Integrating data to acquire new knowledge: Three modes of integration in plant science

Studies in History and Philosophy of Science Part C :Studies in History and Philosophy of Biological and Biomedical Sciences

Volumn 44, Issue 4, 2013, Pages 503-514

  Leonelli, Sabina ^a  

^a UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

Data; Integration; Model organisms; Plant biology; Scientific knowledge; Translational research

Indexed keywords

BOTANY; INFORMATION PROCESSING; METHODOLOGY; PROCEDURES;

BOTANY; DATASETS AS TOPIC; RESEARCH DESIGN;

EID: 84908500483     PISSN: 13698486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.shpsc.2013.03.020     Document Type: Article

References (78)

1. Ankeny R.A., Leonelli S. What is so special about model organisms?. Studies in History and Philosophy of Science: Part A 2011, 42(2):313-323.
2. Avraham S., Tung C.W., Ilic K., Jaiswal P., Kellogg E.A., McCouch S., et al. The plant ontology database: A community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research 2008, 36:D449-D454.
3. Babcock, B. A. (2011). The impact of US biofuel policies on agricultural price levels and volatility. ICTSD Issue Paper No. 35.
4. Bechtel W., Richardson R.C. Discovering complexity: Decomposition and localization as strategies in scientific research 2010, MIT Press/Bradford Books, Cambridge, MA. 2nd ed.
5. Bechtel W. From molecules to behavior and the clinic: Integration in chronobiology. Studies in History and Philosophy of Biological and Biomedical, Sciences 2013, 44:493-502.
6. Bevan M., Walsh S. Positioning Arabidopsis in plant biology. A key step toward unification of plant research. Perspectives on Translational Biology 2004, 135:602-606.
7. Bolker J.A. Model systems in developmental biology. BioEssays 1995, 17:451-455.
8. Botanical Society of America. Botany for the next millennium: I. The intellectual: Evolution, development, ecosystems (1994). Accessed 09.08.12. http://www.botany.org/bsa/millen/mil-chp1.html#Evolution.
9. Bowker G. Biodiversity datadiversity. Social Studies of Science 2000, 3(5):643-683.
10. Brigandt I. Beyond reduction and pluralism: Toward an epistemology of explanatory integration in biology. Erkenntnis 2010, 73:295-311.
11. Brigandt I. Explanation in biology: Reduction, pluralism, and explanatory aims. Science & Education 2013, 22:69-91.
12. Brigandt, I. (2013). Systems biology and the integration of mechanistic explanation and mathematical explanation. Studies in History and Philosophy of Biological and Biomedical Sciences.
13. Browne, J. (2001). History of plant sciences. In: Encyclopedia of life science. John Wiley and Sons. Accessed 09.08.12. http://web.fc.uaem.mx:8080/tareas/55_HistoryPlSc.pdf.
14. Bülow L., Schindler M., Hehl R. PathoPlant®: A platform for microarray expression data to analyze co-regulated genes involved in plant defense responses. Nucleic Acids Research 2007, 35:D841-D845.
15. Bult C.J. From information to understanding: The role of model organism databases in comparative and functional genomics. Animal Genetics 2006, 37(Suppl. 1):28-40.
16. Burian R. Exploratory experimentation and the role of histochemical techniques in the work of Jean Brachet, 1938-1952. History and Philosophy of the Life Sciences 1997, 19:27-45.
17. Callebaut W. Scientific perspectivism: A philosopher of science's response to the challenge of big data biology. Studies in the History and the Philosophy of the Biological and Biomedical Sciences 2012, 43(1):69-80.
18. 2O? Evidence, realism and pluralism 2012, Springer, Dordrecht.
19. Craver C.F. Beyond reduction: Mechanisms, multifield integration and the unity of neuroscience. Studies in the History and Philosophy of Biological and Biomedical Sciences 2005, 36:373-395.
20. Darden L. Relations among fields: Mendelian, cytological and molecular mechanisms. Studies in History and Philosophy of Biological and Biomedical Sciences 2005, 36:349-371.
21. Darden L., Maull N. Interfield theories. Philosophy of Science 1997, 44(1):43-64.
22. Davis R.H. The age of model organisms. Nature Reviews Genetics 2004, 5:69-76.
23. De Luca V., Salim V., Masada-Atsumi S., Yu F. Mining the biodiversity of plants. A revolution in the making. Science 2012, 336:1658-1661.
