Kepa Ruiz-Mirazo

Research Interests – Education – Experience – Publications – Further Info

Personal info

Position Full-time Researcher (IDP) at the UPV/EHU
Email kepa.ruiz-mirazo AT ehu DOT es
Website http://www.ias-research.net/people/kepa_ruiz-mirazo/
Phone 943015628 // 946018005
Address Department of Philosophy (UPV/EHU), Avenida de Tolosa 70, 20018 Donostia – San Sebastián  // Biofisika Instittute (CSIC-UPV/EHU), Leioa, Bizkaia.

Summary

Staff researcher of the University of the Basque Country (UPV/EHU), KRM is a physicist who has devoted most of his career to study the interface between chemistry and biology, particularly interested in grounding the transition from one to the other. After a doctorate in the transdisciplinary field of Complex Systems (PhD advisor: Alvaro Moreno) at the UPV/EHU (1996-2001), he carried out a post-doc in supramolecular chemistry, under the supervision of Prof. P. L. Luisi (ETH-Zürich and Universitá Roma Tre, 2003-2005). He then returned to the Basque Country and soon obtained a Ramon y Cajal Research Fellowship (2007-2012) in the area of Humanities to develop his own line of research, combining experimental and theoretical approaches to origins of life (protocellular systems). He was visiting scholar at the Gulbenkian Institute (Portugal) for three months (2011) and is currently on sabbatical at the D. Philosophy of the University of Calgary (Aug 2022 – June 2023). Affiliated also to the Biofisika Institute (CSIC, UPV/EHU), KRM lectures ‘systems biology’ at the Faculty of Science and Technology, ‘philosophy of biology’ (Masters in Philosophy, Science and Values) and an introduction to ‘philosophy of science’ (Masters in Chemistry and Polymers). Member of the Editorial Board of OLEB, he participates in the European ITN project on the origins of metabolism (‘ProtoMet‘) and was involved in two EU COST Actions: CM1304 (Emergence and Evolution of Complex Chemical Systems) and TD 1308 (Origins and Evolution of Life on Earth and in the Universe).

Research interests

  • THEORETICAL BIOLOGY
  • ORIGINS OF LIFE
  • PROTOCELL MODELS
  • SELF-ORGANIZATION AND COMPLEX SYSTEMS
  • SYSTEMS CHEMISTRY
  • SYNTHETIC BIOLOGY
  • EVOLUTIONARY TRANSITIONS
  • AUTONOMY, FUNCTION, AGENCY, REGULATION & INFORMATION IN BIOLOGY

Education

  • PhD in Sciences (Complex Systems)
  • Masters in Society, Science and Technology in Europe (ESST)
  • Five-year-degree in Physics (Solid State Physics)

Experience

  • 2007-2012: ‘Ramón y Cajal’ Research Fellow at UPV/EHU
  • 2005-2006: Post-doc at UPV/EHU (D. Logic & Phil. Science — A. Moreno)
  • 2004-2005: Post-doc at UniRomaTre (D. Biology — Pier Luigi Luisi)
  • 2003 (II): Lectureship at Mondragon University (D. Basic Sciences)
  • 2003 (I): Post-doc at ETH-Zürich (Institute for Polymers — Pier Luigi Luisi)
  • 2002 (II): Lectureship at Mondragon University (D. Basic Sciences)
  • 2002 (I): Post-doc at Centre for Astrobiology (CSIC, INTA)
  • 1996-2001: Pre-doc position at UPV/EHU (D. Logic & Phil. Science)

—  PhD Supervisor: Alvaro Moreno

Publications

A) RESEARCH PAPERS IN JOURNALS

Lauber, N., Flamm, C. & Ruiz-Mirazo, K. (2021): ‘Minimal metabolism’: a key concept to investigate the origins and nature of biological systems. BioEssays 43: 2100103. (https://doi.org/10.1002/bies.202100103)

Amilburu, A., Moreno, A. & Ruiz-Mirazo, K. (2021). Definitions of life as epistemic tools that reflect and foster the advance of biological knowledge. Synthese 198: 10565–10585 (doi: 10.1007/s11229-020-02736-7).

Ruiz-Mirazo, K., Shirt-Ediss, B., Escribano-Cabeza, M. & Moreno, A. (2020): The construction of biological ‘inter-identity’ as the outcome of a complex process of protocell development in prebiotic evolution. Frontiers in Physiology – Systems Biology 11: 530.

