Hi! I am Yogi.
I am a systems scientist, an evolutionary biologist, and a natural philosopher with an extremely transdisciplinary track record. My investigations, first as the head of an empirical lab, later as the director of an institute for the philosophy of biology, then as a freelance investigator, have always focused around a process perspective on the organism and its evolution.
I am interested in fundamental questions such as the limits of (genetic) reductionism, dynamical systems modelling, and mechanistic explanation in biology. My current projects deal with the use of models as epistemic tools, with causality in complex adaptive systems, and with the nature of organismic agency and its role in evolution.
In recent years, I have also developed an interest in promoting open science and in understanding the epistemology of open inquiry and innovation.
Crossing disciplinary boundaries between biology, mathematics, and philosophy is an essential aspect of my work. Teaching and mentoring are my passions. In addition, I gained valuable managerial experience in running an institute of advanced study. I have a talent for facilitating interdisciplinary interactions, and a proven track record for building a supportive, productive, and creative academic environment.
I am a systems scientist, an evolutionary biologist, and a natural philosopher with an extremely transdisciplinary track record. My investigations, first as the head of an empirical lab, later as the director of an institute for the philosophy of biology, then as a freelance investigator, have always focused around a process perspective on the organism and its evolution.
I am interested in fundamental questions such as the limits of (genetic) reductionism, dynamical systems modelling, and mechanistic explanation in biology. My current projects deal with the use of models as epistemic tools, with causality in complex adaptive systems, and with the nature of organismic agency and its role in evolution.
In recent years, I have also developed an interest in promoting open science and in understanding the epistemology of open inquiry and innovation.
Crossing disciplinary boundaries between biology, mathematics, and philosophy is an essential aspect of my work. Teaching and mentoring are my passions. In addition, I gained valuable managerial experience in running an institute of advanced study. I have a talent for facilitating interdisciplinary interactions, and a proven track record for building a supportive, productive, and creative academic environment.
PROFESSIONAL EXPERIENCE:
Freelance Researcher, Philosopher, and Educator (2017–), associated with the Complexity Science Hub (CSH) Vienna.
Scholar (2023–), Ronin Institute.
Project Leader (2022–2025), John Templeton Foundation, Project: "Pushing the Boundaries", Dept of Philosophy, Uni Vienna
Scientific Director (2015–2017), Konrad Lorenz Institute for Evolution & Cognition Research (KLI), Klosterneuburg, Austria.
Group Leader (2008–2015), EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona.
Postdoctoral Associate (2006–2008), University Museum of Zoology, University of Cambridge, UK.
EDUCATION:
PhD, Graduate Program in Genetics (2005), Stony Brook University, NY.
MSc in Holistic Science (2000), Schumacher College, Dartington, Devon.
University Diploma in Biology (1999), Biocenter, University of Basel.
Freelance Researcher, Philosopher, and Educator (2017–), associated with the Complexity Science Hub (CSH) Vienna.
Scholar (2023–), Ronin Institute.
Project Leader (2022–2025), John Templeton Foundation, Project: "Pushing the Boundaries", Dept of Philosophy, Uni Vienna
Scientific Director (2015–2017), Konrad Lorenz Institute for Evolution & Cognition Research (KLI), Klosterneuburg, Austria.
Group Leader (2008–2015), EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona.
Postdoctoral Associate (2006–2008), University Museum of Zoology, University of Cambridge, UK.
EDUCATION:
PhD, Graduate Program in Genetics (2005), Stony Brook University, NY.
MSc in Holistic Science (2000), Schumacher College, Dartington, Devon.
University Diploma in Biology (1999), Biocenter, University of Basel.
AWARDS & FELLOWSHIPS:
D'Alembert Fellow (2020/21), Université Paris-Saclay/Institut d´Études Avancées (IEA) de Paris.
Fellow (2020). Stellenbosch Institute for Advanced Study (STIAS).
Dr. Chopin Visiting Fellowship (2019), Webster Private University, Vienna.
Fellow (2018/19), Centre de Recherches Interdisciplinaires (CRI), Paris.