24. Douglas H. Science, policy and the value-free ideal 2009, Pittsburgh University Press, Pittsburgh.
25. Elliott K. Is a little pollution good for you? Incorporating societal values in environmental research 2011, Oxford University Press, New York.
26. Fehr, C. & Plaisance, K. (Eds.). (2010). Making Philosophy of Science More Socially Relevant. Special issue of Synthese (Vol. 177, Issue 3).
27. Griesemer J.R. Theoretical integration, cooperation, and theories as tracking devices. Biological Theory 2006, 1:4-7.
28. Hacking, I. (1992). The self-vindication of the laboratory sciences. In A. Pickering (Ed.), Science as practice and culture (pp. 29-64). Chicago, IL: The University of Chicago Press.
29. Harwood J. Europe's green revolution and others since 2012, Routledge, London.
30. Royal Society (2012). Science as an open enterprise. Accessed 10.08.12
31. Ideker T., Bafna V., Lemberger T. Integrating scientific cultures. Molecular Systems Biology 2007, 3:105.
32. Jensen, E.F. (2007) Flowering time diversity in Miscanthus: A tool for the optimization of biomass. Abstracts of the Annual Main Meeting of the Society for Experimental Biology. Consulted on 7 December 2012 http://hdl.handle.net/2160/4532.
33. Jensen E.F., Robson P., Norris J., Cookson A., Farrar K., Donnison I., et al. Characterisation of flowering time diversity in Miscanthus species. GCB Bioenergy 2011, 3:387-400.
34. Keating P., Cambrosio A. Cancer on trial: Oncology as a new style of practice 2012, Chicago University Press, Chicago, IL.
35. Keating P., Cambrosio A. Too many numbers: Microarrays in clinical cancer research. Studies in the History and the Philosophy of the Biological and Biomedical Sciences 2012, 43(1):37-51.
36. Kelling S., Hochachka W.M., Fink D., Riedewald M., Caruana R., Ballard G., et al. Data-intensive science: A new paradigm for biodiversity studies. BioScience 2009, 59(7):613-620.
37. Kingsbury N. Hybrid-The history and science of plant breeding 2009, University of Chicago Press, Chicago.
38. Kohler R.E. Lords of the fly: "Drosophila" genetics and the experimental life 1994, University of Chicago Press, Chicago.
39. Koornneef M., Meinke D. The development of Arabidopsis as a model plant. The Plant Journal 2010, 61:909-921.
40. Kourany J. Philosophy of science after feminism 2010, Oxford University Press, Oxford.
41. Lamesch P., Berardini T.Z., Li D., Swarbreck D., Wilks C., Sasidharan R., et al. The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools. Nucleic Acids Research 2012, 40(D1):D1202-D1210.
42. Lenoir T. Shaping biomedicine as an information science. Proceedings of the 1998 conference on the history and heritage of science information systems 1999, 27-45. Information Today press, Medford, NJ, ASIS Monograph Series. M.E. Bowden, T.B. Hahn, R.V. Williams (Eds.).
43. Leonelli S. Growing weed, producing knowledge. An epistemic history of Arabidopsis thaliana. History and Philosophy of the Life Sciences 2007, 29(2):55-87.
44. Leonelli S. On the locality of data and claims about phenomena. Philosophy of Science 2009, 76(5):737-749.
45. Leonelli S. The impure nature of biological knowledge. Scientific understanding: philosophical perspectives 2009, 189-209. Pittsburgh University Press, Pittsburgh. H. de Regt, S. Leonelli, K. Eigner (Eds.).
46. Leonelli S. Documenting the emergence of bio-ontologies: or, why researching bioinformatics requires HPSSB. History and Philosophy of the Life Sciences 2010, 32(1):105-126.
47. Leonelli S. Packaging data for re-use: Databases in model organism biology. How well do facts travel? The dissemination of reliable knowledge 2010, 325-348. Cambridge University Press, Cambridge, MA. P. Howlett, M.S. Morgan (Eds.).
48. Leonelli S. When humans are the exception: Cross-species databases at the interface of clinical and biological research. Social Studies of Science 2012, 42(2):214-236.
49. Leonelli S. Classificatory theory in data-intensive science: The case of open biomedical ontologies. International Studies in the Philosophy of Science 2012, 26(1):47-65.
50. Leonelli S., Ankeny R.A. Re-thinking organisms: The impact of databases on model organism biology. Studies in History and Philosophy of Biological and Biomedical Sciences 2012, 43:29-36.
