What mechanisms can't do: Explanatory frameworks and the function of the p53 gene in molecular oncology

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

Volumn 44, Issue 3, 2013, Pages 374-384

  Blasimme, Alessandro ^a,c   Maugeri, Paolo ^b,c   Germain, Pierre Luc ^c  

^a UMR INSERM 1027   (France)

^b UNIVERSITY OF MILAN   (Italy)

^c EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

Author keywords

Cancer; Discovery; Explanatory frameworks; Mechanistic explanation; Molecular oncology; P53

Indexed keywords

PROTEIN P53;

ARTICLE; CARCINOGENESIS; DISCOVERY; EXPLANATORY FRAMEWORKS; HUMAN; KNOWLEDGE; MECHANISTIC EXPLANATION; MOLECULAR BIOLOGY; MOLECULAR ONCOLOGY; NEOPLASM; TUMOR SUPPRESSOR GENE;

CANCER; DISCOVERY; EXPLANATORY FRAMEWORKS; MECHANISTIC EXPLANATION; MOLECULAR ONCOLOGY; P53;

CARCINOGENESIS; GENES, P53; HUMANS; KNOWLEDGE; MOLECULAR BIOLOGY;

EID: 84881259293     PISSN: 13698486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.shpsc.2013.02.001     Document Type: Article

References (73)

