Kepa Ruiz-Mirazo

Presentation

Ramón y Cajal Research Fellow at the University of the Basque Country                                   

(Dept. of Logic and Philosophy of Science / Biophysics Research Unit )                       

                  CV (Oct. 2008)

        CV (Short version -- in English)

Main research interests

   

    Complex Systems

    Self-organization processes

    Biophysics -- Bioenergetics

    Prebiological Membranes

    Minimal Cell Models

    Origins of Life

    Theoretical Biology

    Artificial Life

    Astrobiology

Present lines of research

On the origins and definition of life. Analysis and synthesis of the main conceptual/philosophical aspects of the problem -- In collaboration with Alvaro Moreno and his group.
                1) Major transitions in the process of origins of life: characterization of the hypothetical types of system, material organization and evolutionary dynamics involved.
            2) Function, agency, autonomy, information,...: theoretical interpretation/elaboration of these different concepts, their relationship, as well as their relevance and possible naturalization in the context of those prebiotic transitions.

On protocell dynamics. Development of a stochastic simulation model to study 'in silico' the coupling of self-assembly, transport and reaction processes in the context of very primitive proto-cellular systems -- In collaboration with Fabio Mavelli (University of Bari, Italy).
                1) Reproduction and analysis of real 'in vitro' experiments with fatty acid and/or standard phospholipid vesicles.
                2) Theoretical investigation of diverse minimal cell models (e.g., the 'lipid-peptide' protocell model  -- see refs. below).

On prebiological membranes. Exploration of the conditions (temperature, pH, ionic force,...) for the spontaneous formation and the basic properties (stability, permeability, possible growth and reproduction...) of vesicles made of simpler amphiphilic molecules (fatty acids, alkanes, alcohols, isoprenoids,...) than the standard phospholipids found in actual biomembranes -- In collaboration with Felix Goñi and his group at the Biophysics Research Unit (CSIC--UPV/EHU).

Background

First Degree (5-year degree) in Physics. (Specialization: Solid State Physics.)
University of the Basque Country (UPV/EHU) (1989-94).

Master in “European Studies on Society, Science and Technology” (EEST) by the University of Notre Dame de la Paix in Namur (Belgium) and the UPV/EHU (1994-95).

Ph. D. in Sciences (Complex Systems) by the University of the Basque Country (1996-2001). Ph. D. Program in ‘Complex Systems’: Quality Program MEC: 1995-97. UNESCO-Specialization Code: 720501-720102. Ph. D. dissertation: “Physical conditions for the appearance of autonomous systems with open-ended evolutionary capacities” (supervisor: Alvaro Moreno). Available in Spanish.  Excellent Dissertation Award by the University of the Basque Country.

Lectureship of Physics and Mathematics at the Department of Fundamental Sciences of Mondragon Polytechnic School in MU-Mondragon University. (Sept. 2002 – Feb. 2003 and Sept. 2003 – Feb. 2004)

    Previous research grants/fellowships

Erasmus grant (for ‘post-graduates’) to stay at the University of Notre Dame de la Paix of Namur (Belgium) and carry out the second half (6 months) of the Master in “European Studies on Society, Science and Technology” (March-Sept. 1995).

Pre-doctoral fellowship provided by the University of the Basque Country (UPV-EHU) to carry out my PhD research work (October 1996 - November 2000)

Invited student to the “1998 Complex Systems Summer School”, organized by the Santa Fe Institute (SFI), held at The College of Santa Fe, New Mexico, USA, during the four weeks of June 1998.

Invited researcher for a two-month stay (July-September, 1999) at the University of Newcastle (Australia), to work with the Complex Dynamic Systems Research Group led by Professor Cliff Hooker.

