What is stemness?

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

Volumn 40, Issue 4, 2009, Pages 312-320

  Leychkis, Yan ^a   Munzer, Stephen R ^b   Richardson, Jessica L ^c  

^a Morrison and Foerster LLP   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Dedifferentiation; Entity theory; State theory; Transdifferentiation

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CHROMATIN IMMUNOPRECIPITATION; GENE; GENETIC ASSOCIATION; HUMAN; PHILOSOPHY; PROTEOMICS; STEM CELL;

ANIMALS; BIOLOGY; CHROMATIN IMMUNOPRECIPITATION; GENES; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, BIOLOGICAL; PHILOSOPHY; PROTEOMICS; STEM CELLS;

EID: 71749110718     PISSN: 13698486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.shpsc.2009.09.002     Document Type: Article

References (59)

1. Aristotle. (1984). Topics, Book VI. In idem, The complete works of Aristotle, Vol. 1 (J. Barnes, Ed.) (pp. 235-255). Princeton: Princeton University Press.
2. Bealer, G., & Mönnich, U. (1989). Property theories. In D. Gabbay, & F. Guenthner (Eds.), Handbook of philosophical logic, Vol. 4 (pp. 133-251). Dordrecht: D. Reidel.
3. Chargaff E. Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia 6 (1950) 201-209
4. Chin M.H., Mason M.J., Xie W., Volinia S., Singer M., Peterson C., Ambartsumyan G., Aimiuwu O., Richter L., Zhang J., Khvorostov I., Ott V., Grunstein M., Lavon N., Benvenisty N., Croce C.M., Clark A.T., Baxter T., Pyle A.D., Teitell M.A., Pelegrini M., Plath K., and Lowry W.E. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 5 (2009) 111-123
5. Cocchiarella N.B. Logical investigations of predication theory and the problem of universals (1986), Bibliopolis, Naples
6. Cocchiarella N.B. Formal ontology and conceptual realism (2007), Springer, Dordrecht
7. Daly, C. (1998). Natural kinds. Routledge encyclopedia of philosophy, Vol. 6 (pp. 682-685). London & New York: Routledge.
8. Evsikov, A. V., & Solter, D. (2003). Comment on '"Stemness": Transcriptional profiling of embryonic and adult stem cells' and 'A stem cell molecular signature'. Science, 302, 393. (Also available at www.sciencemag.org/cgi/content/full/302/5644/393c. Accessed 28 August 2009).
9. Feyerabend P. Against method: Outline of an anarchistic theory of knowledge (1975), New Left Books, London
10. Fortunel, N. O., Otu, H. H., Ng, H.-H., Chen, J., Mu, X., Chevassut, T., Li, X., Joseph, M., Bailey, C., Hatzfeld, J. A., Hatzfeld, A., Usta, F., Vega, V. B., Long, P. M., Liberman, T. A., & Lim, B. (2003). Comment on '"Stemness": Transcriptional profiling of embryonic and adult stem cells' and 'A stem cell molecular signature'. Science, 302, 393. (Also available at www.sciencemag.org/cgi/content/full/302/5644/393b. Accessed 28 August 2009).
11. Franklin R.E., and Gosling R.G. Molecular configuration in sodium thymonucleate. Nature 171 (1953) 740-741
12. Hochedlinger, K., & Plath, K. (2009). Epigenetic reprogramming and induced pluripotency. Development, 136, 509-523.
13. Ivanova N.B., Dimos J.T., Schaniel C., Hackney J.A., Moore K.A., and Lemischka I.R. A stem cell molecular signature. Science 298 (2002) 601-604
14. Ivanova, N. B., Dimos, J. T., Schaniel, C., Hackney, J. A., Moore, K. A., Ramalho-Santos, M., Yoon, S., Matsuzaki, Y., Mulligan, R. C., Melton, D. A., & Lemischka, I. R. (2003). Response to comments on '"Stemness": Transcriptional profiling of embryonic and adult stem cells' and 'A stem cell molecular signature'. Science, 302, 393. (Also available at www.sciencemag.org/cgi/content/full/302/5644/393d. Accessed 28 August 2009).