1. Andrews P.W. From teratocarcinomas to embryonic stem cells. Philosophical Transactions of the Royal Society of London-Series B: Biological Sciences 2002, 357:405-417.
2. Bechtel W. Discovering cell mechanisms: The creation of modern cell biology 2006, Cambridge University Press, Cambridge.
3. Bechtel W., Abrahamsen A. Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences 2005, 36:421-441. 10.1016/j.shpsc.2005.03.010.
4. Bechtel W., Richardson R.C. Discovering complexity: Decomposition and localization as strategies in scientific research 2000, The MIT Press, Cambridge.
5. Bishop J.M. Cancer: The rise of the genetic paradigm. Genes & Development 1995, 9:1309-1315.
6. Bonizzi G., Cicalese A., Insinga A., Pelicci P.G. The emerging role of p53 in stem cells. Trends in Molecular Medicine 2012, 18:6-12. 10.1016/j.molmed.2011.08.002.
7. Bonnet D., Dick J.E. Human acute myeloid leukaemia is organized as a hierarchy that originates from a primitive hematopoietic cell. Nature Medicine 1997, 3(7):730-737.
8. Breivik J., Gaudernack G. Carcinogenesis and natural selection: A new perspective to the genetics and epigenetics of colorectal cancer. Advances in Cancer Research 1999, 76:187-212.
9. Cambrosio A., Keating P. A matter of FACS: Constituting novel entities in immunology. Medical Anthropology Quarterly 1992, 6:362-384. 10.1525/maq.1992.6.4.02a00040.
10. Cambrosio A., Keating P. Exquisite specificity: The monoclonal antibody revolution 1995, Oxford University Press, New York.
11. Cambrosio A., Keating P. Biomedical platforms: Realigning the normal and the pathological in late-twentieth-century medicine 2003, The MIT Press, Cambridge.
12. Cicalese A., Bonizzi G., Pasi C.E., et al. The tumor suppressor p53 regulates polarity of self-renewing divisions in mammary stem cells. Cell 2009, 138:1083-1095.
13. Craver C.F. Explaining the brain: Mechanisms and the mosaic unity of neuroscience 2007, Clarendon Press, Oxford.
14. Craver, C., & Darden, L. (2001). Discovering mechanisms in neurobiology. In Machamer, P. K., Grush, R., & P. McLaughlin (Eds.), Theory and Method in the Neurosciences. Pittsburgh: University of Pittsburgh Press, pp. 112-137.
15. Darden L. Strategies for discovering mechanisms: Schema instantiation, modular subassembly, forward/backward chaining. Philosophy of Science 2002, 69:354-365.
16. Darden L. Thinking again about biological mechanisms. Philosophy of Science 2008, 75:958-969. 10.1086/594538.
17. Darden L., Craver C. Strategies in the interfield discovery of the mechanism of protein synthesis. Studies in History and Philosophy of Biological and Biomedical Sciences 2002, 33:1-28. 10.1016/S1369-8486(01)00021-8.
18. Dick J.E. Breast cancer stem cells revealed. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:3547-3549.
19. Donehower L.A., Harvey M., Slagle B.L., et al. Mice deficient for p53 are developmentally normal but susceptible to spontaneous tumours. Nature 1992, 356:215-221.
20. Donnenberg V.S., Donnenberg A.D. Multiple drug resistance in cancer revisited: The cancer stem cell hypothesis. Journal of clinical pharmacology 2005, 45:872-877. 10.1177/0091270005276905.
21. Eliyahu D., Goldfinger N., Pinhasi-Kimhi O., et al. Meth A fibrosarcoma cells express two transforming mutant p53 species. Oncogene 1988, 3:313-321.
22. Eliyahu D., Raz A., Gruss P., et al. Participation of p53 cellular tumour antigen in transformation of normal embryonic cells. Nature 1984, 312:646-649.
23. Finlay C.A., Hinds P.W., Levine A.J. The p53 proto-oncogene can act as a suppressor of transformation. Cell 1989, 57:1083-1093. 10.1016/0092-8674(89)90045-7.
24. Finlay C.A., Hinds P.W., Tan T.H., et al. Activating mutations for transformation by p53 produce a gene product that forms an hsc70-p53 complex with an altered half-life. Molecular and Cellular Biology 1988, 8:531-539.
25. Fleck L. Genesis and development of a scientific fact 1979, Chicago University Press, Chicago, (Translation of Entstehung und Entwicklung einer wissenschaftlichen Tatsache. Benno Schwabe und Co., 1935).
26. Fujimura J.H. The Molecular biological bandwagon in cancer research: Where social worlds meet. Social Problems 1988, 35:261-283. 10.1525/sp. 1988.35.3.03a00050.
27. Fujimura J.H. Crafting science: Standardization packages, boundary objects, and "translation". Science as practice and culture 1992, 168-211. University of Chicago Press, Chicago. A. Pickering (Ed.).
28. Germain P.-L. Cancer cells and adaptive explanations. Biology & Philosophy 2012, online first. 10.1007/s10539-012-9334-2.
29. Glennan S. Rethinking mechanistic explanation. Philosophy of Science 2002, 69:S342-S353. 10.1086/341857.
30. Glennan S. Modeling mechanisms. Studies in History and Philosophy of Biological and Biomedical Sciences 2005, 36:443-464. 10.1016/j.shpsc.2005.03.011.
31. Hanahan D., Weinberg R.A. The hallmarks of cancer. Cell 2000, 100:57-70.
32. Hempel C.G. Aspects of scientific explanation: And other essays in the philosophy of science 1965, The Free Press, New York.
33. Herskowitz I. Functional inactivation of genes by dominant negative mutations. Nature 1987, 329:219-222.
34. Hinds P., Finlay C., Levine A.J. Mutation is required to activate the p53 gene for cooperation with the ras oncogene and transformation. Journal of Virology 1989, 63:739-746.
35. Hitchcock C. Salmon on explanatory relevance. Philosophy of Science 1995, 62:304-320.
