. It uses an operational notion of autonomy developed in the philosophy of biology. The main claim is that social interaction can act as an extended mechanism that modulates and transforms individual cognition, autonomy and agency. This leads to the following proposals: 1. Explanations of social cognition should range from individual-dominant to interaction-dominant ones. 2. We can distinguish between contextual, enabling, and constitutive factors in the role of interaction dynamics for cognition. 3. Intentions are not locked and ready-made inside individuals, but can be modulated and transformed in interactions. 4. Interaction processes can acquire a form of systemic autonomy. 5. There is an interplay between individual (organismic, sensorimotor) and interactional autonomy. 6. Socio-cultural norms need to be negotiated in interaction. 7. Individual neural mechanisms are shaped – literally – by social interactions. In this new model of social cognition, the interaction does proper explanatory work. This has consequences for theory, modelling and experiments, and extends the range of explanations.
Recent related publications: De Jaegher, H., Di Paolo, E. & Gallagher, S. 2010. Does social interaction constitute social cognition? Trends in Cognitive Science, 14(10), 441-447.
More information: hannedejaegher.wordpress.com
Autonomy in philosophy of biology and bioethics (2009-2011)
This joint research project aims to develop the concept of autonomy as a central construct for non-reductionist theoretical approaches, both in philosophy of biology and in bioethics. In the first domain, our purpose is to set up the ground for a contemporary organicism in order to advance in our understanding of living organization at different levels. In the second, we examine a cluster of crucial bioethical issues in biomedical research and philosophy of medicine, all dealing with the respect for autonomy, such as the interpretation of informed consent (IC) or the definition of disease. Both research lines require to explore the notion of autonomy, but hitherto this has been done from radically different perspectives: on the one hand, the naturalist approach developed in theoretical biology (a field in which we have worked for quite a long time now); on the other hand, the normative approach, more usual in practical (moral and political) philosophy, which is especially relevant to bioethics. The basic interest behind this project is to delve into the possible connections between those two perspectives, with a particular focus on the problem of the origin of biological normativity. Thus, whereas the two subprojects (MECAUT & AUTBIO) are rooted in those two traditional perspectives, at the same time they will strive together to shed some light on the question of their mutual relationship.
Explaining biological organization: between mechanicism and autonomy (MECAUT)
This project aims to contribute to the development of a concept of autonomy suitable to be applied to the explanation of biological organization, starting from the hypothesis that autonomy should become a core concept within the new systemic paradigm in biology, far from the reductionist approaches of both molecular biology or evolutionary biology in its strictly adaptationist versions. We thus attempt to build up our own theoretical approach, which should enable us to integrate the knowledge acquired regarding those material mechanisms underlying biological organization (or those evolutionary mechanisms, more complicated and indirect, as natural selection), without having to abandon a more holistic, relational and interactive perspective on those processes that constitute the complexity of the phenomenon of life. Within this general framework (and clearly in continuity with the research work made in the context of the previous project: “Information, Autonomy and Systems. Epistemological and ethics aspects for the elaboration of an organicist view in biology”, HUM2005-02449/FISO), this project proposal poses a series of concrete strategies in order to advance in the elaboration of a more complete theory of autonomy, with which it becomes possible to tackle, in particular, the problem of the origin of normativity in biology. First, we attempt to continue the work on minimal organisms or cellular systems, since this would contribute to clarify some fundamental issues, still open, regarding autonomy and its relation to other key concepts such as function, agency or information. In order to do that, we will make use of a methodology which gives a bigger role to the use of computational tools (specifically, the simulation platform ENVIRONMENT) and the effort of developing theoretical models. A second specific realm of applicability and development of the concept of autonomy that we consider very important to investigate is concerned with those forms of biological organization remarkably more complex, as colonies or multi-cellular organisms, whose functional integration/coordination depends on the fact that the basic subunits they are made of should lose part of their plasticity and autonomy in order to benefit the whole. Besides analyzing the relation among diverse kinds of autonomy that may arise in this more complex context (as the relation between metabolic and cognitive autonomy), there is one aspect that we want to address specifically, since one of the main links with the sub-project with which this one is coordinated hinges on it: the problem of dysfunction, or the relation between autonomy and disease. That is, what happens when the functional coordination of the components of a multi-cellular organism fails and the integrity of the organism is at risk or ends up breaking down? Finally, considering our multidisciplinary methodology of work, involving an ample use of computational simulations, another aspect we would like to analyze in detail from the perspective of autonomy is the natural /artificial dichotomy. This issue is, in fact, very up to date considering the current development of a “synthetic biology”, the new biology of the xxi century, as it is called, that should convey a different way of understanding and explaining living systems, intimately linked to our capacity to simulate or physically reconstruct those systems.
