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Weak Emergence Drives the Science, Epistemology, and Metaphysics of Synthetic Biology

  • Thematic Issue Article: Synthesis (σύνθεσις)
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Abstract

Top-down synthetic biology makes partly synthetic cells by redesigning simple natural forms of life, and bottom-up synthetic biology aims to make fully synthetic cells using only entirely nonliving components. Within synthetic biology the notions of complexity and emergence are quite controversial, but the imprecision of key notions makes the discussion inconclusive. I employ a precise notion of weak emergent property, which is a robust characteristic of the behavior of complex bottom-up causal webs, where a complex causal web is one that is incompressible and its behavior cannot be derived except by crawling through all of the gory details of the interactions in the web. The central thesis of this article is that synthetic biology centrally is the activity of engineering the desired weak emergent properties of synthetic cells. Synthetic biology has many different ways to engineer desired weak emergent properties of synthetic cells, including Edisonian trial and error, standardized parts, refactoring, and reprogramming synthetic genomes. The article ends by noting two philosophical consequences of engineering weak emergence. One is epistemological: synthesis is crucial for discovering weak emergent properties. The other is metaphysical: simple life forms are nothing but complex chemical mechanisms.

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References

  • Agapakis C (2012) Pixelating the genome. Scientific American Blogs. http://blogs.scientificamerican.com/WSS/post.php?blog=25&post=786. Accessed Aug 2013

  • Bedau MA (1997) Weak emergence. Noûs 31(Supplement 11):375–399

    Google Scholar 

  • Bedau MA (2003) Downward causation and autonomy in weak emergence. Principia 6:5–50. (Reprinted in Bedau and Humphreys (2008), Emergence: contemporary readings in philosophy and science. MIT Press, Cambridge, pp 155–188)

    Google Scholar 

  • Bedau MA (2008) Is weak emergence just in the mind? Mind Mach 18:443–459

    Article  Google Scholar 

  • Bedau MA (2010) The power and the pitfalls. Nature 465:422

    Article  Google Scholar 

  • Bedau MA (2011a) Weak emergence and computer simulation. In: Humphreys P, Imbert C (eds) Models, simulations, and representations. Routledge, New York, pp 91–114

    Google Scholar 

  • Bedau MA (2011b) The intrinsic scientific value of reprogramming life. Hastings Cent Rep 41(4):29–31

    Google Scholar 

  • Bedau MA, Parke EC (eds) (2009) The ethics of protocells: moral and social implications of creating life in the laboratory. MIT Press, Cambridge, MA

    Google Scholar 

  • Bedau MA, Triant M (2009) Social and ethical implications of artificial cells. In: Bedau MA, Parke EC (eds) The ethics of protocells: moral and social implications of creating life in the laboratory. MIT Press, Cambridge, MA, pp 31–48

    Chapter  Google Scholar 

  • Benner S (2010) Synthesis drives innovation. Nature 465:423

    Google Scholar 

  • Boldt J, Müller O (2008) Newtons of the leaves of grass. Nat Biotechnol 26:387–389

    Article  Google Scholar 

  • Boogerd FC, Bruggeman FJ, Richardson RC, Stephan A, Westerhoff HV (2005) Emergence and its place in nature: a case study of biochemical networks. Synthese 145:131–164

    Article  Google Scholar 

  • Caplan A (2010) The end of vitalism. Nature 465:423

    Google Scholar 

  • Carlson RH (2010) Biology is technology: the promise, peril, and new business of engineering life. Harvard University Press, Cambridge

    Google Scholar 

  • Caschera F, Gazzola G, Bedau MA, Bosch Moreno C, Buchanan A, Cawse J, Packard NH, Hanczyc MM (2010) Automated discovery of novel drug formulations using predictive iterated high throughput experimentation. PLoS ONE 5:e8546

    Article  Google Scholar 

  • Caschera F, Bedau MA, Buchanan A, Cawse J, de Lucrezia D, Gazzola G, Hanczyc MM, Packard NH (2011) Coping with complexity: machine learning optimization of cell-free protein synthesis. Biotechnol Bioeng 108:2218–2228

    Article  Google Scholar 

  • Chaitin GJ (1975) Randomness and mathematical proof. Sci Am 232:47–53

    Article  Google Scholar 

  • Chaitin GJ (1988) Randomness in arithmetic. Sci Am 259:80–85

    Article  Google Scholar 

  • Cho MK, Magnus D, Caplan AL, McGee D (1999) Ethical considerations in synthesizing a minimal genome. Science 286:2087–2090

    Article  Google Scholar 

  • Church G, Regis E (2012) Regenesis: how synthetic biology will reinvent nature and ourselves. Basic Books, New York

    Google Scholar 

  • Collins J (2010) Got parts, need manual. Nature 465:424

    Google Scholar 

  • Deamer D (2010) Origin of life just got closer. Nature 465:424

    Google Scholar 

  • Endy D (2005) Foundations for engineering biology. Nature 438:449–453

    Google Scholar 

  • Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang R-Y, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi Z-Q, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA III, Smith HO, Venter JC (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52–56