Post-doctoral fellowship provided by the National Institute of Aerospace Technology (INTA) of the Spanish Government to work at the Centre for Astrobiology (CAB) in Madrid (April 2002 - September 2002)

Post-doctoral fellowship provided by the MECD (Spanish Government) to collaborate with Pier Luigi Luisi’s group at ETH-Zürich (Switzerland), studying proto-cellular systems in vitro. (February – September 2003). Continuation in Rome, Italy, with the same research group (Dept. of Biology, Roma Tre University). (January 2004 – March 2005).

        Post-doctoral fellowship provided by the Basque Government to re-join Alvaro Moreno’s research group in Philosophy of Biology. (Oct 2005 – Dec. 2006).

Main publications

 

   RUIZ-MIRAZO, K, MORENO, A., & MORAN, F. (1998): Merging the Energetic and the Relational-Constructive Logic of Life. In Adami, C, Belew; R. Kitano, H. & Taylor, C.(eds) Artificial Life VI, Cambridge MA: MIT Bradford Books, pp. 448-451.

 

   RUIZ-MIRAZO, K & MORENO, A. (1998): Autonomy and emergence: how systems become agents through the generation of functional constraints. Acta Polytechnica Scandinavica Ma91 Emergence, Complexity, Hierarchy, Organization. Special Issue Farre, G.L. & Oksala, T.(eds) The Finnish  Academy of Technology, pp.:273-282.

 

   MORENO, A. & RUIZ-MIRAZO, K. (1999): Metabolism and the problem of its universalization. BioSystems  49 (1): 45-61.

 

   RUIZ-MIRAZO, K. MORENO, A, MORAN. F, PERETO, J & MERELO, J. (1999): Designing a Simulation Model of a Self-Maintaining Cellular System. In Advances in Artificial Life.  D. Floreano, J.Nicoud & F. Mondada (eds.) Berlin Spriger Verlag, pp. 379-388.

 

   RUIZ-MIRAZO, K., ETXEBERRIA, A., MORENO, A., & IBAÑEZ, J. (2000): Organisms and their place in biology. Theory  in Biosciences  119: 43-67.

 

  RUIZ-MIRAZO, K., MORENO, A. (2000): Searching for the roots of autonomy: the natural and artificial paradigms revisited. In CC AI: Comunication and Cognition-Artificial Intelligence, 17(3-4): 209-228.

 

   MORENO, A, RUIZ-MIRAZO, K. (2002): Key issues regarding the origin, nature and evolution of complexity in nature: information as a central concept to understand biological organization. Emergence 4.1/4.2: 63-76.

 

   RUIZ-MIRAZO, K, PERETO, J. & MORENO, A. (2004): A Universal Definition of Life: Autonomy and Open-ended Evolution. Origins of Life and Evolution of the Biosphere 34 (3): 323-346.

 

   RUIZ-MIRAZO, K &  MORENO, A. (2004): Basic Autonomy as a fundamental step in the synthesis of life. Artificial Life  10 (3): 235-259.

 

   MORENO, A. & RUIZ-MIRAZO, K. (2006): The maintenance and open-ended growth of complexity in nature: information as a decoupling mechanism  in the origins of life. In Capra F, Sotolongo P, Juarrero A. & van Uden J. (eds) Rethinking Complexity ISCE Publisher. (pp. 55-72)

   RUIZ-MIRAZO, K & MORENO, A. (2006):  On the origins of information and its relevance for biological complexity. Biological Theory 1(3): 227-229.

   RUIZ-MIRAZO, K, STANO, P. & LUISI, P.L. (2006): Lysozyme effect on oleic acid/oleate vesicles. Journal of Liposome Research 16(2) 143–154.

   MAVELLI, F. & RUIZ-MIRAZO, K. (2007):  Stochastic simulations of minimal self-reproducing cellular systems. Philosophical Transactions of the Royal Society of London B. 362 (1486): 1789-1802 (Special Issue: ‘Towards the Artificial Cell’).

   RUIZ-MIRAZO, K. & MAVELLI, F. (2007): Modelling minimal lipid-peptide cells. Origins of Life and Evolution of the Biosphere 37: 433-437.

