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 (Castellano--Sept.2010)

          CV (English--Sept.2010)

Main research interests

   

    Complex Systems

    Self-organization and self-assembly 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).

Publications (most available in pdf - upon request)

 

    A) ARTICLES IN RESEARCH JOURNALS

   Ruiz-Mirazo, K. & Moreno, A. (2010): Autonomy in evolution: from minimal to complex life. Synthese (Forthcoming). ISI WoK -- JCR 5yearIF: 0,782

  Mavelli, F. & Ruiz-Mirazo, K. (2010): ENVIRONMENT: a computational platform to stochastically simulate reacting and self-reproducing lipid compartments. Physical Biology 7(3) 036002. doi:10.1088/1478-3975/7/3/036002 ISI WoK -- JCR 5yearIF: 3,480

  Ruiz-Mirazo, K., Peretó, J. & Moreno, A. (2010): Defining life or bringing biology to life. Origins of Life and Evolution of the Biosphere 40: 203-213.  ISI WoK -- JCR 5yearIF: 2,028

  Moreno, A. & Ruiz-Mirazo, K. (2009): The problem of the emergence of functional diversity in prebiotic evolution. Biology and Philosophy 24: 585-605.  ISI WoK -- JCR 5yearIF: 1,445

  Etxeberria, A. & Ruiz-Mirazo, K. (2009): The challenging biology of transients. EMBO Reports 10, S33-S36.   ISI WoK -- JCR 5yearIF: 7,519

  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. ISI WoK -- JCR 5yearIF: 1,653

  Ruiz-Mirazo, K., Umerez, J. & Moreno, A. (2008): Enabling conditions for ‘open-ended evolution’.  Biology and Philosophy 23(1): 67-85. ISI WoK -- JCR 5yearIF: 1,445

  Mavelli, F. & Ruiz-Mirazo, K. (2007): Stochastic simulations of minimal self-(re-)producing cellular systems. Philosophical Transactions of the Royal Society of London B 362 (1486): 1789-1802. ISI WoK -- JCR 5yearIF: 6,584

  Ruiz-Mirazo, K. & Moreno, A. (2006) On the origins of information and its relevance for biological complexity. Biological Theory 1(3): 227-229.  (not indexed yet)

  Ruiz-Mirazo, K., Stano, P. & Luisi, P.L. (2006):  Lysozyme effect on oleic acid/oleate vesicles. Journal of Liposome Research 16:143–154. ISI WoK -- JCR 5yearIF: 1,944

  Ruiz-Mirazo, K. & Moreno, A. (2004): Basic autonomy as a fundamental step in the synthesis of life. Artificial Life, 10(3): 235-259.   ISI WoK -- JCR 5yearIF: 2,556

  Ruiz-Mirazo, K., Peretó, J. & Moreno, A. (2004): A universal definition of life: autonomy and open-ended evolution. Origins of Life and Evolution of the Biosphere 34: 323-346.  ISI WoK -- JCR 5yearIF: 2,028 *** This article has been selected for the compilation book: The Nature of Life, M. Bedau & C. Cleland (eds.), Cambridge University Press, 2010.

  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.  (not indexed)

  Ruiz-Mirazo, K. & Moreno, A. (2000): Searching for the roots of autonomy: the natural and artificial paradigms revisited. CC-AI (Communication and Cognition – Artificial Intelligence)  17 (3-4): 209-228. (not indexed)

  Ruiz-Mirazo, K., Etxeberria, K., Moreno, A. & Ibáñez, J. (2000) Organisms and their place in biology. Theory in Biosciences, 119: 43-67.  ISI WoK -- JCR 5yearIF: 1,481

  Moreno, A. & Ruiz-Mirazo, K. (1999): Metabolism and the problem of its universalization. BioSystems 49 (1): 45-61.    ISI WoK -- JCR 5yearIF: 1,653

  Ruiz-Mirazo, K. & Moreno, A. (1998): Autonomy and emergence: how systems become agents through the generation of functional constraints. Acta Polytechnica Scandinavica Ma91: 273-282. (not indexed)

 

  B) ARTICLES IN OTHER JOURNALS -- (SCIENCE POPULARIZATION)

  Ruiz-Mirazo, K. (2009): Un nuovo inizio. Sapere (Ottobre 2009): anno 75 (5): 28-33. http://www.galileonet.it/sapere/editoriale/32/riconquistare-la-scuola

  Ruiz-Mirazo, K. (2003): Biziaren sorrera berriro sortzen? (Re-originating life's origins?) Elhuyar, 191, pp. 22-25.

 

  C) BOOK CHAPTERS

  Ruiz-Mirazo, K.; Piedrafita, G.; Ciriaco, F. & Mavelli, F. (2010): Stochastic simulations of mixed-lipid compartments: from self-assembling vesicles to self-producing protocells. In Arabnia H. R. (Ed.) “Software Tools and Algorithms for Biological Systems” (Book series: Advances in Experimental Medicine & Biology, AEMB). Springer. Forthcoming (accepted for public.).

  Moreno, A., Ruiz-Mirazo, K. & Barandiaran, X. (2009): The impact of the paradigm of complexity on the foundational frameworks of biology and cognitive science. Accepted for publication (Elsevier):  C. Hooker (ed) Complex Systems. Vol X of the D. Gavia, P. Thagard & J. Woods (eds) Handbook of the Philosophy of Science. www.johnwoods.ca/HPS

  Ruiz-Mirazo, K. & Moreno, A. (2009): New century biology could do with a universal definition of life. Accepted for publication in: Information and Living Systems: Essays in Philosophy of Biology, G. Terzis & R. Arp (eds.) MIT Press.

