Bibliography

Sporadically updated list of books, journal articles, and popular article I’ve read as part of my research. It’s important to acknowledge the work of others that is influencing me. It’s also nice to remind myself how much reading I’ve accomplished! 

Academic or topic specific

Allen, Judith E., and Tara E. Sutherland. 2014. “Host Protective Roles of Type 2 Immunity: Parasite Killing and Tissue Repair, Flip Sides of the Same Coin.” Seminars in Immunology 26 (4). Elsevier: 329–40.

Anderson, C. C., and P. Matzinger. 2000. “Danger: The View from the Bottom of the Cliff.” Seminars in Immunology 12 (3): 231–38; discussion 257–344.

Andrews, Paul S., Fiona A. C. Polack, Adam T. Sampson, Susan Stepney, and Jon Timmis. 2010. “The CoSMoS Process Version 0.1: A Process for the Modelling and Simulation of Complex Systems.” University of York Technical Report YCS–2010 453. https://www-users.cs.york.ac.uk/susan/bib/ss/nonstd/tr453.pdf.

Andrews, Paul S., Susan Stepney, Tim Hoverd, Fiona A. C. Polack, Adam T. Sampson, and Jon Timmis. 2011. “CoSMoS Process, Models, and Metamodels.” In Proceedings of the 2011 Workshop on Complex Systems Modelling and Simulation, Paris, France, 1–13.

Arazi, Arnon, William F. Pendergraft 3rd, Ruy M. Ribeiro, Alan S. Perelson, and Nir Hacohen. 2013. “Human Systems Immunology: Hypothesis-Based Modeling and Unbiased Data-Driven Approaches.” Seminars in Immunology 25 (3): 193–200.

Austin, Christopher J. 2016. “The Ontology of Organisms: Mechanistic Modules or Patterned Processes?” Biology & Philosophy, June. Springer Netherlands, 1–24.

Ballenberger, Nikolaus, Anna Lluis, Erika von Mutius, Sabina Illi, and Bianca Schaub. 2012. “Novel Statistical Approaches for Non-Normal Censored Immunological Data: Analysis of Cytokine and Gene Expression Data.” PloS One 7 (10): e46423.

Behn, Ulrich. 2007. “Idiotypic Networks: Toward a Renaissance?” Immunological Reviews 216 (1): 142–52.

Bickhard, Mark H. 2008. “The Interactivist Model.” Synthese 166 (3). Springer Netherlands: 547–91.

Bretscher, P. 2000. “Contemporary Models for Peripheral Tolerance and the Classical ‘Historical Postulate.’” Seminars in Immunology 12 (3): 221–29; discussion 257–344.

Brockman, John. 1996. “Francisco Varela: The Emergent Self.” In Third Culture: Beyond the Scientific Revolution. A Touchstone Book. Simon & Schuster.

Callebaut, Werner. 2012/3. “Scientific Perspectivism: A Philosopher of Science’s Response to the Challenge of Big Data Biology.” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 69–80.

Calvert, Jane. 2012/3. “Systems Biology, Synthetic Biology and Data-Driven Research: A Commentary on Krohs, Callebaut, and O’Malley and Soyer.” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 81–84.

Capra, Fritjof. 2004. The Hidden Connections: A Science for Sustainable Living. Anchor.
Capra, Professor Fritjof, and Pier Luigi Luisi. 2016. The Systems View of Life: A Unifying Vision. 1 edition. Cambridge University Press.

Carneiro, Jorge. 1996. “Towards a Comprehensive View of the Immune System.” Institut Pasteur.

Casadevall, Arturo, and Liise-Anne Pirofski. 2011. “A New Synthesis for Antibody-Mediated Immunity.” Nature Immunology 13 (1): 21–28.

Castellani, Brian, and Frederic William Hafferty. 2009. Sociology and Complexity Science: A New Field of Inquiry. Springer Science & Business Media.

Castiglione, Filippo, Francesco Pappalardo, Carlo Bianca, Giulia Russo, and Santo Motta. 2014. “Modeling Biology Spanning Different Scales: An Open Challenge.” BioMed Research International 2014 (July): 902545.

Cohen, I. R. 2000a. Tending Adam’s Garden: Evolving the Cognitive Immune Self. Elsevier Science.

———. 2000b. “Discrimination and Dialogue in the Immune System.” Seminars in Immunology 12 (3): 215–19; discussion 257–344.

Cohen, Irun R. 2013. “Autoantibody Repertoires, Natural Biomarkers, and System

Controllers.” Trends in Immunology 34 (12). Elsevier Ltd: 620–25.

