Publications

Peer-Reviewed Papers

• (with Rachel Ankeny, forthcoming) What Is So Special About Model Organisms? Studies in the History and the Philosophy of Science: Part A. [draft]
  

• (2010, with Ruth Bastow) Sustainable Digital Infrastructure. EMBO Reports. [click here for link to publication]

• (2010) Documenting the Emergence of Bio-Ontologies: Or, Why Studying Bioinformatics Requires HPSSB. History and Philosophy of the Life Sciences 32: 105-126.[draft]

• (2009) On the Locality of Data and Claims About Phenomena. Philosophy of Science 76, 5. [Draft]

• (2008) Performing Abstraction. Two ways of modeling Arabidopsis thaliana. Biology and Philosophy 23, 4: 509-528 [draft]
  

• (2008) Bio-Ontologies as Tools for Integration in Biology. Biological Theory 3, 1: 8-11 [draft]

• (2007) Growing Weed, Producing Knowledge. A Epistemic History of Arabidopsis thaliana. History and Philosophy of the Life Sciences 29, 2: 55-87. [draft here]

• (2005, with Hasok Chang) Infrared Metaphysics: the Elusive Ontology of Radiation (Part 1). Studies in the History and Philosophy of Science: Part A, Volume 36, Issue 3, Pages 477–508
  

• (2005, with Hasok Chang) Infrared Metaphysics: Radiation and Theory-Choice and the Ontology of Radiation (Part 2). Studies in the History and Philosophy of Science: Part A, Volume 36, Issue 4, Pages 687–706
  

Book Chapters

• (2010) Packaging Data for Re-Use: Databases in Model Organism Biology. In Morgan, MS and Howlett, WH (eds) How Well Do Facts Travel? The dissemination of reliable knowledge. Cambridge University Press. [draft]
  

• (2010) The Commodification of Knowledge Exchange: Governing the Circulation of Biological Data. In: Radder, H (ed.) The Commodification of Academic Research. Pittsburgh University Press. [draft]
  

• (2009) The Impure Nature of Biological Knowledge and the Practice of Understanding. In: De Regt, H., Leonelli, S. and Eigner, K. (eds.) Scientific Understanding: A Philosophical Perspective. Pittsburgh University Press. [Draft available here]

• (2009, with Henk de Regt and Kai Eigner) Focusing on Scientific Understanding. In: de Regt, H., Leonelli, S. and Eigner, K. [draft]
  

• (2009) Centralising Labels to Distribute Data: The Regulatory Role of Genomic Consortia. In Atkinson, P., Glasner, P. and Lock, M. (eds.) The Handbook for Genetics and Society: Mapping the New Genomic Era. London: Routledge. [draft]
  

• (2007) What Is In A Model? In: Laubichler, M. and Müller, G. B., (eds.) Modeling Biology. Structures, Behaviours, Evolution. Vienna Series: MIT Press

• (2007) Cultivando Hierba, Produciendo conocimiento. Una historia epistemologica de Arabidopsis thaliana. In: Suarez, E. [ed.] Variedad Sin Limites. Las Rapresentationes en la Ciencia. Universidad Autonoma de Mexico y Editor Limusa.

Edited Book and Special Issues

(2009) Scientific Understanding: Philosophical Perspectives. de Regt, H., Leonelli, S. and Eigner, K. (eds.). Pittsburgh University Press

         (in preparation) Data-Driven Research in the Biological and the Biomedical Sciences. Special Issue of Studies in the History and the Philosophy of the Biological and the Biomedical Sciences: Part C.

         (2005, with Thomas Reydon) Philosophy of Biology in Flanders and the Netherlands. Acta Biotheoretica, Vol. 53, Issue 2, Pages 55–56 (co-author: Thomas Reydon) ISSN: 0001-5342 (Paper) 1572-8358 (Online)

Other Publications and Working Papers

• (2011) ‘Data-Intensive Research’. In: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota (Eds.) Encyclopaedia of System Biology. Springer.

• (2011) ‘Model Organism’. In: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota (Eds.) Encyclopaedia of System Biology. Springer.

• (2011) ‘Bio-Ontologies’. In: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota (Eds.) Encyclopedia of System Biology. Springer.

• (2010, June) Key concerns that should travel between e-social and e-natural science. E-Research Ethics Website. http://eresearch-ethics.org/

• (2008, March) Circulating Evidence Across Contexts: Data and Claims in Model Organism Biology. LSE Working Paper Series 'The Nature of Evidence: How Well Do 'Facts' Travel?'

• (2008, April) Regulating Data Travel in the Life Sciences: The Impact of Commodification. LSE Working Papers on the Nature of Evidence: How Well Do ‘Facts’ Travel?, No. 27/08.

• (2007, March) Arabidopsis, the botanical Drosophila: from mouse cress to model organism. Review Article. Endeavour 31 1: 34–38.

• (2007, April) Naar een open dialoog tussen de wetenschap en de wetenschapsstudies. Congresbespreking. Algemeen Nederland Tijdschrift Wijsbegeerte 99, 3: 237–240. [`Towards an open dialogue between science and science studies' in the Dutch Journal for General Philosophy]

• (2005, with Thomas Reydon) Philosophy of Biology in Flanders and the Netherlands. Acta Biotheoretica, Vol. 53, Issue 2, Pages 55–56 (co-author: Thomas Reydon) ISSN: 0001-5342 (Paper) 1572-8358 (Online)

• (2006, July) Forming Civic Consciousness: A Participant's View on the European Social Forum. Re-Public: Re-Imagining Democracy.

• (2005) Pluralism and Normativity in Interdisciplinary Research in Graduate Journal of Social Science Vol. 2, Issue 1, Pages i–vi, ISSN 1572-3763

• (2005, with Stefanie Ortmann) Unity in Social Science? Graduate Journal of Social Science, Vol.2, Issue 2, Pages i–v ISSN 1572-3763
  

• (2004) Introducing the GJSS: Why a Graduate Journal on Interdisciplinary Methodology? in Graduate Journal of Social Science Vol. 1, Issue1, Pages i–vii, ISSN 1572-3763

• (2002, May) Understanding Infrared Metaphysics: Melloni's Quest for Identity. in: Measurement in Physics and Economics Discussion Paper Series, DP MEAS 22/02, ISSN 1465-637X [pdf]

Doctoral Dissertation

(April 2007) Weed for Thought. Using Arabidopsis thaliana to Understand Plant Biology. Vrije Universiteit Amsterdam. Download full text or email me for a printed copy

In Progress

• When Humans are the Exception: Cross-Species Data Mining. Submitted.
• Classificatory Theory in Data-Driven Research: The Case of Bio-Ontologies. Submitted.
• (with Diehl A, Christie K, Harris MA and Lomax J) How the Gene Ontology Evolves. Submitted.
• (with Maureen O'Malley) The scientific importance of asking questions at meetings. Submitted.
  
• (with Rachel Ankeny) Re-Thinking Organisms: The Epistemic Impact of Databases on Model Organism Biology. For submission to Studies in the History and the Philosophy of the Biological and Biomedical Sciences: Part C.
• Issue-Based Scientific Governance: Cases of Self-Regulation in Genomic Research. In preparation.
• (with Ranjit Singh) Using digital infrastructure to cure cancer? The case of caBIG. In preparation.
  
• The Virtual Plant. An Epistemic History of Arabidopsis thaliana. Monograph, in preparation.