    Article  Google Scholar 

  • Hempel C, Oppenheim P (1965) On the idea of emergence. In: Hempel C (ed) Aspects of scientific explanation and other essays in the philosophy of science. Free Press, New York, pp 258–264. (Reprinted in Bedau and Humphreys (2008) pp 61–68)

  • Jones R (2008) Drew Endy on engineering biology. In: Soft Machines. www.softmachines.org/wordpress/?p=389. Accessed Aug 2013

  • Kuruma Y, Stano P, Ueda T, Luisi PL (2009) A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells. Biochim Biophys Acta 1788:567–574

    Article  Google Scholar 

  • Kwok R (2010) Five hard truths for synthetic biology. Nature 463:288–290

    Article  Google Scholar 

  • Martin VJJ, Pitera DJ, Withers ST, Newman JD, Keasling JD (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21:796–802

    Article  Google Scholar 

  • Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA (2012) Genetic programs constructed from layered logic gates in single cells. Nature 491:249–253

    Article  Google Scholar 

  • Moya A, Krasnogor N, Peretó J, Latorre A (2009) Goethe’s dream: challenges and opportunities for synthetic biology. EMBO Rep 10:S28–S32

    Article  Google Scholar 

  • Mutalik VK, Guimaraes JC, Cambray G, Mai Q-A, Christoffersen MJ, Martin L, Yu A, Lam C, Rodriguez C, Bennett G, Keasling JD, Endy E, Arkin AP (2013a) Quantitative estimation of activity and quality for collections of functional genetic elements. Nat Methods 10:347–353

    Article  Google Scholar 

  • Mutalik VK, Guimaraes JC, Cambray G, Lam C, Christoffersen MJ, Mai Q-A, Tran AB, Paull M, Keasling JD, Arkin AP, Endy D (2013b) Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods 10:354–360

    Article  Google Scholar 

  • Nagel T (2012) Mind and cosmos: why the materialist neo-Darwinian conception of nature is almost certainly false. Oxford University Press, New York

    Book  Google Scholar 

  • Newmann DV (1996) Emergence and strange attractors. Philos Sci 63:245–261

    Article  Google Scholar 

  • Prindle A, Hasty J (2012) Making gene circuits sing. Proc Natl Acad Sci USA 109:16758–16759

    Article  Google Scholar 

  • Purnick PEM, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10:410–422

    Article  Google Scholar 

  • Rasmussen S (2010) ‘Bottom-up’ will be more telling. Nature 465:422–423

    Article  Google Scholar 

  • Rasmussen S, Chen L, Nilsson M, Abe S (2003) Bridging nonliving and living matter. Artificial Life 9:269–316

    Article  Google Scholar 

  • Rasmussen S, Chen L, Deamer D, Krakauer D, Packard NP, Stadler PF, Bedau MA (2004) Transitions from nonliving to living matter. Science 303:963–965

    Article  Google Scholar 

  • Rasmussen S, Bedau MA, Chen L, Deamer D, Krakauer DC, Packard NH, Stadler PF (eds) (2009a) Protocells: bridging nonliving and living matter. MIT Press, Cambridge, MA

    Google Scholar 

  • Rasmussen S, Bedau MA, McCaskill JS, Packard NH (2009b) A roadmap to protocells. In: Rasmussen S et al (eds) Protocells: bridging nonliving and living matter. MIT Press, Cambridge, MA, pp 71–100

    Google Scholar 

  • Rueger A (2000a) Robust supervenience and emergence. Philos Sci 67:466–489

    Article  Google Scholar 

  • Rueger A (2000b) Physical emergence, diachronic and synchronic. Synthese 124:297–322

    Article  Google Scholar 

  • Serrano L (2007) Synthetic biology: promises and challenges. Mol Syst Biol 3:158

    Article  Google Scholar 

  • Temme K, Zhao D, Voigt CA (2012) Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci USA 109:7085–7090

    Article  Google Scholar 

  • Wimsatt WC (1986) Forms of aggregativity. In: Donagan A, Perovich AN, Wedin MV (eds) Human nature and natural knowledge. Reidel, Dordrecht, pp 259–291

    Chapter  Google Scholar 

  • Wimsatt WC (1997) Aggregativity: reductive heuristics for finding emergence. Philos Sci 64:S3720–S384. (Reprinted in Bedau and Humphreys (2008) pp 99–110)

    Google Scholar 

  • Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539–544

    Article  Google Scholar 

  • Wolfram S (1985) Undecidability and intractability in theoretical physics. Phys Rev Lett 54:735–738. (Reprinted in Bedau and Humphreys (2008), pp 387–394)

    Google Scholar 

  • Wolfram S (2002) A new kind of science. Wolfram Media, Champaign

    Google Scholar 

Download references

Acknowledgments

For helpful comments, many thanks to Fridolin Gross, Ulrich Krohs, and Emily Parke.

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Authors and Affiliations

  1. Department of Philosophy, Reed College, Portland, OR, USA

    Mark A. Bedau

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  1. Mark A. Bedau
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Correspondence to Mark A. Bedau.

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Bedau, M.A. Weak Emergence Drives the Science, Epistemology, and Metaphysics of Synthetic Biology. Biol Theory 8, 334–345 (2013). https://doi.org/10.1007/s13752-013-0139-6

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  • DOI: https://doi.org/10.1007/s13752-013-0139-6

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