Piedrafita, G., Monnard, P.-A., Mavelli, F. & Ruiz-Mirazo, K. (2017): Permeability-driven selection in a semi-empirical protocell model: the roots of prebiotic systems evolution. Scientific Reports 7: 3141.

Ruiz-Mirazo, K., Briones, C. & de la Escosura, A. (2017): Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems. Open Biology 7: 170050.

Acosta-Andrade, C. Artetxe, I., Lete, M.G., Monasterio, B.G., Ruiz-Mirazo, K., Goñi, F. M. & Sánchez-Jiménez, F. (2017): Polyamine-RNA-membrane interactions: from the past to the future in biology. Colloids and Surfaces B: Biointerfaces 155: 173-181.

Murillo-Sánchez, S. & Ruiz-Mirazo, K. (2016): La biología sintética como desafío para comprender la autonomía de lo vivo. Isegoría 55: 551-575.

Murillo-Sánchez, S., Beaufils, D., González Mañas, J. M., Pascal, R. & Ruiz-Mirazo, K. (2016): Fatty acids’ double role in the prebiotic formation of a hydrophobic dipeptide. Chemical Science 7, 3406–3413.

Bich, L., Mossio, M., Ruiz-Mirazo, K. & Moreno, A. (2016): Biological regulation: controlling the system from within. Biology and Philosophy 31: 237-265.

Ruiz-Mirazo, K. & Moreno, A. (2015): Reflexiones sobre el origen de la vida: algo más que un problema ‘evolutivo’. Mètode 87: 55–63.

Ibarguren, M., Bomans, P. H. H., Ruiz-Mirazo, K., Frederik, P. M., Alonso, A. and Goñi, F.M. (2015): Thermally-induced aggregation and fusion of protein-free lipid vesicles. Colloids and Surfaces B: Biointerfaces 136: 545-552.

de la Escosura, A., Briones, C. & Ruiz-Mirazo, K. (2015): The systems perspective at the crossroads between chemistry and biology.  Journal of Theoretical Biology 381: 11-22.

Shirt-Ediss, B., Solé, R.V. & Ruiz-Mirazo, K. (2015): Emergent chemical behavior in variable-volume protocells.  Life 5(1): 181-211.

Balleza, D., García-Arribas, A. B., Sot, J., Ruiz-Mirazo, K. and Goñi, F.M. (2014): Ether- versus ester-linked phospholipid bilayers containing either linear or branched apolar chains. Biophysical Journal 107: 1364-1374.

Shirt-Ediss, B., Ruiz-Mirazo, K., Mavelli, F. & Solé, R.V. (2014): Modelling lipid competition dynamics in heterogeneous protocell populations. Scientific Reports 4: 5675.

Arnellos, A., Moreno, A. & Ruiz-Mirazo, K. (2014): Organizational requirements for multicellular autonomy: insights from a comparative case study. Biology & Philosophy 29: 851-884.

Ruiz-Mirazo, K. & Moreno, A. (2013): Synthetic Biology: challenging life in order to grasp, use or extend it. Biological Theory 8: 376–382.

Mavelli, F. & Ruiz-Mirazo, K. (2013): Theoretical conditions for the stationary reproduction of model protocells. Integrative Biology 5, 324-341.

Piedrafita, G., Ruiz-Mirazo, K., Monnard, P.-A., Cornish-Bowden, A. & Montero, F. (2012): Viability conditions for a compartmentalized proto-metabolic system: a semi-empirical approach. PLoS ONE 7(6): e39480.

Rendón, A., Gil Carton, D., Sot, J., García-Palacios, M., Montes, R., Valle, M., Arrondo, J-L. R., Goñi, F.M. and Ruiz-Mirazo, K. (2012): Model systems of precursor cellular membranes: long-chain alcohols stabilize spontaneously formed oleic acid vesicles. Biophysical Journal 102: 278-286.

Ruiz-Mirazo, K. & Moreno, A. (2012): Autonomy in evolution: from minimal to complex life. Synthese 185 (1): 21-52.

Mavelli, F. & Ruiz-Mirazo, K. (2010): ENVIRONMENT: a computational platform to stochastically simulate reacting and self-reproducing lipid compartments. Physical Biology 7(3) 036002.

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.

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

Etxeberria, A. & Ruiz-Mirazo, K. (2009): The challenging biology of transients. EMBO Reports 10, S33-S36.

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.

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

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.

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 16:143–154.

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

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.  *** This article was 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.