Visiting Scholar (2017/18), Center for Systems Biology Dresden (CSBD).
Fellow (2014/15), Institute for Advanced Study/Wissenschaftskolleg zu Berlin.
President's Medal (2013), Section: Cell Biology, Society for Experimental Biology (SEB).
D'Alembert Fellow (2020/21), Université Paris-Saclay/Institut d´Études Avancées (IEA) de Paris.
Fellow (2020). Stellenbosch Institute for Advanced Study (STIAS).
Dr. Chopin Visiting Fellowship (2019), Webster Private University, Vienna.
Fellow (2018/19), Centre de Recherches Interdisciplinaires (CRI), Paris.
Visiting Scholar (2017/18), Center for Systems Biology Dresden (CSBD).
Fellow (2014/15), Institute for Advanced Study/Wissenschaftskolleg zu Berlin.
President's Medal (2013), Section: Cell Biology, Society for Experimental Biology (SEB).
SELECTED PUBLICATIONS:
Jaeger J. Ontogenesis, Organization, and Organismal Agency (forthcoming book chapter, preprint).
Jaeger J., Masselot C., Greshake Tzovaras B., Senabre Hidalgo E., Santolini M. An epistemology for democratic citizen science. Roy Soc Open Sci (in review, preprint).
Jaeger J. The Fourth Perspective: evolution and organismal agency (2023). In: Organization in Biology, Mossio M (ed.), Springer, Berlin (preprint).
Roli A, Jaeger J, Kauffman SA. How organisms come to know the world: fundamental limits on artificial general intelligence. Front Ecol Evol 9: 806283 (2022, published online, preprint).
Jaeger J. Dynamical modularity of the genotype-phenotype map (2021). In: Evolutionary Systems Biology: Advances, Questions, and Opportunities, Crombach A (ed.), Springer Nature Switzerland, Cham (preprint).
Jaeger J, Monk N. Dynamical modules in metabolism, cell and developmental biology (2021). J Roy Soc Interface 11: 20210011 (preprint).
DiFrisco J, Jaeger J. Homology of processes: developmental dynamics in comparative biology (2021). J Roy Soc Interface 11: 20210007 (preprint).
DiFrisco J, Jaeger J (2020). Genetic causation in complex regulatory systems: an integrative dynamic perspective. BioEssays 42: 1900226.
Jaeger J, Verd B. Dynamic positional information: patterning mechanism vs. precision in gradient-driven systems (2020). Current Topics in Developmental Biology 137: 219–246.
Anderson G, Verd B & Jaeger J (2020). Drawing to extend Waddington’s Epigenetic Landscape. Leonardo 53: 1–14.
DiFrisco J, Jaeger J (2019). Beyond networks: mechanism and process in evo-devo (2019). Biology & Philosophy 34: 54.
Verd B, Monk N & Jaeger J. Modularity, criticality and evolvability of a developmental gene regulatory network (2019). eLIFE 8: e42832.
Jaeger J. Dynamic structures in evo-devo: from morphogenetic fields to evolving organisms (2019). In: Perspectives on Evolutionary and Developmental Biology: essays for Alessandro Minelli, Fusco G (ed.), Padova Univ Press, Padova, Italy (preprint).
Verd B, Clark E, Wotton KR, Janssens H, Jiménez-Guri E, Crombach A & Jaeger J (2018). A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila. PLOS Biology 16: e2003174.
Jaeger J. Shift happens: the developmental and evolutionary dynamics of the gap gene system (2018). Current Opinion in Systems Biology 11: 65–73.
Verd B, Crombach A & Jaeger J (2017). Dynamic maternal gradients control timing and shift-rates for Drosophila gap gene expression. PLOS Computational Biology 13: e1005285.
Jaeger J. The importance of being dynamic: systems biology beyond the hairball (2017). In: Philosophy of Systems Biology: Perspectives from Philosophers and Scientists, Green S (ed.), Springer, Berlin.
Crombach A, Wotton KR, Jiménez-Guri E & Jaeger J (2016). Gap gene regulatory dynamics evolve along a genotype network. Molecular Biology & Evolution 33: 1293–1307.
