Bottlenecks: Zwischen glitschigen Konzepten und starren Worten (2019) DiNa 11/2019 , S. 28-41.
Prof. Dr. Niall Palfreyman
Berechtigungen: Peer Reviewed
Exploring autonomy through computational biomodelling (2009) Briefings in Bioinformatics 10 (4), S. 462-474.
DOI: 10.1093/bib/bbp003
The question of whether living organisms possess autonomy of action is tied up with the nature of causal efficacy. Yet the nature of organisms is such that they frequently defy conventional causal language. Did the fig wasp select the fig, or vice versa? Is this an epithelial cell because of its genetic structure, or because it develops within the epithelium? The intimate coupling of biological levels of organisation leads developmental systems theory to deconstruct the biological organism into a life-cycle process which constitutes itself from the resources available within a complete developmental system. This radical proposal necessarily raises questions regarding the ontological status of organisms: Does an organism possess existence distinguishable from its molecular composition and social environment? The ambiguity of biological causality makes such questions difficult to answer or even formulate, and computational biology has an important role to play in operationalising the language in which they are framed. In this article we review the role played by computational biomodels in shedding light on the ontological status of organisms. These models are drawn from backgrounds ranging from molecular kinetics to niche construction, and all attempt to trace biological processes to a causal, and therefore existent, source. We conclude that computational biomodelling plays a fertile role in furnishing a proof of concept for conjectures in the philosophy of biology, and suggests the need for a process-based ontology of biological systems.
Johannes J. Mandel,
Hendrik Fuß,
Prof. Dr. Niall Palfreyman,
Werner Dubitzky
Berechtigungen: Open Access
Berechtigungen: Peer Reviewed
Modeling biochemical transformation processes and information processing with Narrator (2007) BMC Bioinformatics 8 , S. 1-17.
DOI: 10.1186/1471-2105-8-103
Johannes J. Mandel,
Prof. Dr. Niall Palfreyman,
Jesus A. Lopez,
Werner Dubitzky
Berechtigungen: Peer Reviewed
Representing bioinformatics causality (2004) Briefings in Bioinformatics 5 (3), S. 270-283.
DOI: 10.1093/bib/5.3.270
Prof. Dr. Niall Palfreyman
Berechtigungen: Peer Reviewed
The Construction of Meaning in Computational Integrative Biology (2004) OMICS: A Journal of Integrative Biology 8 (2), S. 95-105.
DOI: 10.1089/1536231041388357
It is the contention of this paper that current data mining work in bioinformatics tends to emphasize data representation to the neglect of another essential aspect of biological systems, namely dynamics. This results in a divorce of both the enterprise and the teaching of bioinformatics from its central aim of meaning-construction. The paper argues that this neglect of dynamics is rooted in an information-processing view of cognitive psychology, and needs to be complemented by a more narrative perspective which emphasizes the explanation, rather than the mere description, of observed patterns in data. This increased emphasis on explanatory narrative in the form of dynamical modeling leads to both a deeper understanding of biological information and a more invigorating approach to the teaching of bioinformatics. The paper presents a cross-curricular teaching framework for a first-year undergraduate course in bioinformatic dynamical modeling which is based around the use of narrative plots.
Prof. Dr. Niall Palfreyman
Berechtigungen: Peer Reviewed
Relativity on a single sheet (1994) Physics Education 29 (4), S. 217-221.
DOI: 10.1088/0031-9120/29/4/007
Zeitschriftenbeiträge
Prof. Dr. Niall Palfreyman,
Janice Miller-Young
What is a cognizing subject? Construction, autonomy and original causation (2018) Constructivist Foundations 13 (3), S. 362-373.
Prof. Dr. Niall Palfreyman
Ist entdeckendes Lernen für technische Studiengänge geeignet? (2008) DiNa 11/2008 , S. 12-34.
Johannes J. Mandel,
Prof. Dr. Niall Palfreyman,
Werner Dubitzky
Modelling codependence in biological systems (2007) IET Systems Biology 1 (1), S. 18-32.
DOI: 10.1049/iet-syb:20060002
Prof. Dr. Niall Palfreyman
Health: The Quest for Wholeness (1999) AWIS .
Beiträge in Monografien, Sammelwerken, Schriftenreihen
Prof. Dr. Niall Palfreyman
Teaching Bioinformatics: Using Storytelling to Negotiate Cultural Divisions in the Sciences (2007) Palfreyman D., McBride D.L. (eds) Learning and Teaching Across Cultures in Higher Education. Palgrave Macmillan, London , S. 243-259.
DOI: 10.1057/9780230590427_14
Johannes J. Mandel,
Prof. Dr. Niall Palfreyman
A Pen-and-Paper Notation for Teaching Biosciences (2004) Proceedings of the International Symposium KELSI, Milan, Italy, November 25-26 2004, López J.A., Benfenati E., Dubitzky W. (eds) Knowledge Exploration in Life Science Informatics. KELSI 2004. Lecture Notes in Computer Science, vol 3303. Springer, Berlin, , S. 1-8.
DOI: 10.1007/978-3-540-30478-4_1
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