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.

Ruiz-Mirazo, K., Etxeberria, K., Moreno, A. & Ibáñez, J. (2000) Organisms and their place in biology. Theory in Biosciences, 119: 43-67.

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

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.

B) REVIEW ARTICLES

Ruiz-Mirazo, K. (2020): Boundary versus enabling conditions for the origins of life. Physics of Life Reviews 34-35: 96-98.

Ruiz-Mirazo, K. (2019): A plea for hypothesis-driven research in prebiotic systems chemistry. Chem 5: 1920-1922.

Serrano-Luginbühl, S., Ruiz-Mirazo, K., Ostaszewski, R., Gallou, F. & Walde, P. (2018): Soft and dispersed interface-rich aqueous systems that promote and guide chemical reactions. Nature Reviews Chemistry 2: 306-327.

Shirt-Ediss, B., Murillo-Sánchez, S. Ruiz-Mirazo, K. (2017): Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research. Beilstein Journal of Organic Chemistry 13: 1388-1395.

Ruiz-Mirazo, K., Briones, C. & de la Escosura, A. (2014): Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chemical Reviews 114: 285-366.

Saborido, C., Mossio, M. & Ruiz-Mirazo, K. (2010):  In search for conceptual bridges: A review of ‘Functions in Biological and Artificial Worlds’ (Edited by Ulrich Krohs and Peter Kroes). Artificial Life 16: 337-340.

C) BOOK CHAPTERS

Ruiz-Mirazo, K. (2017): Entre las moléculas y la vida: dos metáforas para indagar sobre la emergencia de la organización biológica. En: G. A. Schwartz & V. E. Bermúdez (Eds.) Nodos. Next Door Publishers (pp. 213-217). ISBN 978-84-946669-7-1.

Ruiz-Mirazo, K.; Piedrafita, G.; Ciriaco, F. & Mavelli, F. (2011): 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. (Chapter 70: pp. 689-696). ISBN 978-1-4419-7046-6.

Moreno, A., Ruiz-Mirazo, K. & Barandiaran, X. (2011): The impact of the paradigm of complexity on the foundational frameworks of biology and cognitive science. In: C. Hooker (ed) Complex Systems. Vol X of the D. Gavia, P. Thagard & J. Woods (eds) Handbook of the Philosophy of Science. Elsevier. (pp. 311-334) ISBN: 978-0-444-52076-0.

Ruiz-Mirazo, K. & Moreno, A. (2011): The need for a universal definition of life in 21st century biology. In: Information and Living Systems: Philosophical and Scientific Perspectives, G. Terzis & R. Arp (eds.) MIT Press. (pp.: 3-23). ISBN: 978-0-262-20174-2.

Moreno, A. & Ruiz-Mirazo, K. (2011):  The informational nature of biological causality. In: Information and Living Systems: Philosophical and Scientific Perspectives, G. Terzis & R. Arp (eds.) MIT Press. (pp.: 157-175).  ISBN: 978-0-262-20174-2.

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). ISBN: 0-9766814-6-3.

D) BOOK CHAPTERS in PROCEEDINGS/REPORTS

Shirt-Ediss, B., Solé, R. & Ruiz-Mirazo, K. (2013): Steady state analysis of a vesicle bioreactor with mechanosensitive channels. In: ECAL 2013 Proceedings — Advances in Artificial Life Liò, P., et al. (Eds.), MIT Press, pp. 1162-1169.   ISBN: 9780262317092

Piedrafita, G., Mavelli, F., Morán, F. & Ruiz-Mirazo, K. (2011): On the transition from prebiotic to proto-biological membranes: from ‘self-assembly’ to ‘self-production’. In: ECAL 2009 Proceedings — LNCS 5777 (Lecture Notes in Computer Science), Kampis et al. (Eds.), Springer, pp. 256-264. ISBN: 978-3-642-21283-3.

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. ISBN: 1-60132-053-1.

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. ISBN: 9780819467393.

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. ISBN: 978-3-540-74912-7.

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. ISBN-13: 978-84-9349419-3.

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. ISBN: 84-600-9579-7.

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. ISBN: 3-540-66452-1.

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. ISBN: 0-262-51099-5.

E) EDITORIALS

Ruiz-Mirazo, K. (2013): Definir vida: un ejercicio constructivo (Presentación del dossier Qué es la vida?) Revista de la Sociedad Española de Bioquímica y Biología Molecular (SEBBM) Marzo de 2013. Número 175.

