Designing de novo: interdisciplinary debates in synthetic biology

Adrianantoandro ES et al (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2:1–13

Anderson JN et al (2012) Engineering and ethical perspectives in synthetic biology. EMBO Rep 13:584–590

Anonymous (2009) What’s in a name? Nat Biotechnol 27:1071–1072. doi: 10.1038/nbt1209-1071

Arkin AP, Fletcher D (2006) Fast, cheap and somewhat in control. Genome Biol 7:114–119

Ball P (2004) Synthetic biology, starting from scratch. Nature 431:624–626

Bedau M, Church G, Rasmussen S, Caplan A, Benner S, Fussenegger M, Collins J, Deamer D (2010) Life after the synthetic cell. Nature 465:27

Bensaude-Vincent B (2007) Reconfiguring nature through synthesis: from plastics to biomimetics. In: Newman WR (ed) The natural and the artificial. An ever-evolving polarity. MIT Press, Cambridge

Blakes J, Twycross J, Romero-Campero FJ, Krasnogor N (2011) The infobiotics workbench: an integrated in silico modelling platform for systems and synthetic biology. Bioinformatics 27:3323–3324

Bok von Wûlfingen B (2009) Biology and the systems view. EMBO Rep 10:37–41

Boldt J, Muller O (2008) Newtons of the leaves of grass. Certain ethical implications of synthetic biology research go beyond those of genetic engineering. Nat Biotechnol 26:387–389

Boogerd FC, Bruggeman F, Hofmeyr JH, Westerhoff HV (2007) Systems biology. Elsevier, Amsterdam

Brown N (2003) Hope against hype—accountability in biopasts, presents and futures. Sci Stud 16(2):2–21

Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS Comput Biol 5(10)

Calvert J (2010) Synthetic biology: constructing nature? Sociol Rev 58:95–112

Calvert J, Martin P (2009) The role of social scientists in synthetic biology. EMBO Rep 10(3):201–204

Campos L (2010) That was the synthetic biology that was. In: Schmidt M, Kelle A, Ganguli-Mitra A, Vriend H (eds) Synthetic biology. Springer, Netherlands

Cardinale S, Arkin AP (2012) Contextualizing context for synthetic biology-identifying causes of failure of synthetic biological systems. Biotechnol J 7:856–866

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

Carrera J, Elena SF, Jaramillo A (2012) Computational design of genomic transcriptional networks with adaptation to varying environments. Proc Natl Acad Sci USA 109:15277–15282

De Lorenzo V (2010a) Synthetic biology: something old, something new. BioEssays 32:267–270

De Lorenzo V (2010b) Beware of metaphors. Chasses and orthogonality in synthetic biology. Bioeng Bugs 2:3–7

De Lorenzo V, Danchin A (2008) Synthetic biology: discovering new worlds and new words. EMBO Rep 9:822–827

DeLanda M (2011) Philosophy and simulation. The emergence of the synthetic reason. Continuum, New York

Delgado A, Funtowicz S, Dankel D (2012) Super-computers, evolution and the fabrication of life: how can science and technology studies (STS) contribute to more reflexive developments in systems and synthetic biology? Int J Soc Ecol Sustain Dev 3(2):12–24

Deplazes A (2009) Piecing together a puzzle. EMBO Rep 10:428–432

Deplazes A, Huppenbauer M (2009) Synthetic organisms—living machines. Positioning the products of synthetic biology at the borderline between living and non-living matter. Syst Synth Biol 3:55–63

Dietrich JA et al (2009) A novel semi-biosyntehtic route for artemisin production using engineered substrate-promiscouos P450. ACS Chem Biol 4:261–267

Dupre J (2003) Darwin’s legacy. What evolution means today. Oxford University Press, Oxford

Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335–338

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

ETC Group (2007) Extreme genetic engineering: An introduction to synthetic biology. http://www.etcgroup.org/node/602 . Accessed 15 June 2012

Fox Keller E (2003) Making sense of life. Explaining biological development with models, metaphors and machines. Harvard University Press, Cambridge MA

Fox Keller E (2007) The disappearance of function from ‘self-organising systems’. In: Boogerd FC, Bruggeman FJ, Hofmeyr J-HS, Westerhoff HV (eds) Systems biology philosophical foundations. Elsevier, Amsterdam

Fox Keller E (2009) What does synthetic biology have to do with biology? Biosocieties 4:291–302

Gibson DG et al (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52–56

Giuliani A et al (2011) What is artificial about life? Sci World J 11:670–673

Gramelsberger G (2012) Lifelike algorithms and cellular machines. Paper presented at the workshop: different forms of live. Comparative perspectives in systems and synthetic biology. Centre for Biotechnology, Society and Environment. Hamburg, January 2012

Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L (2009) Transcriptome complexity in a genome-reduced bacterium. Science 326(5957):1268–1271

