On the position of biology in systems biology

Constantinos Mekios

Resumen


Although the term “systems biology” describes a wide range of diverse research projects, a common feature of systems approaches in biology is that they rely on contributions from various non-biological disciplines. Inspired by Ernst Mayr’s concerns about biological autonomy, this essay explores the status of biology within this evolving, multidisciplinary scientific landscape. After briefly considering competing theoretical views about the optimal role of biology in systems biology, the focus turns on two examples that illustrate distinct strategies for its implementation. On the basis of these examples, I argue that traditional biological concepts remain essential for elucidating meaning from the mathematical models used to represent the experimental results, both in top-down and in bottom-up versions of systems biology. The paper concludes with a discussion of the philosophical implications of the preceding analysis for the normative issue regarding biological autonomy: should biological autonomy be maintained for systems biology to fulfill its aims? The viability of the alternative cannot be excluded a priori. The observed effectiveness of pluralistic explanation in current systems biology, however, suggests that the continuing contributions of an autonomous biology, with its own irreducible concepts and methods, would not obstruct the development of an integrative systems approach but would rather advance its agenda.

 

Key Words. Biological autonomy, systems biology, reductionism, complexity, explanatory pluralism.


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Referencias


Aderem, A. (2005), “Systems biology: Its practice and challenges”, Cell 121: 511-513.

Aebersold, R. (2005), “Molecular systems biology: A new journal for a new biology?” Molecular Systems Biology 1: 1-2. http://www.nature.com/msb/journal/v1/n1/full/msb4100009.html. (Accessed 10 June 2014)

Albert, R. (2005), “Scale-free networks in cell biology”, Journal of Cell Science 118: 4947-4957.

Alon, U. (2006), An Introduction to Systems Biology, Boca Raton: Chapman and Hall.

Ayala F.J. (1968), “Biology as an autonomous science”, American Scientist 56: 207-221.

Baliga, N.S., Bjork, S.J., Bonneau, R., Pan, M., Iloanusi, C., Kottemann, M.C.H., Hood, L., Di Ruggiero, J. (2004), “System level insights into the stress response to UV radiation in the Hallophilic Archaeon Halobacterium NRC-1”, Genome Research 14: 1025-1035.

Barabasi, A.-L., Oltvai, Z.N. (2004), “Network biology: understanding the cell’s functional organization”, Nature Reviews Genetics 5: 101-113.

Bechtel, W. (2011), “Mechanism and biological explanation”, Philosophy of Science, 78: 533-557.

Braillard, P.-A. (2010), “Systems biology and the mechanistic framework”, History and Philosophy of the Life Sciences 32: 43-62.

Brent, R. (1999), “Functional genomics: Learning to think about gene expression data”, Current Biology 9: R338-341.

Brigandt, I. (2010), “Beyond reduction and pluralism: Toward an epistemology of explanatory integration in biology”, Erkenntnis 73: 295-311.

Bruggeman, F.J., Westerhoff, H.V. (2006), “The nature of systems biology”, Trends in Microbiology 15: 45-50.

Calvert, J., Fujimura, J.H. (2009), “Calculating life? A sociological perspective on systems biology”, EMBO 10: S46-S49.

Calvert, J., Fujimura, J.H. (2011), “Calculating life? Duelling discources in interdisciplinary systems biology”, Studies in History and Philosophy of Biological and Biomedical Sciences 42: 155-163.

Carrera, J., Rodrigo, G., Jaramillo, A., Elena, S.F. (2009), “Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions”, Genome Biology 10(9): R96.

Dorogovtsev, S.N., Mendes, J.F.F. (2003), Evolution of Networks: From Biological Nets to the Internet and WWW, Oxford: Oxford University Press.

Fischbach, M.A., Krogan, N.J. (2010), “The next frontier of systems biology: Higher-order and interspecies interactions” Genome Biology, 11: 208.

Fraser, A.G., Marcotte, E.M. (2004), “A probabilistic view of gene function”, Nature Genetics 36: 559-564.

Gatherer, D. (2010), “So what do we really mean when we say that systems biology is holistic?”, BMC Systems Biology 4: 22.

Grantham, T.A. (2004), “Conceptualizing the (dis)unity of science”, Philosophy of Science 71: 133-155.

Green, S., Wolkenhauer, O. (2013), “Tracing organizing principles: Learning from the history of systems biology”, History and Philosophy of the Life Sciences 35: 553-576.

Guido, N.J., Wang, X., Adalsteinsson, D., McMillen, D., Hasty, J., Cantor, C.R., Elston, T.C., Collins, J.J. (2006), “A bottom-up approach to gene regulation”, Nature 439: 856-860.

Hamilton, A. (2007), “Laws of biology, laws of nature: Problems and (dis)solutions”, Philosophy Compass 2: 592-610.

Haubelt, A., Bullinger, E., Sauter, T., Allgöwer, F., Gilles, E.D. (2004), “Systems biology — A glosary from two perspectives: What biology says and systems theory understands — and vice versa”, http://www.sysbio.de/projects/glossary. (Accessed 10 June 2014)

Huang, S. (2004), “Back to the biology in systems biology: What can we learn from biomolecular networks?” Briefings in Functional Genomics and Proteomics 2: 279-297.

Hyman, A.A. (2011), “Whither systems biology”, Philosophical Transactions of The Royal Society B 366: 3635-3637.