Luisi, P. L. & Ruiz-Mirazo, K. (2010): Open questions on the origins of life: Introduction to the special issue. Origins of Life & 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.

F) ABSTRACTS in PROCEEDINGS

Shirt-Ediss, B., Mavelli, F. & Ruiz-Mirazo (2010): To Burst or Not To Burst: Osmotic Regulation in a Protocell Model Through Precursor Mechano-Sensitive Channels. Extended Abstract in Fellermann et. al. (eds.) Artificial Life XII: Proceedings of the Twelfth Int. Conference on the Synthesis and Simulation of Living Systems, pp.156-157. MIT Press, Cambridge, MA. ISBN: 9780262290753.

Piedrafita, G., Shirt-Ediss, B., Mavelli, F., Monnard, P.-A., & Ruiz-Mirazo (2010): In vitro and in silico complementary studies on the physical properties of prebiotic compartments. In Fellermann et. al. (eds.) Artificial Life XII: Proceedings of the Twelfth Int. Conference on the Synthesis and Simulation of Living Systems, p.162. MIT Press, Cambridge, MA. ISBN: 9780262290753.

Ruiz-Mirazo, K. (2010): A systems view on defining the boundaries of the problem of origins of life.  Origins of Life and Evolution of Biospheres 40(4-5): 495-496. (Abstracts of OQOL’09). ISSN: 0169-6149.

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 Biospheres 40(4-5): 445-449. (Abstracts of OQOL’09). ISSN: 0169-6149.

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). ISSN: 0169-6149.

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). ISBN: 978-0-262-28719-7

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. ISSN: 0169-6149.

Ruiz-Mirazo, K. & Mavelli, F. (2007) Modelling minimal lipid-peptide cells. Origins of Life and Evolution of the Biosphere  37: 433–437.  ISSN: 0169-6149.

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. ISSN: 0169-6149.

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. ISSN: 0169-6149.

G) GENERAL PUBLIC JOURNAL ARTICLES AND ENCYCLOPEDIA ENTRIES

Ruiz-Mirazo, K. (2013): ‘Self-organization’, In: Encyclopedia of Systems Biology (Dubitzky, W.; Wolkenhauer, O.; Yokota, H.; Cho, K.-H.; Eds.). Springer.  Heidelberg, Germany (pp. 1915-1919)   —   http://link.springer.com/referencework/10.1007/978-1-4419-9863-7/page/115

Ruiz-Mirazo, K. & Moreno, A. (2012): Biología sintética: enfrentándose a la vida para comprenderla, utilizarla o extenderla. Pasajes 38: 28-37.

Ruiz-Mirazo, K. & Moreno, A. (2011): ‘Life’, In: Encyclopedia of Astrobiology (Gargaud, M., Amils, R., Cernicharo Quintanilla, J., Cleaves, H.J., Irvine, W.M., Pinti, D., Viso, M., Eds.). Springer.  Heidelberg, Germany. Vol 2, pp. 919-921.

Ruiz-Mirazo, K. (2011): ‘Protocell’, In: Encyclopedia of Astrobiology (Gargaud, M., Amils, R., Cernicharo Quintanilla, J., Cleaves, H.J., Irvine, W.M., Pinti, D., Viso, M., Eds.). Springer. Heidelberg, Germany. Vol 3, pp. 1353-1354.

Ruiz-Mirazo, K. (2009): Un nuovo inizio. Sapere (Ottobre 2009): anno 75 (5): 28-33. ISSN: 0036-4681. http://www.galileonet.it/sapere/editoriale/32/riconquistare-la-scuola

Ruiz-Mirazo, K. (2003): Biziaren sorrera berriro sortzen?  Elhuyar, 191, pp. 22-25

H) DISSERTATIONS

Ruiz-Mirazo, K. (2001): Condiciones físicas para la aparición de sistemas autónomos con capacidades evolutivas abiertas. Tesis Doctoral (PhD dissertation). University of the Basque Country (UPV-EHU).

Ruiz-Mirazo, K. (1995): World-views while introducing quantum mechanics. ESST Masters dissertation. University of the Basque Country (UPV-EHU) & Facultés Universitaires Notre-Dame de la Paix (FUNDP), Namur (Belgium).

Further info

A) KRM_brief_CV_Feb_2021 (CV — abbreviated)

B) CV_krm_English_Feb_2021 (CV — complete version)

Personal profile at Google Scholar