RECENT RELATED PUBLICATIONS: Etxeberria, A. & Moreno, A. 2007. La idea de autonomía en biología. Logos 40: 21-37. Barandiaran, X. & Ruiz-Mirazo, K. (Eds.) 2008. Modelling autonomy: Simulating the essence of life and cognition. Introduction to the special issue. BioSystems 91(2): 295-304. Moreno, A., Etxeberria, A. & Umerez, J. 2008. The autonomy of biological individuals and artificial models. BioSystems 91(2): 309-319. Ruiz-Mirazo, K. & Mavelli, F. 2008. On the way towards ‘basic autonomous agents’: Stochastic simulations of minimal lipid-peptide cells. BioSystems 91(2): 374-387.
The concept of autonomy in biomedical research and bioethics (AUTBIO)
The concept of autonomy is a basic one in moral philosophy since Kant, but developments in biotechnology at the beginning of the 21st century are opening new lines of inquiry in its study and application. Bioethics emerged at the beginning of the 1970s as a defence of the autonomy of patients and research subjects. The institutionalization of bioethics has given more importance and relevance to autonomy, but within this academic field there are great disagreements concerning its nature and implications, both in theory and in practice. The concept of autonomy at stake in bioethics (i.e., healthcare ethics, environmental ethics, and research ethics) reflects different positions concerning the relationship between facts and values in the life sciences. The research project AUTBIO aims to provide a concept of autonomy useful for bioethics and, at the same time, to ground it in well established biological science, including current developments and practices in biomedical research. More specifically, it aims to study whether the protection of autonomy is compromised by the implementation of bioinformatics tools such as biobanks, whose regulation is characterized by its novelty, ambiguity and lack of harmonization at the international level. This sub-project creates a truly multidisciplinary research group, comprised of six PhDs of diverse backgrounds (Philosophy, Biological Sciences, Law, Medicine, and Computer Science) but with research experience in common and previous contributions to this subject from a theoretical perspective. In addition, the sub-project has a practical edge to it, by means of a case-study on the protection of the autonomy of research participants in studies involving biobanks within the Basque Country; in order to accomplish this task, the collaboration of an external partner is secured so as to make possible the transfer of knowledge. The main goals of this research group are to advance both the study of the philosophical aspects of the concept of autonomy, clarifying its relationship with other principles or values in healthcare and environmental ethics, and the study of the social aspects of the concept in biomedical research, focusing on the justification and varieties of informed consent procedures to collect and use biosamples. In order to assess how respect for autonomy is grounded in our country, special attention will be devoted to recent legal developments, such as the Act on Biomedical Research enacted in Spain in 2007. In coordination with its twin project (MECAUT), this subproject also aims to deepen the study of the relationship between autonomy and normativity, a basic issue for any attempt to provide a philosophical foundation for bioethics, most particularly in what respects to the debate between naturalist and normativist approaches to the concept of disease — a contested issue in current philosophy of medicine. To elaborate a phenomenological account of disease might help looking at it as the result of a complex interaction between biological, psychological and social factors. To sum up, AUTBIO aims to open new paths of reflection beyond the mere introduction in bioethics of autonomy as it is understood by other disciplines.
Retecog: Red temática en ciencias cognitivas
Un espacio de intereses compartidos frente al desafío de comprender y modelar la mente -humana, animal, artificial- a partir de un enfoque transdisciplinar (ingeniería, informática, psicología, filosofía y neurociencia), con un carácter científico sólido (experimentación, modelización, formalización, etc.) y con el objetivo de constituir una comunidad de investigadores colaborando en proyectos conjuntos, tanto en el estudio y comprensión de los principios fundamentales de la cognición como en su transformación en “conocimiento operativo” base para el modelado y diseño de tecnologías inteligentes.
Un foro de intercambio de perspectivas y recursos en el estudio y aprendizaje sobre la cognición: análisis conceptual, formalización y desarrollo ingenieril para la comprensión y modelización de sistemas cognitivos así como para el diseño de agentes con capacidades cognitivas.
Un entorno de movilidad e interacción entre los investigadores miembros de la red, que permita tener acceso a herramientas y conocimientos que se están generando en distintas disciplinas interesadas en la comprensión de la mente y la cognición así como la coordinación de diversos proyectos de investigación y la colaboración para el desarrollo de publicaciones, prototipos y experimentos.
IAS-Research members of the project: Xabier Barandiaran, Ezequiel Di Paolo, Alvaro Moreno, Thomas Buhrmann
More information: http://retecog.net