Wotton KR, Jiménez-Guri E, Crombach A, Janssens H, Alcaine Colet A, Lemke S, Schmidt-Ott U & Jaeger J (2015). Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita. eLIFE 4: e04785.
Wotton KR, Jiménez-Guri E & Jaeger J (2015). Maternal co-ordinate gene regulation and axis polarity in the scuttle fly Megaselia abdita. PLOS Genetics 11: e1005042.
Jaeger J & Monk N (2015). Everything flows: a process perspective on life. EMBO Reports 16: 1064–7.
Jaeger J & Monk N (2014). Bioattractors: dynamical systems theory and the evolution of regulatory processes. Journal of Physiology 592: 2267–81.
Verd B, Crombach A & Jaeger J (2014). Classification of transient behaviours in a time-dependent toggle switch model. BMC Systems Biology 8: 43.
Becker K, Balsa-Canto E, Cicin-Sain D, Hoermann A, Janssens H, Banga JR, Jaeger J (2013). Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster. PLoS Computational Biology 9: e1003281.
Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J (2013). Comparative transcriptomics of early dipteran development. BMC Genomics 14: 123.
Jaeger J & Monk N (2013). Keeping the gene in its place. In: The Intuitive Way of Knowing: A Tribute to Brian Goodwin, Lambert D & Chetland C (eds), Floris, Edinburgh.
Crombach A, Wotton KR, Cicin-Sain D, Ashyraliyev M & Jaeger J (2012). Efficient reverse-engineering of a developmental gene regulatory network. PLoS Computational Biology 8: e1002589.
Jaeger J & Crombach A (2012). Life’s attractors: understanding developmental systems through reverse engineering and in silico evolution. In: Evolutionary Systems Biology, Soyer O (ed.), Springer, Berlin.
Jaeger J, Irons D & Monk N (2012). The inheritance of process: a dynamical systems approach. Journal of Experimental Zoology (Molecular Development & Evolution) 318B: 591–612.
Jaeger J (2011). The gap gene network. Cellular & Molecular Life Science 68: 243–74
Jaeger J (2009). Modelling the Drosophila embryo. Molecular BioSystems 5: 1549–68.
Jaeger J, Irons D & Monk N (2008). Regulative feedback in pattern formation: towards a general relativistic theory of positional information. Development 135: 3175–83.
Jaeger J & Reinitz J (2006). On the dynamic nature of positional information. BioEssays 28: 1102–11.
Janssens H, Hou S, Jaeger J, Kim A-R, Myasnikova E, Sharp DH & Reinitz J (2006). Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nature Genetics 38: 1159–65.
Perkins TJ, Jaeger J, Reinitz J & Glass L (2006). Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Computational Biology 2: e51.
Jaeger J, Surkova S, Blagov M, Janssens H, Kosman D, Kozlov KN, Manu, Myasnikova E, Vanario-Alonso CE, Samsonova M, Sharp DH & Reinitz J (2004). Dynamic control of positional information in the early Drosophila blastoderm. Nature 430: 368–71.
Jaeger J, Blagov M, Kosman D, Kozlov KN, Manu, Myasnikova E, Surkova S, Vanario-Alonso, CE, Samsonova M, Sharp DH & Reinitz J (2004). Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics
167: 1721–37.
Jaeger J & Goodwin BC (2001). A cellular oscillator model for periodic pattern formation. Journal of Theoretical Biology 213: 171–81.
Jaeger J. Ontogenesis, Organization, and Organismal Agency (forthcoming book chapter, preprint).
Jaeger J., Masselot C., Greshake Tzovaras B., Senabre Hidalgo E., Santolini M. An epistemology for democratic citizen science. Roy Soc Open Sci (in review, preprint).
Jaeger J. The Fourth Perspective: evolution and organismal agency (2023). In: Organization in Biology, Mossio M (ed.), Springer, Berlin (preprint).
