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Biological Complexity and the Need for Computational Approaches

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Philosophy of Systems Biology

Part of the book series: History, Philosophy and Theory of the Life Sciences ((HPTL,volume 20))

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“Biological systems are highly complicated, non-linear, and require very high-dimensional and high volume data analysis. In reality, we are as human beings not good at handling such data. How can we understand biological systems in face of this complexity? This is the major challenge for biological and biomedical research. I would claim that a combination of artificial intelligence and human research is the most powerful way to proceed, rather than relying solely on the human brain in trying to understand biology… The most powerful research team will consist of highly intelligent AI systems and human researchers. Just like we need high-throughput measurement devices and next generation sequencers for any high profile research institution in systems biology today, so will highly intelligent AI systems sooner or later be mandatory for any future high profile research institution.”

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References

  • Bak, P., Tang, C., & Wiesenfeld, K. (1988). Self-organized criticality. Physical Review A, 38, 364–374.

    Article  Google Scholar 

  • Bode, H. W. (1945). Network analysis and feedback amplifier design. Melbourne: Krieger.

    Google Scholar 

  • Cannon, W. (1932). The wisdom of the body. New York: Norton.

    Google Scholar 

  • Carlson, J. M., & Doyle, J. (1999). Highly optimized tolerance: A mechanism for power laws in designed systems. Physical Review E – Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 60, 1412–1427.

    Google Scholar 

  • Carlson, J. M., & Doyle, J. (2002). Complexity and robustness. Proceedings of the National Academy of Sciences USA, 99(Suppl 1), 2538–2545.

    Article  Google Scholar 

  • Chen, K. C., Calzone, L., Csikasz-Nagy, A., Cross, F. R., Novak, B., & Tyson, J. J. (2004). Integrative analysis of cell cycle control in budding yeast. Molecular Biology of the Cell, 15, 3841–3862.

    Article  Google Scholar 

  • Clarke, A. C. (1962). Hazards of prophecy: The failure of imagination. In A. C. Clarke (Ed.), Profiles of the future: An enquiry into the limits of the possible. London: Phoenix.

    Google Scholar 

  • Covert, M. W., & Palsson, B. O. (2002). Transcriptional regulation in constraint-based metabolic models of Escherichia coli. The Journal Biological Chemistry, 277, 28058–28064.

    Article  Google Scholar 

  • Covert, M. W., Schilling, C. H., Famili, I., Edwards, J. S., Goryanin, I. I., Selkov, E., & Palsson, B. O. (2001). Metabolic modeling of microbial strains in silico. Trends in Biochemical Sciences, 26, 179–186.

    Article  Google Scholar 

  • Csermely, P., Agoston, V., & Pongor, S. (2005). The efficiency of multi-target drugs: The network approach might help drug design. Trends in Pharmacological Sciences, 26, 178–182.

    Article  Google Scholar 

  • Csete, M. E., & Doyle, J. C. (2002). Reverse engineering of biological complexity. Science, 295, 1664–1669.

    Article  Google Scholar 

  • Csete, M. E., & Doyle, J. (2004). Bow ties, metabolism and disease. Trends in Biotechnology, 22, 446–450.

    Article  Google Scholar 

  • Doyle, J., Francis, B., & Tannenbaum, A. (2009). Feedback control theory. New York: Dover.

    Google Scholar 

  • Duarte, N. C., Herrgard, M. J., & Palsson, B. O. (2004). Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Research, 14(7), 1298–1309.

    Article  Google Scholar 

  • Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., … Palsson, B. O. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences USA, 104, 1777–1782.

    Google Scholar 

  • Ferrucci, D., Brown, E., Chu-Carroll, J., Fan, J., Gondek, D., Kalyanpur, A., … Welty, C. (2010). Building Watson: An overview of the DeepQA project. AI Magazine, 31, 59–79.

    Google Scholar 

  • Ferrucci, D., Levas, A., Bagchi, S., Gondek, D., & Mueller, E. (2011). Watson: Beyond Jeopardy! Artificial Intelligence, 199, 93–105.