  Moreno, A. & Ruiz-Mirazo, K. (2009):  The informational nature of biological causality. Accepted for publication in: Information and Living Systems: Essays in Philosophy of Biology, G. Terzis & R. Arp (eds.) MIT Press.

  Moreno, A. & Ruiz-Mirazo, K. (2006): The long-term 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).

 

  D) BOOK CHAPTERS (in PROCEEDINGS/REPORTS)

  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 LNCS (Lecture Notes in Computer Science) (in press).

  Mavelli, F., Lerario, M. & Ruiz-Mirazo, K. (2008): ‘ENVIRONMENT’: 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.

  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.). ISBN:9780819467393. Bellingham, Washington.

  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.

  Ruiz-Mirazo, K. & Mavelli, F. (2006): Stochastic Simulations of proto-cellular self-assemling systems. In: Science and Supercomputing in Europe: Report 2006 (Bologna-Cineca), pp.170-179. ISBN: 978-88-86037-19-8

  Ruiz-Mirazo, K. & Moreno, A. (2006) ¿Puede la vida ser definida? In: Martinez Manrique, F. & Paris-Viñé, L. M. (eds) Actas del V Congreso de la Sociedad de Lógica, Metodología y Filosofía de la Ciencia en España. Sider, SC (Granada) pp. 311-313.

  Ruiz-Mirazo, K. (2000): Raíces del concepto de autonomía en biología: una crítica al concepto de autopoiesis. In Mary Sol de Mora, Andoni Ibarra, Eulalia Pérez Sedeño, Isabel Sánchez Balmaseda (eds.), Actas del III Congreso de la Sociedad de Lógica, Metodología y Filosofía de la Ciencia en España, Publicaciones del Departamento de Filosofía de la UPV-EHU, San Sebastián -- Donostia, pp. 609-617.

  Ruiz-Mirazo, K., Moreno, A., Morán, F., Peretó, J. & Merelo, J.J. (1999): Designing a simulation model of a self-maintaining cellular system. In: Floreano, D., Nicoud, J-D Nicoud & Mondada, F. (eds.), Advances in Artificial Life, Proceedings of the 5th European Conference ECAL’99, Berlin, Springer-Verlag, pp. 379-389.

  Ruiz-Mirazo, K., Moreno, A. & Morán, F. (1998) Merging the energetic and the relational-constructive logic of life. In: Adami, C., Belew, R., Kitano, H. & Taylor, C. (eds.), Proceedings of The Sixth International Conference on Artificial Life (ALIFE VI), Cambridge, MA: MIT Bradford Books, pp. 448-451.

 

  E) SHORT ARTICLES/(EXTENDED) ABSTRACTS in PROCEEDINGS

  Ruiz-Mirazo, K. (2010): A systems view on defining the boundaries of the problem of origins of life.  Origins of Life and Evolution of the Biosphere 40(4-5): 495-496. (Abstracts of OQOL’09).

  Piedrafita, G., Olasagasti, F., Ruiz-Mirazo, K., Peretó, J., Moreno, A., Montero, F. & Morán; F.^. (2010): Conceptual bases for the emergence of early protocells. Origins of Life and Evolution of the Biosphere 40(4-5): 445-449. (Abstracts of OQOL’09).

  Ruiz-Mirazo, K., Lerario, M. & Mavelli, F. (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).

  Ruiz-Mirazo, K., Umerez, J. & Moreno, A. (2008): Organizational requirements for open-ended evolution. In S. Bullock, J. Noble, R. A. Watson, and M. A. Bedau (Eds.) Proceedings of the 11th International Conference on Artificial Life, Alife XI, Winchester, UK, MIT Press, Cambridge, MA (p. 58).

  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) Modelling minimal lipid-peptide cells. Origins of Life and Evolution of the Biosphere  37: 433–437.

  Ruiz-Mirazo, K. (2005): Working towards the ‘minimal cell’: a bottom-up proposal. Origins of Life and Evolution of the Biosphere (Abstracts of ISSOL’05) 36, pp. 216-218.

  Ruiz-Mirazo, K., Peretó J. & Moreno, A. (2003): Proposal for a universal definition of life. Origins of Life and Evolution of the Biosphere (Abstracts of ISSOL’02) 33 (3), pp. 282-283.

 

  F) REVIEWS

  Saborido, C., Mossio, M. & Ruiz-Mirazo, K. (2010):  Bridging worlds and concepts: a review of ‘Functions in Biological and Artificial Worlds’ (Edited by Ulrich Krohs and Peter Kroes). Artificial Life (forthcoming).

 

  G) EDITORIAL INTROS (to SPECIAL ISSUES)

  Luisi, P. L. & Ruiz-Mirazo, K. (2010): Open questions on the origins of life: Introduction to the special issue. Origins of Life and Evolution of Biospheres 40(4-5): 353-355.

  Barandiaran, X. & Ruiz-Mirazo, K. (2008): Modelling autonomy: simulating the essence of life and cognition. (Editorial Introduction to the Special Issue). BioSystems 91(2): 295-304.

 

  H) DISSERTATIONS

  Ruiz-Mirazo, K. (2001): Condiciones físicas para la aparición de sistemas autónomos con capacidades evolutivas abiertas. PhD Dissertation. Only available in Spanish, unfortunately. University of the Basque Country (UPV-EHU). Excellent Dissertation Award by the University of the Basque Country.

  Ruiz-Mirazo, K. (1995): World-views while introducing quantum mechanics. Masters Dissertation. Master ESST (European Studies on Society Science and Technology). UPV-EHU & Notre Dame de la Paix (Namur-Belgium) Publishing Services.

 

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
         Some tentative 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