Abstract
In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior—both conceptually and explanatory—to entities, and that in the biological realm entities are defined primarily by the context they are embedded within—and hence by the web of relations they are part of.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Morange M (1998) A history of molecular biology. Harvard University Press, Cambridge, MA
Rheinberger H-J (2007) What happened to molecular biology? BIF Futura 22:218–223
Weinberg RA (2014) Coming full circle-from endless complexity to simplicity and back again. Cell 157(1):267–271. https://doi.org/10.1016/j.cell.2014.03.004
Darden L (2006) Reasoning in biological discoveries. Cambridge University Press, Cambridge, UK
Bechtel W, Richardson R (2010) Discovering complexity - decomposition and localization as strategies in scientific research. The MIT Press, Cambridge, MA
Nicholson DJ (2010) Biological atomism and cell theory. Stud Hist Philos Biol Biomed Sci 41(3):202–211. https://doi.org/10.1016/j.shpsc.2010.07.009
Garraway LA, Lander ES (2013) Lessons from the cancer genome. Cell 153(1):17–37. https://doi.org/10.1016/j.cell.2013.03.002
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW (2013) Cancer genome landscapes. Science (New York, NY) 339(6127):1546–1558. https://doi.org/10.1126/science.1235122
Bizzarri M, Cucina A (2016) SMT and TOFT: why and how they are opposite and incompatible paradigms. Acta Biotheor 64(3):221–239. https://doi.org/10.1007/s10441-016-9281-4
Nicholson DJ (2012) The concept of mechanism in biology. Stud Hist Philos Biol Biomed Sci 43(1):152–163. https://doi.org/10.1016/j.shpsc.2011.05.014
Bizzarri M, Palombo A, Cucina A (2013) Theoretical aspects of systems biology. Prog Biophys Mol Biol 112(1–2):33–43. https://doi.org/10.1016/j.pbiomolbio.2013.03.019
Bertolaso M (2016) Philosophy of cancer: a dynamic and relational view. Springer, New York
Esfeld M (2003) Do relations require underlying intrinsic properties?—a physical argument for a metaphysics of relations. Metaphysica 4(1):5–25
Boem F, Ratti E, Andreoletti M, Boniolo G (2016) Why genes are like lemons. Stud Hist Philos Biol Biomed Sci 57:88–95. https://doi.org/10.1016/j.shpsc.2016.04.005
Barabási A-L, Oltvai ZN (2004) Network biology: understanding the cell’s functional organization. Nat Rev Genetics 5(2):101–113. https://doi.org/10.1038/nrg1272
Wolff J (2011) Do objects depend on structures? Br J Philos Sci 63(3):607–625. https://doi.org/10.1093/bjps/axr041
Craver CF (2016) The explanatory power of network models. Philos Sci 83(5):698–709
Palumbo MC et al (2005) Functional essentiality from topology features in metabolic networks: a case study in yeast. FEBS Lett 579(21):4642–4646
Palumbo MC et al (2007) Essentiality is an emergent property of metabolic network wiring. FEBS Lett 581(13):2485–2489
Bertolaso M, Giuliani A, Filippi S (2013) The mesoscopic level and its epistemological relevance in systems biology, Recent advances in systems biology. Nova Science Publishers, Inc., New York, pp 19–36
Giuliani A (2010) Collective motions and specific effectors: a statistical mechanics perspective on biological regulation. BMC Genomics 11(Suppl 1):S2
Bissell MJ, Hall HG, Parry G (1982) How does the extracellular matrix direct gene expression? J Theor Biol 99(1):31–68
Bissell MJ et al (2002) The organizing principle: microenvironmental influences in the normal and malignant breast. Differentiation 70(9–10):537–546
Correia AL, Bissell MJ (2012) The tumor microenvironment is a dominant force in multidrug resistance. Drug Resist Updat 15(1–2):39–49
Boogerd FC et al (2005) Emergence and its place in nature: a case study of biochemical networks. Synthese 145(1):131–164