Roli A, Jaeger J, Kauffman SA. How organisms come to know the world: fundamental limits on artificial general intelligence. Front Ecol Evol 9: 806283 (2022, published online, preprint).
Jaeger J. Dynamical modularity of the genotype-phenotype map (2021). In: Evolutionary Systems Biology: Advances, Questions, and Opportunities, Crombach A (ed.), Springer Nature Switzerland, Cham (preprint).
Jaeger J, Monk N. Dynamical modules in metabolism, cell and developmental biology (2021). J Roy Soc Interface 11: 20210011 (preprint).
DiFrisco J, Jaeger J. Homology of processes: developmental dynamics in comparative biology (2021). J Roy Soc Interface 11: 20210007 (preprint).
DiFrisco J, Jaeger J (2020). Genetic causation in complex regulatory systems: an integrative dynamic perspective. BioEssays 42: 1900226.
Jaeger J, Verd B. Dynamic positional information: patterning mechanism vs. precision in gradient-driven systems (2020). Current Topics in Developmental Biology 137: 219–246.
Anderson G, Verd B & Jaeger J (2020). Drawing to extend Waddington’s Epigenetic Landscape. Leonardo 53: 1–14.
DiFrisco J, Jaeger J (2019). Beyond networks: mechanism and process in evo-devo (2019). Biology & Philosophy 34: 54.
Verd B, Monk N & Jaeger J. Modularity, criticality and evolvability of a developmental gene regulatory network (2019). eLIFE 8: e42832.
Jaeger J. Dynamic structures in evo-devo: from morphogenetic fields to evolving organisms (2019). In: Perspectives on Evolutionary and Developmental Biology: essays for Alessandro Minelli, Fusco G (ed.), Padova Univ Press, Padova, Italy (preprint).
Verd B, Clark E, Wotton KR, Janssens H, Jiménez-Guri E, Crombach A & Jaeger J (2018). A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila. PLOS Biology 16: e2003174.
Jaeger J. Shift happens: the developmental and evolutionary dynamics of the gap gene system (2018). Current Opinion in Systems Biology 11: 65–73.
Verd B, Crombach A & Jaeger J (2017). Dynamic maternal gradients control timing and shift-rates for Drosophila gap gene expression. PLOS Computational Biology 13: e1005285.
Jaeger J. The importance of being dynamic: systems biology beyond the hairball (2017). In: Philosophy of Systems Biology: Perspectives from Philosophers and Scientists, Green S (ed.), Springer, Berlin.
Crombach A, Wotton KR, Jiménez-Guri E & Jaeger J (2016). Gap gene regulatory dynamics evolve along a genotype network. Molecular Biology & Evolution 33: 1293–1307.
Wotton KR, Jiménez-Guri E, Crombach A, Janssens H, Alcaine Colet A, Lemke S, Schmidt-Ott U & Jaeger J (2015). Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita. eLIFE 4: e04785.
Wotton KR, Jiménez-Guri E & Jaeger J (2015). Maternal co-ordinate gene regulation and axis polarity in the scuttle fly Megaselia abdita. PLOS Genetics 11: e1005042.
Jaeger J & Monk N (2015). Everything flows: a process perspective on life. EMBO Reports 16: 1064–7.
Jaeger J & Monk N (2014). Bioattractors: dynamical systems theory and the evolution of regulatory processes. Journal of Physiology 592: 2267–81.
Verd B, Crombach A & Jaeger J (2014). Classification of transient behaviours in a time-dependent toggle switch model. BMC Systems Biology 8: 43.
Becker K, Balsa-Canto E, Cicin-Sain D, Hoermann A, Janssens H, Banga JR, Jaeger J (2013). Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster. PLoS Computational Biology 9: e1003281.
Jiménez-Guri E, Huerta-Cepas J, Cozzuto L, Wotton KR, Kang H, Himmelbauer H, Roma G, Gabaldón T, Jaeger J (2013). Comparative transcriptomics of early dipteran development. BMC Genomics 14: 123.
Jaeger J & Monk N (2013). Keeping the gene in its place. In: The Intuitive Way of Knowing: A Tribute to Brian Goodwin, Lambert D & Chetland C (eds), Floris, Edinburgh.