36. Jenkins J.R., Rudge K., Redmond S., Wade-Evans A. Cloning and expression analysis of full length mouse cDNA sequences encoding the transformation associated protein p53. Nucleic Acids Research 1984, 12:5609-5626.
37. Keating P., Cambrosio A. Cancer on trial: Oncology as a new style of practice 2012, University of Chicago Press, Chicago.
38. Keating P., Cambrosio A., Mackenzie M. The tools of the discipline: standards, models, and measures in the affinity/avidity controversy in immunology. The right tools for the job: at work in the Twentieth century life sciences 1992, 312-354. Princeton University Press, Princeton. A.E. Clark, J.H. Fujimura (Eds.).
39. Keller E.F. Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines 2003, Harvard University Press, Cambridge.
40. Kuhn T.S. The Structure of scientific revolutions. University of Chicago Press 1965, (3rd ed.). 10.1023/A:1006474128258 First published 1962.
41. Lane D.P. P53, guardian of the genome. Nature 1992, 358:15-16.
42. Lane D.P., Benchimol S. P53: Oncogene or anti-oncogene?. Genes & Development 1990, 4:1-8.
43. Lewis, D. (1986). Causal explanation. In Philosophical papers (Vol. II) (pp. 214-240). New York: Oxford University Press.
44. Linzer D.I., Levine A.J. Characterization of a 54K dalton cellular SV40 tumor antigen present in SV40-transformed cells and uninfected embryonal carcinoma cells. Cell 1979, 17:43-52.
45. Machamer P., Darden L., Craver C.F. Thinking about mechanisms. Philosophy of Science 2000, 67:1-25. 10.1086/392759.
46. Maugeri P., Blasimme A. Humanised models of cancer in molecular medicine: The experimental control of disanalogy. History and Philosophy of the Life Sciences 2011, 33:603-622.
47. Maenhaut C., Dumont J.E., Roger P.P., van Staveren W.C.G. Cancer stem cells: A reality, a myth, a fuzzy concept or a misnomer? An analysis. Carcinogenesis 2010, 31:149-158.
48. McCann J., Choi E., Yamasaki E., Ames B.N. Detection of carcinogens as mutagens in the Salmonella/microsome test: Assay of 300 chemicals. Proceedings of the National Academy of Sciences of the United States of America 1975, 72:5135-5139.
49. Mora P.T., Chandrasekaran K., McFarland V.W. An embryo protein induced by SV40 virus transformation of mouse cells. Nature 1980, 288:722-724.
50. Morange M. The discovery of cellular oncogenes. History and Philosophy of the Life Sciences 1993, 15:45-58.
51. Morange M. From the regulatory vision of cancer to the oncogene paradigm, 1975-1985. Journal of the History of Biology 1997, 30:1-29.
52. Muller H.J. Radiation and genetics. The American Naturalist 1930, 64:220-251.
53. Nicholson D.J. The concept of mechanism in biology. Studies in History and Philosophy of Biological and Biomedical Sciences 2012, 43:152-163. 10.1016/j.shpsc.2011.05.014.
54. Parada L.F., Land H., Weinberg R.A., et al. Cooperation between gene encoding p53 tumour antigen and ras in cellular transformation. Nature 1984, 312:649-651.
55. Pitot H.C., Heidelberger C. Metabolic regulatory circuits and carcinogenesis. Cancer Research 1963, 23:1694-1700.
56. Railton P. Deductive-nomological model of probabilistic explanation. Philosophy of Science 1978, 45:206-226.
57. Rheinberger H.-J. Toward a history of epistemic things: Synthesizing proteins in the test tube 1997, Stanford University Press, Stanford.
58. Salmon W.C. Scientific explanation and the causal structure of the world 1984, Princeton University Press, Princetone.
59. Salmon W.C. Four decades of scientific explanation 1989, University of Minnesota Press, Minneapolis.
60. Singh S.K., Clarke I.D., Terasaki M., et al. Identification of a cancer stem cell in human brain tumors. Cancer Research 2003, 63:5821-5828. 10.1038/nature03128.
61. Skipper R.A., Millstein R.L. Thinking about evolutionary mechanisms: Natural selection. Studies in History and Philosophy of Biological and Biomedical Sciences 2005, 36:327-347.
62. Sonnenschein C., Soto A.M. Theories of carcinogenesis: An emerging perspective. Seminars in Cancer Biology 2008, 18:372-377. 10.1016/j.semcancer.2008.03.012.
63. Srivastava S., Wang S., Tong Y.A., et al. Dominant negative effect of a germ-line mutant p53: A step fostering tumorigenesis. Cancer Research 1993, 53:4452-4455.
64. Stehelin D., Varmus H.E., Bishop J.M., Vogt P.K. DNA related to the transforming gene(s) of avian sarcoma viruses is present in normal avian DNA. Nature 1976, 260:170-173.
65. Temin H.M. On the origin of the genes for neoplasia: G. H. A. Clowes memorial lecture. Cancer Research 1974, 34(11):2835-2841.
66. Thompson P. The structure of biological theories 1989, State University of New York Press, Albany.
67. Vogelstein B., Kinzler K.W. The multistep nature of cancer. Trends in Genetics 1993, 9:138-141.
68. Vogelstein B., Lane D., Levine A.J. Surfing the P53 Network. Nature 2000, 408:307-310.
69. Willis A., Jung E.J., Wakefield T., Chen X. Mutant p53 exerts a dominant negative effect by preventing wild-type p53 from binding to the promoter of its target genes. Oncogene 2004, 23:2330-2338.
70. Wittgenstein L. Philosophical investigations 2001, Blackwell Publishing, Oxford, (Translation of Philosophische Untersuchungen, 1953).
71. Woodward J. A theory of singular causal explanation. Erkenntnis 1984, 21:231-262. 10.1007/BF00169275.
72. Woodward J. Making things happen: A theory of causal explanation 2003, Oxford University Press, New York.
73. World Health Organization (2012). Cancer: fact sheet. Geneva: World Health Organization. Accessed 09.10.12. http://www.who.int/mediacentre/factsheets/fs297/en/.