    Google Scholar 

  • Ghosh, S., Matsuoka, Y., Asai, Y., Hsin, K. Y., & Kitano, H. (2011). Software for systems biology: From tools to integrated platforms. Nature Reviews Genetics, 12, 821–832.

    Google Scholar 

  • Hale, V., Keasling, J. D., Renninger, N., & Diagana, T. T. (2007). Microbially derived artemisinin: A biotechnology solution to the global problem of access to affordable antimalarial drugs. The American Journal of Trophical and Medicine and Hygiene, 77, 198–202.

    Google Scholar 

  • Hsu, F.-H. (2004). Behind deep blue: Buidling the computer that defeated the World Chess Champion. Princeton: Princeton University Press.

    Google Scholar 

  • Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., … Wang, J. (2003). The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524–531.

    Google Scholar 

  • Imai, S., & Kitano, H. (1998). Heterochromatin islands and their dynamic reorganization: A hypothesis for three distinctive features of cellular aging. Experimental Gerontology, 33, 555–570.

    Article  Google Scholar 

  • Imai, S., Johnson, F. B., Marciniak, R. A., McVey, M., Park, P. U., & Guarente, L. (2000). Sir2: An NAD-dependent histone deacetylase that connects chromatin silencing, metabolism, and aging. Cold Spring Harbor Symposia on Quantitative Biology, 65, 297–302.

    Article  Google Scholar 

  • Kitano, H. (1993). Speech-to-speech translation: A massively parallel memory-based approach. New York: Springer.

    Google Scholar 

  • Kitano, H. (2002a). Computational systems biology. Nature, 420, 206–210.

    Article  Google Scholar 

  • Kitano, H. (2002b). Systems biology: A brief overview. Science, 295, 1662–1664.

    Article  Google Scholar 

  • Kitano, H. (2004a). Biological robustness. Nature Reviews Genetics, 5, 826–837.

    Article  Google Scholar 

  • Kitano, H. (2004b). Cancer as a robust system: Implications for anticancer therapy. Nature Reviews Cancer, 4, 227–235.

    Article  Google Scholar 

  • Kitano, H. (2007a). A robustness-based approach to systems-oriented drug design. Nature Reviews Drug Discovery, 6, 202–210.

    Article  Google Scholar 

  • Kitano, H. (2007b). Towards a theory of biological robustness. Molecular Systems Biology, 3, 137.

    Article  Google Scholar 

  • Kitano, H. (2016). Artificial Intelligence to Win the Nobel Prize and Beyond: Creating the Engine for Scientific Discovery. AI Magazine, 37(1), 39–49.

    Google Scholar 

  • Kitano, H., & Hendler, J. (Eds.). (1994). Massively parallel artificial intelligence. Boston: The MIT Press.

    Google Scholar 

  • Kitano, H., & Imai, S. (1998). The two-process model of cellular aging. Experimental Gerontology, 33, 393–419.

    Article  Google Scholar 

  • Kitano, H., Asada, M., Kuniyoshi, Y., Noda, I., Osawa, E., & Matsubara, H. (1997a). RoboCup: A challenge problem for AI. AI Magazine, 18, 73–85.

    Google Scholar 

  • Kitano, H., Hamahashi, S., Kitazawa, J., Takao, K., & Imai, S. (1997b). The virtual biology laboratories: A new approach of computational biology. Paper presented at the proceedings of the fourth European conference on artificial life, Brighton, UK.

    Google Scholar 

  • Kitano, H., Hamahashi, S., & Luke, S. (1998). The perfect C. elegans project. An initial report. Artificial Life, 4(2), 141–156.

    Article  Google Scholar 

  • Kitano, H., Ghosh, S., & Matsuoka, Y. (2011). Social engineering for virtual ‘big science’ in systems biology. Nature Chemical Biology, 7, 323–326.

    Google Scholar 

  • Korzybski, A. (1933). Science and sanity: An introduction to non-Aristotelian systems and general semantics. Chicago: Institute of General Semantics.

    Google Scholar 

  • Lakoff, G. (1987). Women, fire, and dangerous things: What categories reveal about the mind. Chicago: University of Chicago Press.

