Current research projects

 

– IAS-Research: Centre for Life, Mind and Society (Basque Government — ‘Consolidated Groups’ — Ref.: IT1228-19 [2019-2021]
– Protometabolic pathways: exploring the chemical roots of systems biology [2018-2022]
– Identity in Interaction: ontological and normative aspects of biological, cognitive and social individuality (Ref.: FFI2014-52173-P) [2014-2019]

 

IAS-Research: Centre for Life, Mind and Society

Funding for our basic research activity (Basque Government).

PI: Kepa Ruiz-Mirazo

 

Protometabolic pathways: exploring the chemical roots of systems biology

European Research Project — ITN (Marie Curie Innovative Training Network)
‘ProtoMet’ [2018-2022]

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)
Joseph Moran (University of Strasbourg — France)
Dora Tang (Max Planck Institute, Dresden — Germany)
Matthew Powner (University College London — United Kingdom)
Peter Walde (ETH-Zürich — Switzerland)
Kepa Ruiz-Mirazo (University of the Basque Country — Spain)

More info: ‘ProtoMet’ web page.

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

PIs: Arantza Etxeberria & Kepa Ruiz-Mirazo