Cohn, Melvin. 2005. “The Common Sense of the Self-Nonself Discrimination.” Springer Seminars in Immunopathology 27 (1). Springer: 3–17.

———. 2009. “Why Aire? Compensating for Late Bloomers.” European Journal of Immunology 39 (11). Wiley Online Library: 2969–72.

———. 2015. “Analysis of Paris Meeting Redefining the ‘Self’ of the Immune System.” Immunologic Research. Springer US, 106–24.

Coutinho, A. 2000. “Germ-Line Selection Ensures Embryonic Autoreactivity and a Positive Discrimination of Self Mediated by Supraclonal Mechanisms.” Seminars in Immunology 12 (3): 205–13; discussion 257–344.

Coutinho, Antonio. 2002. “Immunology at the Crossroads.” EMBO Reports 3 (11). embor.embopress.org: 1008–11.

Davis, Daniel M. 2013. The Compatibility Gene. Penguin UK.

Dupré, John. 2014. “A Process Ontology for Biology.” The Philosophers’ Magazine 67: 81–88.

Eberl, G., M. Colonna, J. P. Di Santo, and a. N. J. McKenzie. 2015. “Innate Lymphoid Cells: A New Paradigm in Immunology.” Science 348 (6237): aaa6566–aaa6566.
Eichmann, Klaus. 2008. The Network Collective: Rise and Fall of a Scientific Paradigm. Basel, Switzerland: Birkhäuser Verlag AG.

García-Sancho, Miguel. 2012/3. “From the Genetic to the Computer Program: The Historicity of ‘data’ and ‘computation’ in the Investigations on the Nematode Worm C. Elegans (1963–1998).” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 16–28.

Gatherer, Derek. 2010. “So What Do We Really Mean When We Say That Systems Biology Is Holistic?” Gatherer BMC Systems Biology 4: 22.

Genser, Bernd, Philip J. Cooper, Maria Yazdanbakhsh, Mauricio L. Barreto, and Laura C. Rodrigues. 2007. “A Guide to Modern Statistical Analysis of Immunological Data.” BMC Immunology 8 (October): 27.

Goguen, Joseph A., and Francisco J. Varela. 1979. “Systems and Distinctions; Duality and Complementarity.” International Journal of General Systems 5 (1): 31–43.

Goldstein, Martin, and Inge Goldstein. 1984. “Where Do Hypotheses Come From?” In The Experience of Science, 361–70. Springer.

Gottschalk, Rachel A., Andrew J. Martins, Virginie H. Sjoelund, Bastian R. Angermann, Bin Lin, and Ronald N. Germain. 2013. “Recent Progress Using Systems Biology Approaches to Better Understand Molecular Mechanisms of Immunity.” Seminars in Immunology 25 (3): 201–8.

Grignolio, Andrea, Michele Mishto, Ana Maria Caetano Faria, Paolo Garagnani, Claudio Franceschi, and Paolo Tieri. 2014. “Towards a Liquid Self: How Time, Geography, and Life Experiences Reshape the Biological Identity.” Frontiers in Immunology 5 (APR): 1–17.

Grossman, Z., and W. E. Paul. 2000. “Self-Tolerance: Context Dependent Tuning of T Cell Antigen Recognition.” Seminars in Immunology 12 (3): 197–203; discussion 257–344.

Grossman, Zvi. 2000. “Hopeful Monsters and Other Ideas.” Seminars in Immunology 12 (3): 265–67.

Hammond, Debora. 2016. “Special Issue: General Systems Transdisciplinarity.” Systema 4 (1): 1–3.

Hood, Leroy. 2003. “Systems Biology: Integrating Technology, Biology, and Computation.” Mechanisms of Ageing and Development 124 (1): 9–16.

Howes, M. 2000. “Self, Intentionality, and Immunological Explanation.” Seminars in Immunology 12 (3): 249–56; discussion 257–344.

Jaeger, Johannes, and Nick Monk. 2015. “Everything Flows: A Process Perspective on Life.” EMBO Reports 16 (9): 1064–67.

Keating, Peter, and Alberto Cambrosio. 2012. “Too Many Numbers: Microarrays in Clinical Cancer Research.” Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 37–51.

Keller, Evelyn Fox. 2009. Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines. Harvard University Press.

Kidd, Brian A., Lauren A. Peters, Eric E. Schadt, and Joel T. Dudley. 2014. “Unifying Immunology with Informatics and Multiscale Biology.” Nature Immunology 15 (2): 118–27.

