Synthetic biology and the search for alternative genetic systems: Taking how-possibly models seriously
Tóm tắt
Many scientific models in biology are how-possibly models. These models depict things as they could be, but do not necessarily capture actual states of affairs in the biological world. In contemporary philosophy of science, it is customary to treat how-possibly models as second-rate theoretical tools. Although possibly important in the early stages of theorizing, they do not constitute the main aim of modelling, namely, to discover the actual mechanism responsible for the phenomenon under study. In the paper it is argued that this prevailing picture does not do justice to the synthetic strategy that is commonly used in biological engineering. In synthetic biology, how-possibly models are not simply speculations or eliminable scaffolds towards a single how-actually model, but indispensable design hypotheses for a field whose ultimate goal is to build novel biological systems. The paper explicates this by providing an example from the study of alternative genetic systems by synthetic biologist Steven Benner and his group. The case will also highlight how the method of synthesis, even when it fails, provides an effective way to limit the space of possible models for biological systems.
Tài liệu tham khảo
Bayer, T. S. (2010). Using synthetic biology to understand the evolution of gene expression. Current Biology, 20, R772–R779.
Beatty, J. (1995). The evolutionary contingency thesis. In G. Wolters, J.G. Lennox, & P. McLaughlin (Eds.), Concepts, theories, and rationality in the biological sciences. The second Pittsburgh-Konstanz colloquium in the philosophy of science (pp. 45–81). Pittsburgh: University of Pittsburgh Press.
Bechtel, W., & Richardson, R. C. (2010). Discovering complexity: Decomposition and localization as strategies in scientific research (2nd ed.). Cambridge: The MIT Press.
Benner, S. A., Yang, Z., & Chen, F. (2011). Synthetic biology, tinkering biology, and artificial biology. What are we learning? Comptes Rendus Chimie, 14, 372–387.
Benner, S. A., Karalkar, N. B., Hoshika, S., Laos, R., Shaw, R. W., Matsuura, M., et al. (2016). Alternative Watson–Crick synthetic genetic systems. Cold Spring Harbor Perspectives in Biology. doi:10.1101/cshperspect.a023770.
Cameron, D. E., Bashor, C. J., & Collins, J. J. (2014). A brief history of synthetic biology. Nature Reviews Microbiology, 12, 381–390.
Craver, C. F. (2006). When mechanistic models explain. Synthese, 153, 355–376.
Craver, C. F. (2007). Explaining the brain: Mechanisms and the mosaic unity of neuroscience. Oxford: Oxford University Press.
Craver, C. F., & Darden, L. (2013). In search of mechanisms: Discoveries across the life sciences. Chicago: The University of Chicago Press.
Dawkins, R. (1986). The blind watchmaker: Why the evidence of evolution reveals a universe without design. New York: Norton & Company.
Dennett, D. C. (1995). Darwin’s dangerous idea: Evolution and the meanings of life. New York: Simon and Schuster.
Dray, W. (1957). Laws and explanation in history. Oxford: Clarendon Press.
Elowitz, M. B., & Lim, W. A. (2010). Build life to understand it. Nature, 468, 889–890.
Endy, D. (2005). Foundation for engineering biology. Nature, 438, 449–453.
Forber, P. (2010). Confirmation and explaining how-possible. Studies in History and Philosophy of Biological and Biomedical Sciences, 41, 32–40.
Glennan, S. (2010). Mechanisms, causes, and the layered model of the world. Philosophy and Phenomenological Research, LXXXI, 362–381.
Green, S. (2015). Revisiting generality in biology: Systems biology and the quest for design principles. Biology and Philosophy, 30, 629–652.
Grüne-Yanoff, T. (2013). Appraising models nonrepresentationally. Philosophy of Science, 80, 850–861.
Knuuttila, T., & Loettgers, A. (2013). Synthetic modeling and mechanistic account: Material recombination and beyond. Philosophy of Science, 80, 874–885.
Kwok, R. (2012). DNA’s new alphabet. Nature, 491, 516–518.
Malyshev, A., Dhami, K., Lavergne, T., Chen, T., Dai, N., Foster, J. M., Corrêa Jr., I. R., & Romesberg, F. L. (2014). A semi-synthetic organism with an expanded genetic alphabet. Nature, 509, 385–388.
Marlière, P., Patrouix, J., Döring, V., Herdewijn, P., Tricot, S., Cruveiller, S., Bouzon, M., & Mutzel, R. (2011). Chemical evolution of a bacterial genome. Angewandte Chemie International Edition, 50, 7109–7114.
Morange, M. (2009). Synthetic biology: A bridge between functional and evolutionary biology. Biological Theory, 4, 368–377.
Raerinne, J. (2015). Evolutionary contingency, stability, and biological laws. Journal for General Philosophy of Science, 46, 45–62.
Resnik, D. B. (1991). How-possibly explanations in biology. Acta Biotheoretica, 39, 141–149.
Reydon, T. A. C. (2012). How-possibly explanations as genuine explanations and helpful heuristics: A comment on Forber. Studies in History and Philosophy of Biological and Biomedical Sciences, 43, 302–310.
Rosenberg, A. (2006). Darwinian reductionism: Or, how to stop worrying and love molecular biology. Chicago: The University of Chicago Press.
Ruiz-Mirazo, K., & Moreno, A. (2013). Synthetic biology: Challenging life in order to grasp, use, or extend it. Biological Theory, 8, 376–382.
Schmidt, M. (2010). Xenobiology: A new form of life as the ultimate biosafety tool. BioEssays, 32, 322–331.
Schrödinger, E. (1944). What is life? Cambridge: Cambridge University Press.
Sprinzak, D., & Elowitz, M. B. (2005). Reconstruction of genetic circuits. Nature, 438, 443–448.
Sterelny, K, and P.E. Griffiths. (1999). Sex and death: An introduction to philosophy of biology. Chicago and London: The University of Chicago Press.
Switzer, C., Moroney, S. E., & Benner, S. A. (1989). Enzymatic incorporation of a new base pair into DNA and RNA. Journal of the American Chemical Society, 111, 8322–8323.
Szathmáry, E. (2003). Why are there four letters in the genetic alphabet? Nature Reviews Genetics, 4, 995–1001.
Thyer, R., & Ellefson, J. (2014). New letters for life’s alphabet. Nature, 509, 291–292.
Wagner, A. (2005). Robustness and evolvability in living systems. Princeton, NJ: Princeton University Press.
Weiskopf, D. A. (2011). The functional unity of special science kinds. The British Journal for the Philosophy of Science, 62, 233–258.
Wimsatt, W. C. (2007). Re-engineering philosophy for limited beings: Piecewise approximations to reality. Cambridge: Harvard University Press.
Woodward, J. (2003). Making things happen: A theory of causal explanation. Oxford: Oxford University Press.