15. Kim J. Concepts of supervenience. Philosophy and Phenomenological Research 45 (1984) 153-176
16. Kripke S. Naming and necessity (1980), Harvard University Press, Cambridge, MA
17. Kuhn T.S. The essential tension: Selected studies in scientific tradition and change (1977), University of Chicago Press, Chicago & London
18. Lewitzky, M., & Yamanaka, S. (2007). Reprogramming somatic cells towards pluripotency by defined factors. Current Opinion in Biotechnology, 18, 467-473.
19. Locke, J. (1959). An essay concerning human understanding (A. C. Fraser, Ed.). New York: Dover. (First published 1689).
20. Loh Y.-H., Wu Q., Chew J.-L., Vega V.B., Zhang W., Chen X., Bourque G., George J., Leong B., Liu J., Wong K.-Y., Sung K.W., Lee C.W.H., Zhao X.-D., Chiu K.-P., Lipovich L., Kuznetsov V.A., Robson P., Stanton L.W., Wei C.-L., Ruan Y., Lim B., and Ng H.-H. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nature Genetics 38 (2006) 431-440
21. Maherali N., Sridharan R., Xie W., Utikal J., Eminli S., Arnold K., Stadtfeld M., Yachechko R., Tchieu J., Jaenisch R., Plath K., and Hocheldinger K. Directly reprogrammed fibrolasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell 1 (2007) 55-70
22. Masui S., Nakataki Y., Toyooka Y., Shimosato D., Yagi R., Takahashi K., Okochi H., Okuda A., Matoba R., Sharov A.A., Ko M.S., and Niwa H. Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nature Cell Biology 9 (2007) 625-635
23. Mazurier F., Doedens M., Gan O.I., and Dick J.E. Rapid myeloerythroid repopulation after intrafemoral transplantation of NOD-SCID mice reveals a new class of human stem cells. Nature Medicine 9 (2003) 959-969
24. Moore, K. A., & Lemischka, I. R. (2006). Stem cells and their niches. Science, 311, 1880-1885.
25. Morgan T.H. Experimental studies of the regeneration of planaria maculata. Wilhelm Roux' Archiv für Entwicklungsmechanik der Organismen 7 (1898) 364-397
26. Neumann J.von. Mathematische Grundlagen der Quantenmechanik (1932), Springer, Berlin
27. Newmark, P. A., & Alvarado, A. S. (2002). Not your father's planarian: A classic model enters the era of functional genomics. Nature Reviews Genetics, 3, 210-219.
28. Nishikawa S., Goldstein R.A., and Nierras C.R. The promise of human induced pluripotent stem cells for research and therapy. Nature Reviews Molecular Cell Biology 9 (2008) 725-729
29. Player A., Wang Y., Bhattacharya B., Rao M., Puri R.K., and Kawasaki E.S. Comparisons between transcriptional regulation and RNA expression in human embryonic stem cell lines. Stem Cells and Development 15 (2006) 315-323
30. Popper K.R. The logic of scientific discovery (1959), Basic Books, New York
31. Pritsker M., Ford N.R., Jenq H.T., and Lemischka I.R. Genomewide gain-of-function genetic screen identifies functionally active genes in mouse embryonic stem cells. Proceedings of the National Academy of Sciences USA 103 (2006) 6946-6951
32. Putnam, H. (1975). Philosophical papers, Vol. 2. Mind, language, and reality. Cambridge: Cambridge University Press.
33. Real C., Glavieux-Pardanaud C., Douarina N.M., and Dupin E. Clonally cultured differentiated pigment cells can dedifferentiate and generate multipotent progenitors with self-renewing potential. Developmental Biology 300 (2006) 656-669
34. Romalho-Santos M., Yoon S., Matsuzaki Y., Mulligan R.C., and Melton D.A. 'Stemness': Transcriptional profiling of embryonic and adult stem cells. Science 298 (2002) 597-600
