Biological Theory

, Volume 8, Issue 4, pp 334–345 | Cite as

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

Thematic Issue Article: Synthesis (σύνθεσις)


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.


Complex causal web Protocell Refactoring Standardized part Synthetic biology Synthetic genome Weak emergence 


  1. Agapakis C (2012) Pixelating the genome. Scientific American Blogs. Accessed Aug 2013
  2. Bedau MA (1997) Weak emergence. Noûs 31(Supplement 11):375–399Google Scholar
  3. 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
  4. Bedau MA (2008) Is weak emergence just in the mind? Mind Mach 18:443–459CrossRefGoogle Scholar
  5. Bedau MA (2010) The power and the pitfalls. Nature 465:422CrossRefGoogle Scholar
  6. Bedau MA (2011a) Weak emergence and computer simulation. In: Humphreys P, Imbert C (eds) Models, simulations, and representations. Routledge, New York, pp 91–114Google Scholar
  7. Bedau MA (2011b) The intrinsic scientific value of reprogramming life. Hastings Cent Rep 41(4):29–31Google Scholar
  8. Bedau MA, Parke EC (eds) (2009) The ethics of protocells: moral and social implications of creating life in the laboratory. MIT Press, Cambridge, MAGoogle Scholar
  9. 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 31–48CrossRefGoogle Scholar
  10. Benner S (2010) Synthesis drives innovation. Nature 465:423Google Scholar
  11. Boldt J, Müller O (2008) Newtons of the leaves of grass. Nat Biotechnol 26:387–389CrossRefGoogle Scholar
  12. Boogerd FC, Bruggeman FJ, Richardson RC, Stephan A, Westerhoff HV (2005) Emergence and its place in nature: a case study of biochemical networks. Synthese 145:131–164CrossRefGoogle Scholar
  13. Caplan A (2010) The end of vitalism. Nature 465:423Google Scholar
  14. Carlson RH (2010) Biology is technology: the promise, peril, and new business of engineering life. Harvard University Press, CambridgeGoogle Scholar
  15. 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:e8546CrossRefGoogle Scholar
  16. 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 108:2218–2228CrossRefGoogle Scholar
  17. Chaitin GJ (1975) Randomness and mathematical proof. Sci Am 232:47–53CrossRefGoogle Scholar
  18. Chaitin GJ (1988) Randomness in arithmetic. Sci Am 259:80–85CrossRefGoogle Scholar
  19. Cho MK, Magnus D, Caplan AL, McGee D (1999) Ethical considerations in synthesizing a minimal genome. Science 286:2087–2090CrossRefGoogle Scholar
  20. Church G, Regis E (2012) Regenesis: how synthetic biology will reinvent nature and ourselves. Basic Books, New YorkGoogle Scholar
  21. Collins J (2010) Got parts, need manual. Nature 465:424Google Scholar
  22. Deamer D (2010) Origin of life just got closer. Nature 465:424Google Scholar
  23. Endy D (2005) Foundations for engineering biology. Nature 438:449–453Google Scholar
  24. 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 329:52–56CrossRefGoogle Scholar
  25. 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)Google Scholar
  26. Jones R (2008) Drew Endy on engineering biology. In: Soft Machines. Accessed Aug 2013
  27. 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 1788:567–574CrossRefGoogle Scholar
  28. Kwok R (2010) Five hard truths for synthetic biology. Nature 463:288–290CrossRefGoogle Scholar
  29. Martin VJJ, Pitera DJ, Withers ST, Newman JD, Keasling JD (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21:796–802CrossRefGoogle Scholar
  30. Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA (2012) Genetic programs constructed from layered logic gates in single cells. Nature 491:249–253CrossRefGoogle Scholar
  31. Moya A, Krasnogor N, Peretó J, Latorre A (2009) Goethe’s dream: challenges and opportunities for synthetic biology. EMBO Rep 10:S28–S32CrossRefGoogle Scholar
  32. 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 10:347–353CrossRefGoogle Scholar
  33. 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 10:354–360CrossRefGoogle Scholar
  34. Nagel T (2012) Mind and cosmos: why the materialist neo-Darwinian conception of nature is almost certainly false. Oxford University Press, New YorkCrossRefGoogle Scholar
  35. Newmann DV (1996) Emergence and strange attractors. Philos Sci 63:245–261CrossRefGoogle Scholar
  36. Prindle A, Hasty J (2012) Making gene circuits sing. Proc Natl Acad Sci USA 109:16758–16759CrossRefGoogle Scholar
  37. Purnick PEM, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10:410–422CrossRefGoogle Scholar
  38. Rasmussen S (2010) ‘Bottom-up’ will be more telling. Nature 465:422–423CrossRefGoogle Scholar
  39. Rasmussen S, Chen L, Nilsson M, Abe S (2003) Bridging nonliving and living matter. Artificial Life 9:269–316CrossRefGoogle Scholar
  40. Rasmussen S, Chen L, Deamer D, Krakauer D, Packard NP, Stadler PF, Bedau MA (2004) Transitions from nonliving to living matter. Science 303:963–965CrossRefGoogle Scholar
  41. 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, MAGoogle Scholar
  42. 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 71–100Google Scholar
  43. Rueger A (2000a) Robust supervenience and emergence. Philos Sci 67:466–489CrossRefGoogle Scholar
  44. Rueger A (2000b) Physical emergence, diachronic and synchronic. Synthese 124:297–322CrossRefGoogle Scholar
  45. Serrano L (2007) Synthetic biology: promises and challenges. Mol Syst Biol 3:158CrossRefGoogle Scholar
  46. Temme K, Zhao D, Voigt CA (2012) Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci USA 109:7085–7090CrossRefGoogle Scholar
  47. Wimsatt WC (1986) Forms of aggregativity. In: Donagan A, Perovich AN, Wedin MV (eds) Human nature and natural knowledge. Reidel, Dordrecht, pp 259–291CrossRefGoogle Scholar
  48. 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
  49. Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539–544CrossRefGoogle Scholar
  50. 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
  51. Wolfram S (2002) A new kind of science. Wolfram Media, ChampaignGoogle Scholar

Copyright information

© Konrad Lorenz Institute for Evolution and Cognition Research 2013

Authors and Affiliations

  1. 1.Department of PhilosophyReed CollegePortlandUSA

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