    Book  Google Scholar 

  • Le Novere, N., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., … Kitano, H. (2009). The systems biology graphical notation. Nature Biotechnology, 27, 735–741.

    Google Scholar 

  • Novak, B., & Tyson, J. J. (1993). Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos. Journal of Cell Science, 106, 1153–1168.

    Google Scholar 

  • Novak, B., Toth, A., Csikasz-Nagy, A., Gyorffy, B., Tyson, J. J., & Nasmyth, K. (1999). Finishing the cell cycle. The Journal of Theoretical Biology, 199, 223–233.

    Article  Google Scholar 

  • Oda, K., & Kitano, H. (2006). A comprehensive map of the toll-like receptor signaling network. Molecular Systems Biology, 2(2006), 0015.

    Google Scholar 

  • Oda, K., Matsuoka, Y., Funahashi, A., & Kitano, H. (2005). A comprehensive pathway map of epidermal growth factor receptor signaling. Molecular Systems Biology, 1, E1–E17.

    Article  Google Scholar 

  • Prigogine, I., & Nicolis, G. (1971). Biological order, structure and instabilities. Quarterly Reviews of Biophysics, 4, 107–148.

    Article  Google Scholar 

  • Prigogine, I., Nicolis, G., & Babloyantz, A. (1974). Nonequilibrium problems in biological phenomena. Annals of the New York Academy of Sciences, 231, 99–105.

    Article  Google Scholar 

  • Ro, D. K., Paradise, E. M., Ouellet, M., Fisher, K. J., Newman, K. L., Ndungu, J. M., … Keasling, J. D. (2006). Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature, 440, 940–943.

    Google Scholar 

  • Schoeberl, B., Pace, E. A., Fitzgerald, J. B., Harms, B. D., Xu, L., Nie, L., … Nielsen, U. B. (2009). Therapeutically targeting ErbB3: A key node in ligand-induced activation of the ErbB receptor-PI3K axis. Science Signaling, 2, ra31.

    Google Scholar 

  • Schoeberl, B., Faber, A. C., Li, D., Liang, M. C., Crosby, K., Onsum, M., … Wong, K. K. (2010). An ErbB3 antibody, MM-121, is active in cancers with ligand-dependent activation. Cancer Research, 70, 2485–2494.

    Google Scholar 

  • Thiele, I., & Palsson, B. O. (2010). Reconstruction annotation jamborees: A community approach to systems biology. Molecular Systems Biology, 6, 361.

    Article  Google Scholar 

  • Tyson, J. J., & Novak, B. (2001). Regulation of the eukaryotic cell cycle: Molecular antagonism, hysteresis, and irreversible transitions. The Journal of Theoretical Biology, 210, 249–263.

    Article  Google Scholar 

  • Tyson, J. J., & Novak, B. (2002). Cell cycle control. In C. Fall, E. Marland, J. Wagner, & J. Tyson (Eds.), Computational cell biology (pp. 261–284). New York: Springer.

    Google Scholar 

  • von Bertalanffy, L. (1969). General system theory: Foundations, development, applications. New York: Braziller.

    Google Scholar 

  • Wiener, N. (1948). Cybernetics: Or control and communication in the animal and the machine. Cambridge, MA: The MIT Press.

    Google Scholar 

Suggested Readings by Hiroaki Kitano

  • Kitano, H. (2002). Computational systems biology. Nature, 420, 206–210.

    Google Scholar 

  • Kitano, H. (2007). Towards a theory of biological robustness. Molecular Systems Biology, 3, 137.

    Google Scholar 

  • Kitano, H., Ghosh, S., & Matsuoka, Y. (2011). Social engineering for virtual ‘big science’ in systems biology. Nature Chemical Biology, 7, 323–326.

    Google Scholar 

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Kitano, H. (2017). Biological Complexity and the Need for Computational Approaches. In: Green, S. (eds) Philosophy of Systems Biology. History, Philosophy and Theory of the Life Sciences, vol 20. Springer, Cham. https://doi.org/10.1007/978-3-319-47000-9_16

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