  MAVELLI, F. & RUIZ-MIRAZO, K. (2007):  Bridging the gap between in silico and in vitro approaches to minimal cells. Origins of Life and Evolution of the Biosphere 37: 455-458.

   RUIZ-MIRAZO, K. & MAVELLI, F. (2007): Simulation model for functionalized vesicles: lipid-peptide integration in minimal protocells. In: Advances in Artificial Life (Proceedings of ECAL 2007), Almeida e Costa et al. (eds), pp. 32-41 . Springer, Berlin.

   MAVELLI, F. & RUIZ-MIRAZO, K. (2007):  Stochastic simulation of fatty-acid protocell models. In: Noise and Fluctuations in Biological, Biophysical, and Biomedical Systems. (SPIE Proceedings vol. 6602, pp. 1B1-1B10). Sergey M. Bezkurov (eds.). Bellingham, Washington (USA). ISBN:9780819467393.

   RUIZ-MIRAZO, K., UMEREZ, J. & MORENO, A. (2008): Enabling conditions for ‘open-ended evolution’. Biology and Philosophy 23(1): 67-85.

  BARANDIARAN, X. & RUIZ-MIRAZO, K. (2008): Modelling autonomy: simulating the essence of life and cognition. (Editorial Intro to the Special Issue). BioSystems 91(2): 295-304.

   RUIZ-MIRAZO, K. & MAVELLI, F. (2008): Towards ‘basic autonomy’: stochastic simulations of minimal lipid-peptide cells. BioSystems 91(2): 374-387.

  MAVELLI, F., LERARIO, M. & RUIZ-MIRAZO, K. (2008):  A stochastic simulation platform to Study Protocell Dynamics. In: Proceedings BIOCOMP 2008 (International Conference on Bioinformatics & Computational Biology), H. R. Arabnia et al (eds.), CSREA Press, pp. 934-941.

   ETXEBERRIA, A. & RUIZ-MIRAZO, K. (2009): The challenging biology of transients. EMBO Reports 10: 33-36.

  MAVELLI, F., LERARIO, M. & RUIZ-MIRAZO, K. (2009):  Prebiotically plausible functional compartments: a simulation model to study lipid-peptide protocell dynamics. Origins of Life and Evolution of the Biosphere 39: 326-327 (Abstracts of ISSOL'08).

 MORENO, A. & RUIZ-MIRAZO, K. (2009):  The problem of the emergence of functional diversity in prebiotic evolution. Biology and Philosophy (in press): DOI 10.1007/S10539-009-9178-6.

  PIEDRAFITA, G., MAVELLI, F., MORAN, F. & RUIZ-MIRAZO, K. (2009): On the transition from prebiotic to proto-biological membranes: from 'self-assembly' to 'self-production'. ECAL 2009 Proceedings. Springer (in press).

   RUIZ-MIRAZO, K. & MORENO, A. (2009):  Autonomy as a bridge between the living and cognitive domains. Synthese (forthcoming).

  RUIZ-MIRAZO, K, PERETO, J. & MORENO, A. (2009): Defining life or bringin biology to life. Origins of Life and Evolution of the Biosphere (forthcoming).

Courses

 

   Philosophy of Biology (in Spanish) -- series of interactive lectures for undergraduate students of Biology and Biochemistry (first semester -- last year), UPV/EHU.
                Filosofía de la Biología (Programa y Bibliografía Básica)

    A session on the origins of cellular membranes (Spanish/English) -- as part of the subject 'Molecular and Cellular Biology of Membranes', within the Master in Molecular Biology and Biomedicine (UPV/EHU -- Cantabria University).
       Overall subject program
         This year's slides (of my session)

Supplementary information (for articles)

 

   Piedrafita, G., Mavelli, F., Morán, F. & Ruiz-Mirazo, K. (2009): On the transition from prebiotic to proto-biological membranes: from 'self-assembly' to 'self-production'. ECAL 2009 Proceedings. Springer (accepted for publication).  Supplementary infomation