Ideker, T., Thorsson, V., Ranish, J.A., Christmas, R., Buhler, J., Eng, J.K., Bumgarner, R., Goodlett, D.R., Aebersold, R., Hood, L. (2001), “Integrated genomic and proteomic analyses of a systematically perturbed metabolic network”, Science 292: 929-934.

Jaeger, J., Crombach, A. (2012), “Life’s attractors”, in Soyer, O. (ed.), Evolutionary Systems Biology, Dordrecht: Springer, pp. 93-119.

Joyner, M.J., Pedersen, B.K. (2011), “Ten questions about systems biology”, The Journal of Physiology 24: 1017-1030.

Kitano, H., 2001, “Systems biology: Toward system-level understanding of biological systems”, in Kitano, H. (ed.), Foundations of Systems Biology, Cambridge: MIT Press, pp. 1-36.

Klipp, E., Herwig, R., Kowald, A., Wierling, C., Lehrach, H. (2005), Systems Biology in Practice, Weinheim: Wiley-VCH.

Krohs, U., Callebaut, W. (2007), “Data without models merging with models without data”, in Boogerd, F.C., Bruggeman, F.J., Hofmeyer, J.-H.S, Westerhoff, H.V. (Eds.), Systems Biology: Philosophical Foundations, Amsterdam: Elsevier, pp. 181-213.

Levesque, M.P., Benfey, P.N., 2004, “Systems biology”, Current Biology 14: R179R180.

Love, A.C. (2008), “Explaining evolutionary innovations and novelties: Criteria of explanatory adequacy and epistemological prerequisites”, Philosophy of Science 75: 874-886.

Machamer, P., Darden, L., Craver, C.F. (2000), “Thinking about mechanisms”, Philosophy of Science 67: 1-25.

MacLeod, M., Nersessian, N.J. (2013), “Coupling simulation and experiment: The bimodal strategy in integrative systems biology”, Studies in History and Philosophy of Biological and Biomedical Sciences 44: 572-584.

Mayr, E. (1988), Toward a New Philosophy of Biology, Cambridge: Harvard University Press.

Mayr, E. (2004), What Makes Biology Unique? Considerations on the Autonomy of a Scientific Discipline, Cambridge: Cambridge University Press.

McCarthy, J., (2004), “Tackling the challenges of interdisciplinary bioscience”, Nature Reviews Molecular Cell Biology, 5: 933-937.

Mesarovic, M.D., Sreenath, S.N., Keene, J.D., (2004), “Search for organizing principles: Understanding in systems biology”, Systems Biology 1: 19-27. Mitchell, S. (1997), “Pragmatic laws”, Philosophy of Science 64: S468-S479.

Morange, M. (2011), “Recent opportunities for an increasing role for physical explanations in biology”, Studies in History and Philosophy of Biological and Biomedical Sciences 42: 139-144.

Needham, C.J., Manfield, I.W., Pulpitt, A.J., Gilmartin, P.M., Westhead, D.R., 2009, “From gene expression to gene regulatory networks in Arabidopsis thaliana”, BMC Systems Biology, 3: 85.

Nielson, F., Nielson, H.R., Priami, C., Rosa, D. (2004), “Static analysis for systems biology”, ACM International Conference Proceeding Series Archive (Proceedings for the Winter International Symposium on Information and Communication Technologies – Systeomatics Workshop, Cancun: 1-6).

O’Malley, M.A., Dupre, J. (2005), “Fundamental issues in systems biology”, BioEssays 27: 1270-1276.

O’Malley, M.A. (2012), “Evolutionary systems biology: Historical and philosophical perspectives on an emerging synthesis”, in Soyer, O. (ed.), Evolutionary Systems Biology, Dordrecht: Springer, pp. 1-28.

Street, N., Jansson, S., Hvidsten, T.R. (2011), “A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation”, BMC Plant Biology 11: 13.

Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E.S., Golub, T.R. (1999), “Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation”, Proceedings of the National Academy of Sciences of the United States of America 96: 2907-2912.

von Bertalanffy, L., 1968, General System Theory, New York: George Braziller, Inc.

Westerhoff, H.V., Palsson, B.O. (2004), “The evolution of molecular biology into systems biology”, Nature Biotechnology 22: 1249-1252.

Westerhoff H.V., Kell, D.B., 2007, “The methodologies of systems biology”, in Boogerd, F.C., Bruggeman, F.J., Hofmeyr, J.-H.S., Westerhoff, H.V. (eds.) (2007) Systems Biology: Philosophical Foundations, Amsterdam: Elsevier, pp. 23-70.

Wimsatt, W. (1972), “Complexity and organization”, in Schaffner, K.F., Cohen, R.S. (eds.), Proceedings of the Philosophy of Science Association, Dordrecht: Reidel, pp. 67-86.

Winther, R. (2006), “Parts and theories in compositional biology”, Biology and Philosophy 21: 471-499.

Woodward, J. (2003), Making Things Happen, Oxford: Oxford University Press.

Wouters, A. (2007), “Design explanation: Determining the constraints on what can be alive”, Erkenntnis 67: 65-80.

Yi, T.M., Huang, Y., Simon, M.I., Doyle, J. (2000), “Robust perfect adaptation in bacterial chemotaxis through integral feedback control”, Proceedings of the National Academy of Sciences 97: 4649-4653.


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