Heinemann M, Panke S (2006) Synthetic biology—putting engineering into biology. Bioinformatics 22(22):2790–2799

Isaac F et al (2006) RNA synthetic biology. Nat Biotechnol 24:545–552

Jasanoff S (2007) Technologies of humility. Nature 450:33

Kaznessis YN (2009) Computational methods in synthetic biology. Biotechnol J 4:1392–1405

Keasling J (2009) Synthetic biology in pursuit of inexpensive, effective, anti-malarial drugs. Biosocieties 4:275–282

Knight TF (2005) Engineering novel life. Mol Syst Biol doi: 10.1038/msb4100028

Knorr-Cetina K (1999) Epistemic cultures: how the sciences make knowledge. Harvard University Press, Cambridge, Mass

Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC (2009) Proteome organization in a genome-reduced bacterium. Science 326(5957):1235–1240

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

Law J (2002) Aircraft stories: decentering the object in technoscience. Duke University Press, Durham, London

MacDonald JT, Barner C, Kitney R, Freemont PS, Stan GB (2011) Computational design approaches and tools for synthetic biology. Integr Biol 3:97–108

Mackenzie A (2010) Design in synthetic biology. Biosocieties 5:180–198

Morange M (2009) A critical perspective on synthetic biology. Int J Philos Chem 15:21–30

Moreno A (2007) A systemic approach to the origin of biological organization. In: Boogerd FC, Bruggeman FJ, Hofmeyr J-HS, Westerhoff HV (eds) Systems biology philosophical foundations. Elsevier, Amsterdam

Moya A et al (2009) Goethe’s dream. EMBO Rep 10:28–32

Mukherji S, Oudenaarden AV (2009) Synthetic biology: understanding biological design from synthetic circuits. Nat Rev Genet 10:859–871

Noble D (2008) The music of life. Oxford University Press, Oxford

O’Malley M, Powell A, Davies J, Calvert J (2008) Knowledge making distintions in synthetic biology. BioEssays 30:57–65

Pennisi E (2012) 111 organizations call for synthetic biology moratorium. Science Insider 13 March 2012

Porcar M (2009) Beyond directed evolution: Darwinian selection as a tool for synthetic biology. Syst Synth Biol 4:1–6

Porcar M, Danchin A, de Lorenzo V, Dos Santos VA, Krasnogor N, Rasmussen S, Moya A (2011) The ten grand challenges of synthetic life. Syst Synth Biol 5:1–5

Potthast T (2009) Paradigm shifts versus fashion shifts? Systems and synthetic biology as new epsitemic entities in understanding and making life? EMBO Rep 19:42–45

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

Rabinow P, Bennett G (2012) Designing human practices. An experiment with synthetic biology. Chicago University Press, Chicago

Rheinberger H (1997) Toward a history of epistemic things. Stanford University Press, Stanford, California

Rinaldi A (2012) To hype, or not to(o) hype. Communication of science is often tarnished by sensationalization, for which both scientists and the media are responsible. EMBO Rep 13:303–307

Romanini DW, Peralta-Yahya P, Mondol V, Cornish VW (2012) A heritable recombination system for synthetic Darwinian evolution in yeast. ACS Synth Biol 1(12):602–609

Schaerli Y, Isalan M (2013) Building synthetic gene circuits from combinatorial libraries: screening and selection strategies. Mol Biosyst. 2013 Jan 23. doi: 10.1039/C2MB25483B

Schille P (2011) Bottom-up synthetic biology: engineers in a tinkerer’s world. Science 333:1252–1254

Schyfter P (2012) Standing reserves of function: a Hedeggerian reading of synthetic biology. Philos Technol 25:199–219

Schyfter P (2013) Properllers and promoters: emerging engineering knowledge in aeronautics and synthetic biology. Eng Stud. doi: 10.1080/19378629.2012.762651

Serrano L (2007) Synthetic biology: promises and challenges. Mol Syst Biol 3:1–5

Shetty RP et al (2008) Engineering BioBrick vectors from BioBrick parts. J Biol Eng 2:1–12

Silver PA (2009) Making biology easier to engineer. Biosocieties 4:283–289

Smolke C, Silver P (2011) Informing biological design by integration of systems and synthetic biology. Cell 144:855–859

Stirling A (2008) “Opening up and closing down” power, participation and pluralism in the social appraisal of technology. Sci Technol Human Values 33(2):262–294

Trogemann G (2010) Code and machine. In: Gleiniger A, Vrachliotis G (eds) Code: between operation and narration. Birkhauser, Basel

Vincenti WG (1990) What engineers know and how they know it. The Johns Hopkins University Press, Baltimore

Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L (2009) Impact of genome reduction on bacterial metabolism and its regulation. Science 326(5957):1263–1268