Kitano, Hiroaki. 2002. “Systems Biology: A Brief Overview.” Science 295 (5560). science.sciencemag.org: 1662–64.

———. 2004. “Biological Robustness.” Nature Reviews. Genetics 5 (11): 826–37.
———. 2007. “A Robustness-Based Approach to Systems-Oriented Drug Design.” Nature Reviews. Drug Discovery 6 (3): 202–10.

Krohs, Ulrich. 2012. “Convenience Experimentation.” Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 52–57.

Kuhn, Thomas S. 1962. The Structure of Scientific Revolutions. The University of Chicago Press.

Langman, R. E., and M. Cohn. 2000a. “A Minimal Model for the Self-Nonself Discrimination: A Return to the Basics.” Seminars in Immunology 12 (3): 189–95; discussion 257–344.

———. 2000b. “Self-Nonself Discrimination Revisited. Introduction.” Seminars in Immunology 12 (3): 159–62.

Laszlo, Alexander, and Stanley Krippner. 1998. “Systems Theories: Their Origins, Foundations, and Development.” In Systems Theories and A Priori Aspects of Perception, edited by J. S. Jordan, 47–74. Amsterdam: Elsevier Science.

Leonelli, S. 2012. “Introduction: Making Sense of Data-Driven Research in the Biological and Biomedical Sciences.” Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 1–3.

Leonelli, Sabina, and Rachel A. Ankeny. 2012. “Re-Thinking Organisms: The Impact of Databases on Model Organism Biology.” Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 29–36.

Levesque, Mitchell P., and Philip N. Benfey. 2004. “Systems Biology.” Current Biology: CB 14 (5). Elsevier: R179–80.

Lima, Manuel. 2011. Visual Complexity: Mapping Patterns of Information. Princeton: Princeton Architectural Press.

Luhmann, N. 2006. “System as Difference.” Organization 13 (1): 37–57.
Macy, J. 1991. Mutual Causality in Buddhism and General Systems Theory: The Dharma of Natural Systems. SUNY Series in Buddhist Studies. State University of New York Press.

Maturana, Humberto R., and Francisco J. Varela. 1987. The Tree of Knowledge: The Biological Roots of Human Understanding. New Science Library/Shambhala Publications.

Maturana, Humberto, and Francisco J. Varela. 1980. “Autopoiesis and Cognition, D.” Reidel, Dordrecht, Holland.

McFall-Ngai, Margaret. 2007. “Adaptive Immunity: Care for the Community.” Nature 445 (January): 153.

Meadows, Donella H. 2008. Thinking in Systems: A Primer. Chelsea Green Publishing.
Medawar, P. B. 2008. Induction and Intuition in Scientific Thought. Reprint edition. Routledge.

Medzhitov, R., and C. A. Janeway Jr. 2000. “How Does the Immune System Distinguish Self from Nonself?” Seminars in Immunology 12 (3): 185–88; discussion 257–344.

Mitchison, N. A., D. R. Katz, and B. Chain. 2000. “Self/nonself Discrimination among Immunoregulatory (CD4) T Cells.” Seminars in Immunology 12 (3): 179–83; discussion 257–344.

Müller, Karl H., and Alexander Riegler. 2014a. “A New Course of Action.” Radical Constructivism 10 (1): 1–6.

———. 2014b. “Second-Order Science: A Vast and Largely Unexplored Science Frontier.” Radical Constructivism 10 (1): 7–15.

Nardini, Christine, Jennifer Dent, and Paolo Tieri. 2015. “Editorial: Multi-Omic Data Integration.” Frontiers in Cell and Developmental Biology 3 (July): 46.

Nicholson, Daniel J. 2012. “The Concept of Mechanism in Biology.” Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 152–63.

Noble, Denis. 2012. “A Theory of Biological Relativity: No Privileged Level of Causation.” Interface Focus 2 (1): 55–64.

O’Malley, Maureen A., and John Dupré. 2005. “Fundamental Issues in Systems Biology.” BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology 27 (12): 1270–76.

O’Malley, Maureen A., and Orkun S. Soyer. 2012/3. “The Roles of Integration in Molecular Systems Biology.” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 58–68.

Pearce, Trevor. 2012/3. “Philosophy of Biology in the Twenty-First Century.” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 312–15.

Rescher, Nicholas. 1996. Process Metaphysics: An Introduction to Process Philosophy. Suny Press.

Rook, Graham a. W. 2009. “Review Series on Helminths, Immune Modulation and the Hygiene Hypothesis: The Broader Implications of the Hygiene Hypothesis.” Immunology 126 (1): 3–11.

