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Animating embryos: the in toto representation of life


With the recent advent of systems biology, developmental biology is taking a new turn. Attempts to create a ‘digital embryo’ are prominent among systems approaches. At the heart of these systems-based endeavours, variously described as ‘in vivo imaging’, ‘live imaging’ or ‘in toto representation’, are visualization techniques that allow researchers to image whole, live embryos at cellular resolution over time. Ultimately, the aim of the visualizations is to build a computer model of embryogenesis. This article examines the role of such visualization techniques in the building of a computational model, focusing, in particular, on the cinematographic character of these representations. It asks how the animated representation of development may change the biological understanding of embryogenesis. By situating the animations of the digital embryo within the iconography of developmental biology, it brings to light the inextricably entwined, yet shifting, borders between the animated, the living and the computational.

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1 Gilbert, Scott, Developmental Biology, 10th edn, Sunderland, MA: Sinauer Associates, 2014, p. xvi .

2 See Kitano, Hiroaki, ‘Systems biology: a brief overview’, Science (1 March 2002) 295(5560), pp. 16621664 ; Wake, Marvalee H., ‘Integrative biology: science for the 21st century’, BioScience (2008) 58(4), pp. 349353 .

3 Gilbert, op. cit. (1), p. xvi.

4 Gilbert, op. cit. (1), p. 630.

5 Gilbert, op. cit. (1), p. 632.

6 Khairy, Khaled and Keller, Philipp J., ‘Reconstructing embryonic development’, Genesis (2011) 49, pp. 488513, 488.

7 See Stevens, Hallam, Life out of Sequence: A Data-Driven History of Bioinformatics, Chicago and London: The University of Chicago Press, 2013 .

8 Recent publications include Coopmans, Catelijne, Vertesi, Janet, Lynch, Michael and Woolgar, Steve (eds.), Representation in Scientific Practice Revisited, Cambridge, MA and London: MIT Press, 2014 ; and Carusi, Annamaria, Hoel, Aud Sissel, Webmoor, Timothy and Woolgar, Steve (eds.), Visualization in the Age of Computerization, New York and London: Routledge, 2015 .

9 The different concepts of rendering, performativity, materiality, representation, enactment, ontology etc. have recently been discussed in Coopmans et al., op. cit. (8); and Carusi et al., op. cit. (8).

10 Lorraine Daston, ‘Beyond representation’, in Coopmans et al., op. cit. (8), pp. 319–321, 321.

11 See Irun Cohen and David Harel, ‘Two views of a biology–computer science alliance’, CoSMoS, Proceedings of the 2009 Workshop on Complex Systems Modelling and Simulation, 2009, pp. 1–8.

12 Keller, Evelyn Fox, Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines, Cambridge, MA and London: Harvard University Press, 2002, p. 218 .

13 Alberts, Bruce, ‘Celebrating a year of science’, Science (19 December 2008), 322(5909), p. 1757 .

14 See Keller, Philipp J., Schmidt, Annette D., Wittbrodt, Joachim and Stelzer, Ernst H.K., ‘Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy’, Science (14 November 2008) 322, pp. 10651069 .

15 See Megason, Sean G., ‘In toto imaging of embryogenesis with confocal time-lapse microscopy’, in Lieschke, Graham J., Oates, Andrew C. and Kawakami, Koichi (eds.), Zebrafish: Methods and Protocols, New York: Humana Press, 2009, pp. 317332 .

16 See Keller, op. cit. (12), p. 219; on microscopy see also Carusi, Annamaria, ‘Computational biology and the limits of shared vision’, Perspectives on Science (2011) 19(3), pp. 300336 ; Annamaria Carusi and Aud Sissel Hoel, ‘Toward a new ontology of scientific vision’, in Coopmans et al. op. cit. (8), pp. 201–221; Keller, Evelyn Fox, ‘The biological gaze’, in Roberston, George, Mash, Melinda, Tickner, Lisa, Bird, Jon, Curtis, Barry and Putnam, Tim (eds.), FutureNatural: Nature, Science, Culture, London and New York: Routledge, 1996, pp. 107122 ; Hacking, Ian, Representing and Intervening: Introductory Topics in the Philosophy of Natural Science, Cambridge: Cambridge University Press, 1983 .