Crombach A, Wotton KR, Cicin-Sain D, Ashyraliyev M & Jaeger J (2012). Efficient reverse-engineering of a developmental gene regulatory network. PLoS Computational Biology 8: e1002589.
Jaeger J & Crombach A (2012). Life’s attractors: understanding developmental systems through reverse engineering and in silico evolution. In: Evolutionary Systems Biology, Soyer O (ed.), Springer, Berlin.
Jaeger J, Irons D & Monk N (2012). The inheritance of process: a dynamical systems approach. Journal of Experimental Zoology (Molecular Development & Evolution) 318B: 591–612.
Jaeger J (2011). The gap gene network. Cellular & Molecular Life Science 68: 243–74
Jaeger J (2009). Modelling the Drosophila embryo. Molecular BioSystems 5: 1549–68.
Jaeger J, Irons D & Monk N (2008). Regulative feedback in pattern formation: towards a general relativistic theory of positional information. Development 135: 3175–83.
Jaeger J & Reinitz J (2006). On the dynamic nature of positional information. BioEssays 28: 1102–11.
Janssens H, Hou S, Jaeger J, Kim A-R, Myasnikova E, Sharp DH & Reinitz J (2006). Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nature Genetics 38: 1159–65.
Perkins TJ, Jaeger J, Reinitz J & Glass L (2006). Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Computational Biology 2: e51.
Jaeger J, Surkova S, Blagov M, Janssens H, Kosman D, Kozlov KN, Manu, Myasnikova E, Vanario-Alonso CE, Samsonova M, Sharp DH & Reinitz J (2004). Dynamic control of positional information in the early Drosophila blastoderm. Nature 430: 368–71.
Jaeger J, Blagov M, Kosman D, Kozlov KN, Manu, Myasnikova E, Surkova S, Vanario-Alonso, CE, Samsonova M, Sharp DH & Reinitz J (2004). Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics
167: 1721–37.
Jaeger J & Goodwin BC (2001). A cellular oscillator model for periodic pattern formation. Journal of Theoretical Biology 213: 171–81.
GRANTS/PROJECTS
From Dec 2022 to Aug 2025, I will be leading the project "Pushing the Boundaries: Agency, Evolution, and the Dynamic Emergence of Expanding Possibilities" (with co-leader Tarja Knuuttila), which will be hosted at the Department of Philosophy at the University of Vienna. This project is funded by the John Templeton Foundation (ID: 62581). You can read more about it in this blog post.
I've coordinated an FP7 project called "BioPreDyn: From Data to Models - New Bioinformatics Methods and Tools for Data-Driven, Predictive Dynamic Modelling in Biotechnological Applications" (2011–2015). It turned out to be a great project, but I swear I'll never do anything like this again.
I participated as a partner in a number of other European projects, including two ComplexityNET/ERANet grants that investigated multi-objective optimization (MOPDEV), and heart development in Drosophila (MODHEART), and a recent H2020 project on "Citizen Science for Monitoring Climate Impacts and Achieving Climate Resilience (Crowd4SDG)".
In addition, I managed to somehow secure continuous financial support from the Spanish and/or Catalan governments for my research group in Barcelona in the time right after the 2008 financial crisis, which was a fun time to do science in Spain... No kidding.
From Dec 2022 to Aug 2025, I will be leading the project "Pushing the Boundaries: Agency, Evolution, and the Dynamic Emergence of Expanding Possibilities" (with co-leader Tarja Knuuttila), which will be hosted at the Department of Philosophy at the University of Vienna. This project is funded by the John Templeton Foundation (ID: 62581). You can read more about it in this blog post.
I've coordinated an FP7 project called "BioPreDyn: From Data to Models - New Bioinformatics Methods and Tools for Data-Driven, Predictive Dynamic Modelling in Biotechnological Applications" (2011–2015). It turned out to be a great project, but I swear I'll never do anything like this again.