Ross, Lauren N., and James F. Woodward. 2016. “Koch’s Postulates: An Interventionist Perspective.” Studies in History and Philosophy of Biological and Biomedical Sciences 59 (June). philsci-archive.pitt.edu: 35–46.

Rousseau, David, Julie Billingham, Jennifer Wilby, and Stefan Blachfellner. 2016a. “In Search of General Systems Theory.” Systema 4 (1): 76–99.

———. 2016b. “The Synergy between General Systems Theory and the General Systems Worldview.” Systema 4 (1): 61–75.

Rousseau, David, Stefan Blachfellner, Julie Billingham, and Jennifer Wilby. 2016c. “A Research Agenda for General Systems Transdisciplinarity.” Systema 4 (1): 100–110.

Rousseau, David, Jennifer Wilby, Julie Billingham, and Stefan Blachfellner. 2016a. “A Typology for the Systems Field.” Systema 4 (1): 15–47.

———. 2016b. “Manifesto for General Systems Transdisciplinarity.” Systema 4 (1): 4–14.

———. 2016c. “The Scope and Range of General Systems Transdisciplinarity.” Systema 4 (1): 48–60.

Silverstein, A. M., and N. R. Rose. 2000. “There Is Only One Immune System! The View from Immunopathology.” Seminars in Immunology 12 (3): 173–78; discussion 257–344.

Silverstein, Arthur M., and Noel R. Rose. 1997. “On the Mystique of the Immunological Self.” Immunological Reviews 159 (1). Wiley Online Library: 197–206.

Sintonen, Matti. 2004. “Reasoning to Hypotheses: Where Do Questions Come?” Foundations of Science 9 (3). Kluwer Academic Publishers: 249–66.

Strasser, Bruno J. 2012. “Data-Driven Sciences: From Wonder Cabinets to Electronic Databases.” Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1): 85–87.

Tauber, A. I. 2000. “Moving beyond the Immune Self?” Seminars in Immunology 12 (3): 241–48; discussion 257–344.

Tieri, Paolo, Andrea Grignolio, Michele Mishto, and Claudio Franceschi. 2011. “The Immunological Self: A Reappraisal.” In Sysbiohealth Symposium, 11–15. Bononia University Press.

Trewavas, Anthony. 2006. “A Brief History of Systems Biology. ‘Every Object That Biology Studies Is a System of Systems.’ Francois Jacob (1974).” The Plant Cell 18 (10): 2420–30.

Umpleby, Stuart A. 2014. “Second-Order Science: Logic, Strategies, Methods.” Constructivist Foundations 10 (1): 16–23.

Vaz, Nelson M., Gustavo C. Ramos, Vitor Pordeus, and Claudia R. Carvalho. 2006. “The Conservative Physiology of the Immune System. A Non-Metaphoric Approach to Immunological Activity.” Clinical & Developmental Immunology 13 (2-4): 133–42.

Veldhoen, Marc, and Henrique Veiga-Fernandes. 2015. “Feeding Immunity: Skepticism, Delicacies and Delights.” Nature Immunology 16 (3): 215–19.

Walpole, Joseph, Jason A. Papin, and Shayn M. Peirce. 2013. “Multiscale Computational Models of Complex Biological Systems.” Annual Review of Biomedical Engineering 15: 137–54.

Westerhoff, Hans V., and Bernhard O. Palsson. 2004. “The Evolution of Molecular Biology into Systems Biology.” Nature Biotechnology 22 (10): 1249–52.

Zinkernagel, R. M. 2000. “Localization Dose and Time of Antigens Determine Immune Reactivity.” Seminars in Immunology 12 (3): 163–71; discussion 257–344.

 

Translational/soft skills

Brown, Juanita. 2001. “The World Café: Living Knowledge Through Conversations That Matter.” Fielding Graduate School.

Brown, Juanita, and David Isaacs. 2005. The World Café. San Francisco, California: Berrett-Koehler Publishers, Inc.

Buzan, Tony (2000). Use Your Head. London: BBC Worldwide Limited.

Harrison, Anna. From scholar to dollar: in 15 easy steps. Available from: fromscholartodollar.com.

Pinker, Steven (2014). The Sense of Style: The Thinking Person’s Guide to Writing in the 21st Century. New York, NY: Penguin.

Vogt, Eric E., Juanita Brown, and David Isaacs. 2003. The Art of Powerful Questions. Mill Valley, CA: Whole Systems Associates.

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