17 See Maienschein, Jane, Embryos under the Microscope: The Diverging Meanings of Life, Cambridge, MA and London: Harvard University Press, 2014 ; on the nineteenth century see Schickore, Jutta, The Microscope and the Eye: A History of Reflections, 1740–1870, Chicago and London: The University of Chicago Press, 2007 .

18 See Keller, Philipp J., ‘Imaging morphogenesis: technological advances and biological insights’, Science (7 June 2013) 340(6137), pp. 1234168-1–1234168-10, doi: 10.1126/science.1234168 . For an overview of the rapidly advancing field of visualization techniques, including other than laser-scanning and light sheet microscopy, such as magnetic resonance imaging (μMRI) or optical projection tomography (OPT), see Ruffins, Seth W., Jacobs, Russell E. and Fraser, Scott E., ‘Towards a Tralfamadorian view of the embryo: multidimensional imaging of development’, Current Opinion in Neurobiology (2002) 12(5), pp. 580586 ; Megason, Sean G. and Fraser, Scott E., ‘Digitizing life at the level of the cell: high-performance laser-scanning microscopy and image analysis for in toto imaging of development’, Mechanisms of Development (2003) 120(11), pp. 14071420 ; Keller, Philipp J. and Dodt, Hans-Ulrich, ‘Light sheet microscopy of living or cleared specimens’, Current Opinion in Neurobiology (2011) 22(1), pp. 138143 ; and recently Khairy, Khaled, Lemon, William C., Amat, Fernando and Keller, Philipp J., ‘Light sheet-based imaging and analysis of early embryogenesis in the fruit fly’, in Nelson, Celeste M. (ed.), Tissue Morphogenesis: Methods and Protocols, New York: Springer, 2015, pp. 7997 .

19 See the literature in Ruffins, Jacobs and Fraser, op. cit. (18).

20 Phillips, Melissa, ‘Deciphering development: quantifying gene expression through imaging’, BioScience (2007) 57(8), pp. 648652, 648.

21 On GFP and different markers see Megason and Fraser, op. cit. (18); Matus, Andrew, ‘GFP in motion CD-ROM. Introduction: GFP illuminates everything’, Trends in Cell Biology (1999) 9 (2), p. 43 .

22 This is done in confocal LSM by a pinhole aperture; in two-photon LSM, the fluorescent markers are excited only at the focal plane, making use of an optical property of the fluorescent dye.

23 For more technical detail, also on two-photon LSM, see Megason and Fraser, op. cit. (18), pp. 1408–1409; Megason, op. cit. (15). Before applications with drosophila and zebrafish, in toto imaging was done in C. elegans, for example by the Nobel Prize winner Fire, Andrew Z., ‘A four-dimensional digital image archiving system for cell lineage tracing and retrospective embryology’, Computer Applications in the Biosciences (1994) 10, pp. 443447 .

24 See Keller et al., op. cit. (14); Keller and Dodt, op. cit. (18); Khairy et al., op. cit. (18); Keller, Philipp J., ‘In vivo imaging of zebrafish embryogenesis’, Methods (2013) 62(3), pp. 268278 ; Kobitski, Andrei Y., Otte, Jens C., Takamiya, Masanari et al. , ‘An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution’, Scientific Reports (2015) 5(8601), pp. 110, doi: 10.1038/srep08601 .

25 See Keller et al., op. cit. (14).

26 For details see Khairy et al., op. cit. (18); Tomer, Raju, Khairy, Khaled, Amat, Fernando and Keller, Philipp J., ‘Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy’, Nature Methods (2012) 9(7), pp. 755763 .

27 I will not go into detail here about the use of in vivo imaging and fluorescent markers for genetic research. See Megason and Fraser, op. cit. (18), pp. 1410–1411.

28 Phillips, op. cit. (20), p. 649.

29 See Xiong, Fengzhu and Megason, Sean G., ‘Abstracting the principles of development using imaging and modeling’, Integrative Biology (2015) 7(6), pp. 633642 .

30 Megason and Fraser, op. cit. (18), pp. 1412–1413.

31 Megason, op. cit. (15), p. 329.

32 Megason and Fraser, op. cit. (18), p. 1413.

33 Megason and Fraser, op. cit. (18), p. 1413.

34 Megason and Fraser, op. cit. (18), p. 1415.

35 See in detail also Khairy and Keller, op. cit. (6); Khairy et al., op. cit. (18).

36 Vogel, Gretchen, ‘Lights! Camera! Action! Zebrafish embryos caught on film’, Science (10 October 2008) 322(5899), p. 176 .