Sonnenschein C, Soto AM (1999) The society of cells: cancer and control of cell proliferation. Springer, New York
Soto AM, Sonnenschein C (2004) The somatic mutation theory of cancer: growing problems with the paradigm? BioEssays 26(10):1097–1107
Jaffe L (2005) Response to paper by Henry Harris. BioEssays 27(11):1206
Feinberg AP, Ohlsson R, Henikoff S (2006) The epigenetic progenitor origin of human cancer. Nat Rev Genet 7(1):21–33
Heng HHQ et al (2006) Cancer progression by non-clonal chromosome aberrations. J Cell Biochem 98(6):1424–1435
Harris DP et al (2005) Regulation of IFN-gamma production by B effector 1 cells: essential roles for T-bet and the IFN-gamma receptor. J Immunol 174(11):6781–6790
Huang A et al (2002) Serum tryptophan decrease correlates with immune activation and impaired quality of life in colorectal cancer. Br J Cancer 86(11):1691–1696
Martien S, Abbadie C (2007) Acquisition of oxidative DNA damage during senescence: the first step toward carcinogenesis? Ann N Y Acad Sci 1119:51–63
Mintz B, Illmensee K (1975) Normal genetically mosaic mice produced from malignant tera-tocarcinoma cells. Proc Natl Acad Sci U S A 72:3585–3589
Hochedlinger K, Blelloch R, Brennan C, Yamada Y, Kim M, Chin L, Jaenisch R (2004) Reprogramming of a melanoma genome by nuclear transplantation. Genes Dev 18:1875–1885
Kenny PA, Bissell MJ (2003) Tumor reversion: correction of malignant behaviour by microenvironmental cues. Int J Cancer 107:688–695
Lotem J, Sachs L (2002) Epigenetics wins over genetics: induction of differentiation in tumor cells. Semin Cancer Biol 12:339–346
Sharpless NE, De Pinho RA (2007) How stem cells age and why this makes us grow old. Nat Rev Mol Cell Biol 8:703–713
Oakley EJ, Van Zant G (2007) Unraveling the complex regulation of stem cells: implications for aging and cancer. Leukemia 21:612–621
Finkel T, Serrano M, Blasco MA (2007) The common biology of cancer and ageing. Nature 448:767–774
Soto AM, Maffini MV, Sonnenschein C (2008) Neoplasia as development gone awry: the role of endocrine disruptors. Int J Androl 31(2):288–293
Biava, P. M. (1999). Complexity and cancer. Leadership Medica 1. Vedi (accesso di marzo 2008)
Biava PM (2002) Complessità e biologia. Il cancro come patologia della comunicazione. Mondadori, Milano
Abbs S, Bussoli T, Kavalier F (2004) Nature encyclopaedia of the human genome. BJM 328:172
Marker PC (2008) Does prostate cancer co-opt the developmental program? Differentiation 76:736–744
Soto AM, Sonnenschein C (2011) The tissue organization field theory of cancer: a testable replacement for the somatic mutation theory. BioEssays 33(5):332–340
Rubin H (2011) Fields and field cancerization: the preneoplastic origins of cancer: asymptomatic hyperplastic fields are precursors of neoplasia, and their progression to tumors can be tracked by saturation density in culture. BioEssays 33(3):224–231
Capp J-P (2005) Stochastic gene expression, disruption of tissue averaging effects and cancer as a disease of development. BioEssays 27(12):1277–1285
Maitra A et al (2005) Genomic alterations in cultured human embryonic stem cells. Nat Genet 37(10):1099–1103
Prehn RT (1994) Cancers beget mutations versus mutations beget cancers. Cancer Res 54(20):5296–5300
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Bertolaso, M., Ratti, E. (2018). Conceptual Challenges in the Theoretical Foundations of Systems Biology. In: Bizzarri, M. (eds) Systems Biology. Methods in Molecular Biology, vol 1702. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7456-6_1
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7456-6_1
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7455-9
Online ISBN: 978-1-4939-7456-6
eBook Packages: Springer Protocols