35. Russell B. The principles of mathematics (1903), Cambridge University Press, Cambridge
36. Salvetti A., Rossi L., Lena A., Batistoni R., Deri P., Rainaldi G., Locci M.T., Evangelista M., and Gremigni V. DjPum, a homologue of Drosophila Pumilio, is essential to planarian stem cell maintenance. Development 132 (2005) 1863-1874
37. Sato, N., & Brivanlou, A.H. (2006). Microarray approach to identify the signaling network responsible for self-renewal of human embryonic stem cells. In K. Turksen (Ed.), Human embryonic stem cell protocols. Methods in Molecular Biology, Vol. 331 (pp. 267-283). Totowa, NJ: Humana Press.
38. Sharif A., Legendre P., Prévot V., Allet C., Romao L., Studler J.M., Chneiweiss H., and Junier M.P. Transforming growth factor α promotes sequential conversion of mature astrocytes into neural progenitors and stem cells. Oncogene 26 (2006) 2695-2706
39. Slack, J. M. W., & Tosh, D. (2001). Transdifferentiation and metaplasia: Switching cell types. Current Opinion in Genetics & Development, 11, 581-586.
40. Smith K.P., Luong M.X., and Stein G.S. Pluripotency: Toward a gold standard for human ES and iPS cells. Journal of Cellular Physiology 220 (2009) 21-29
41. Suppe F. The semantic conception of theories and scientific realism (1989), University of Illinois Press, Urbana & Chicago
42. Takahashi, K., & Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 126, 663-676.
43. Tosh, D., & Slack, J. M. W. (2002). How cells change their phenotype. Nature Reviews Molecular Cell Biology, 3, 187-194.
44. Thomson, J. A. Wisconsin Alumni Research Foundation. (1998). Primate embryonic stem cells. US Patent No. 5,843,780. Washington, DC: US Patent Office.
45. Thomson, J. A. Wisconsin Alumni Research Foundation. (2001). Primate embryonic stem cells. US Patent No. 6,200,806. Washington, DC: US Patent Office.
46. Van Fraassen B. The scientific image (1980), Clarendon Press, Oxford
47. Vogel G. 'Stemness' genes still elusive. Science 302 (2003) 371
48. Voncken, J. W., & Hofker, M. (2005). Transgenic mice in biomedical research. In R. A. Meyers (Ed.), Encyclopedia of molecular cell biology and molecular medicine, Vol. 14 (pp. 505-546). Weinheim: Wiley-VCH Verlag.
49. Wagers, A. J., & Weissman, I. L. (2004). Plasticity of adult stem cells. Cell, 116, 639-648.
50. Wang, J., & Orkin, S. H. (2008). A protein roadmap to pluripotency and faithful reprogramming. Cells Tissues Organs, 188, 23-30.
51. Watson, J. D., & Crick, F. H. C. (1953). Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature, 171, 737-738.
52. Wilkerson T.E. Natural kinds (1995), Avebury Press, Aldershot
53. Wittgenstein, L. (1953). Philosophical investigations (G. E. M. Anscombe, Trans.) New York: Macmillan.
54. Worrall J. The value of a fixed methodology. British Journal for the Philosophy of Science 39 (1988) 263-275
55. Zhang L., Rayner S., Katoku-Kikyo N., Romanova L., and Kikyo N. Successful co-immunoprecipitation of Oct4 and Nanog using cross-linking. Biochemistry and Biophysics Research Communications 28 (2007) 611-614
56. Zhou Q., and Melton D.A. Extreme makeover: Converting one cell into another. Cell Stem Cell 3 (2008) 382-388
57. Zipori D. The nature of stem cells: State rather than entity. Nature Reviews Genetics 5 (2004) 873-878
58. Zipori D. The stem state: Plasticity is essential, whereas self-renewal and hierarchy are optional. Stem Cells 23 (2005) 719-726
59. Zipori, D. (2006). Personal communication. Letter dated 18 October 2006 to Stephen R. Munzer.