51. Leonelli S., Diehl A.D., Christie K.R., Harris M.A., Lomax J. How the gene ontology evolves. BMC Bioinformatics 2011, 12:325.
52. Leonelli S., Charnley B., Webb A., Bastow R. Under one leaf. A historical perspective on the UK plant science federation. New Phytologist 2012, 195(1):10-13.
53. Longino H. The fate of knowledge 2002, Princeton University Press, Princeton, NJ.
54. McCain K.W. Mandating sharing: Journal policies in the natural sciences. Science Communication 1995, 16(4):403-431.
55. Mitchell S. Biological complexity and integrative pluralism 2003, Cambridge University Press, Cambridge.
56. Mitchell S. Unsimple truths 2009, Chicago University Press, Chicago, IL.
57. Morgan M.S., Morrison M. Models as mediators 1999, Cambridge University Press, Cambridge, UK.
58. Müller-Wille S.W. Collection and collation: theory and practice of Linnaean botany. Studies in the History and Philosophy of the Biological and Biomedical Sciences 2007, 38:541-562.
59. Nordmann A., Radder H., Schiemann G. Science transformed? Debating claims of an epochal break 2011, Pittsburgh University Press, Pittsburgh.
60. O'Malley M.A. Exploration, iterativity and kludging in synthetic biology. Comptes Rendus Chimie 2011, 14(4):406-412.
61. O'Malley M.A., Soyer O. The roles of integration in molecular systems biology. Studies in the History and the Philosophy of the Biological and Biomedical Sciences 2012, 43(1):58-68.
62. O'Malley M.A., Stotz K. Intervention, integration and translation in obesity research: Genetic, developmental and metaorganismal approaches. Philosophy, Ethics, and Humanities in Medicine 2011, 6(2):10.
63. O'Malley M.A. When integration fails: Prokaryote phylogeny and the tree of life. Studies in History and Philosophy of Biological and Biomedical Sciences 2013, 44:551-562.
64. Plutynski, A. (2013). Cancer and the goals of integration. Studies in History and Philosophy of Biological and Biomedical Sciences.
65. Potter C., Harwood T., Knight J., Tomlinson I. Learning from history, predicting the future: The UK Dutch elm disease outbreak in relation to contemporary tree disease. Philosophical Transactions of the Royal Society B 2011, 366:1966-1974.
66. Quirin E.A., et al. Evolutionary meta-analysis of Solanaceous Resistance Gene and Solanum Resistance Gene analog sequences and a practical framework for cross-species comparisons. Molecular Plant-Microbe Interactions 2012, 25(5):603-612.
67. Rhee S.Y. Carpe diem: Retooling the "publish or perish" model into the "share and survive" model. Plant Physiology 2004, 134:543-547.
68. Rhee S.Y., Dickerson J., Xu D. Bioinformatics and its applications in plant biology. Annal Review of Plant Biology 2006, 57:335-360.
69. Rheinberger H. Infra-experimentality: From traces to data, from data to patterning facts. History of Science 2011, 49:337-348.
70. Royal Society (2012). Science as an open enterprise. Accessed 10.08.12. http://royalsociety.org/policy/projects/science-public-enterprise/report/
71. Ryle G. The concept of mind 1949, The Chicago University Press, Chicago, Illinois.
72. Smocovitis V. Keeping up with Dobzhansky: G. Ledyard Stebbins, Jr., Plant evolution, and the evolutionary synthesis. History and Philosophy of the Life Sciences 2006, 28(1):11-50.
73. Stitt M., Lunn J., Usadel B. Arabidopsis and primary photosynthetic metabolism-More than the icing on the cake. Plant Journal 2010, 61(6):1067-1091.
74. Strasser B.J. The experimenter's museum: GenBank, natural history, and the moral economies of biomedicine, 1979-1982. Isis 2011, 102:60-96.
75. Taylor C.F., Field D., Sansone S., Aerts J., Apweiler R., Ashburner M., et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: The MIBBI project. Nature Biotechnology 2008, 26(8):889-896.
76. Taking the next step: Building an Arabidopsis information portal. Plant Cell 2012, 24(6):2248-2256. The International Arabidopsis Informatics Consortium.
77. World Economic Forum (2011). Global Risks 2011 (6th ed.)Accessed 08.08.12.http://reports.weforum.org/global-risks-2011/.
78. Zhang P., Foerster H., Tissier C., Mueller L., Paley S., Karp P., et al. MetCyc and AraCyc: Metabolic pathway databases for plant research. Plant Physiology 2005, 138:27-37.