I participated as a partner in a number of other European projects, including two ComplexityNET/ERANet grants that investigated multi-objective optimization (MOPDEV), and heart development in Drosophila (MODHEART), and a recent H2020 project on "Citizen Science for Monitoring Climate Impacts and Achieving Climate Resilience (Crowd4SDG)".
In addition, I managed to somehow secure continuous financial support from the Spanish and/or Catalan governments for my research group in Barcelona in the time right after the 2008 financial crisis, which was a fun time to do science in Spain... No kidding.
TEACHING/SUPERVISING/MENTORING:
I worked as a substitute science teacher for middle schoolers at the local Galemo Montessori School (Sep – Dec 2022).
Over the last twenty years, I've taught a wide range of mainly graduate-level courses at institutions like Stony Brook University, the University of Cambridge, the Center for Genomic Regulation (CRG) in Barcelona, the École Normale Supérieure (ENS), Oxford Brookes University, the Instituto Gulbenkian de Ciência in Lisbon, the CRI Paris, and (as a recurring guest lecturer/Gastprofessor) at the University of Vienna.
I used to co-organize the Summer School in Systems Biology at the CRG in Barcelona (2011–2014), and I've been the director of the biannual Venice Summer School in Evo-Devo since 2011 (2011, 2013, 2015, 2017, 2019 edition; we're currently preparing the COVID-delayed 2021 edition for August 2022).
Apart from continuing to supervise graduate students across fields from molecular biology to mathematical modelling, philosophy, artificial intelligence, and cognitive science, I have acted and am acting as a mentor to numerous students and researchers who have chosen to take up particularly unusual academic or non-academic career paths.
I worked as a substitute science teacher for middle schoolers at the local Galemo Montessori School (Sep – Dec 2022).
Over the last twenty years, I've taught a wide range of mainly graduate-level courses at institutions like Stony Brook University, the University of Cambridge, the Center for Genomic Regulation (CRG) in Barcelona, the École Normale Supérieure (ENS), Oxford Brookes University, the Instituto Gulbenkian de Ciência in Lisbon, the CRI Paris, and (as a recurring guest lecturer/Gastprofessor) at the University of Vienna.
I used to co-organize the Summer School in Systems Biology at the CRG in Barcelona (2011–2014), and I've been the director of the biannual Venice Summer School in Evo-Devo since 2011 (2011, 2013, 2015, 2017, 2019 edition; we're currently preparing the COVID-delayed 2021 edition for August 2022).
Apart from continuing to supervise graduate students across fields from molecular biology to mathematical modelling, philosophy, artificial intelligence, and cognitive science, I have acted and am acting as a mentor to numerous students and researchers who have chosen to take up particularly unusual academic or non-academic career paths.
OTHER:
I was a founding member and organizer for the Junior European Drosophila Investigators (JEDI).
I am the biology editor of "Philosophy, Theory, and Practice in Biology" (PTPbio), the only open-access journal in the philosophy of biology.
I am a member of the scientific advisory board of the PhD Programme in Theoretical & Evolutionary Biology at Charles University in Prague.
I appear on episode 118 of the "Brain Inspired" podcast, in a wide-ranging interview with Paul Middlebrooks. talking about the limits of dynamical systems theory and mechanistic explanation, about process philosophy and perspectivism, about agency, evolution and AI, as well as the need to go beyond synthetic theories in evolutionary biology. You can access the episode here.
I was a founding member and organizer for the Junior European Drosophila Investigators (JEDI).
I am the biology editor of "Philosophy, Theory, and Practice in Biology" (PTPbio), the only open-access journal in the philosophy of biology.
I am a member of the scientific advisory board of the PhD Programme in Theoretical & Evolutionary Biology at Charles University in Prague.
I appear on episode 118 of the "Brain Inspired" podcast, in a wide-ranging interview with Paul Middlebrooks. talking about the limits of dynamical systems theory and mechanistic explanation, about process philosophy and perspectivism, about agency, evolution and AI, as well as the need to go beyond synthetic theories in evolutionary biology. You can access the episode here.
You can download my full CV here, and find an up-to-date list of publications at my Google Scholar profile.