37 To view the movies and for additional material see Keller et al., op. cit. (14); and

38 See Keller, op. cit. (24), Figure 5.

39 Keller, op. cit. (24), Figure 5.

40 Hinterwaldner, Inge, Das systemische Bild: Ikonizität im Rahmen computerbasierter Echtzeitsimulationen, Munich: Fink, 2010, p. 126 .

41 Carusi, op. cit. (16), p. 329.

42 See Hinterwaldner, op. cit. (40), p. 83.

43 ‘Woher bezieht die Form ihre Gestalt?’, Gabriele Gramelsberger, ‘Semiotik und Simulation: Fortführung der Schrift ins Dynamische’, dissertation, Freie Universität Berlin, 2001, p. 93, quoted in Hinterwaldner, op. cit. (40), p. 132.

44 For a recently renewed interest in animation see Beckmann, Karen (ed.), Animating Film Theory, Durham, NC and London: Duke University Press, 2014 ; Buchan, Suzanne (ed.), Pervasive Animation, New York and London: Routledge, 2013 ; or the special issue of Animation (2011) 6(2).

45 Tom Gunning, ‘Animating the instant: the secret symmetry between animation and photography’, in Beckman, op. cit. (44), pp. 37–53, 40, original emphasis. Here my use of the term is more precise than in Ostherr and Gaycken, where it is used interchangeably with ‘cinematography’; see Ostherr, Kirsten, ‘Animating informatics: scientific discovery through documentary film’, in Jahusz, Alexandra and Lebow, Alisa (eds.), A Companion to Contemporary Documentary Film, New York: John Wiley & Sons, 2015, pp. 280297 ; Oliver Gaycken, ‘“A living, developing egg is present before you”: animation, scientific visualization, modeling’, in Beckman, op. cit. (44), pp. 68–81.

46 Kelty, Christopher and Landecker, Hannah, ‘A theory of animation: cells, l-systems, and film’, Grey Room (2004) 17, pp. 3063, 42, 36.

47 See the work of Hopwood, Nick, most recently Haeckel's Embryos: Images, Evolution, and Fraud, Chicago: The University of Chicago Press, 2015 ; also Hopwood, Nick, Schaffer, Simon and Secord, James (eds.), Seriality and Scientific Objects in the Nineteenth Century, special issue, History of Science (2010) 48(3–4).

48 Curtis, Scott, ‘Die Kinematographische Methode: Das ‘bewegte Bild’ und die Brownsche Bewegung’, montage/av (2005) 14(1), pp. 2343 . On the rich entanglement of film, modernity and culture see Wellmann, Janina (ed.), Cinematography, Seriality, and the Sciences, special issue, Science in Context (2011) 24(3); recently Lisa Cartwright, ‘Visual science studies: always already materialist’, in Carusi et al., op. cit. (8), pp. 243–268; Curtis, Scott, The Shape of Spectatorship: Art, Science, and Early Cinema in Germany, New York: Columbia University Press, 2015 ; Gaycken, Oliver, Devices of Curiosity: Early Cinema and Popular Science, Oxford: Oxford University Press, 2015 .

49 Kelty and Landecker, op. cit. (46), p. 38.

50 See Ostherr, op. cit. (45); Gaycken, op. cit. (45).

51 Ries, Julius, ‘Kinematographie der Befruchtung und Zellteilung’, Archiv für mikroskopische Anatomie (1909) 74, pp. 131 ; Wellmann, Janina, ‘Plastilin und Kreisel, Pinsel und Projektor: Julius Ries und die Materialität der seriellen Anschauung’, in Scholtz, Gerhard (ed.), Serie und Serialität: Konzepte und Analysen in Gestaltung und Wissenschaft, Berlin: Reimer, 2017, pp. 7793 .

52 Landecker, Hannah, ‘Microcinematography and the history of science and film’, Isis (2006) 97, pp. 121132, 123.

53 This paper is part of a bigger research project on the history of concepts, images and ways of moving in the life sciences. On the terminology of ‘migration’, ‘motion’ or ‘locomotion’ see Alt, Wolfgang and Hoffmann, Gerhard (eds.), Biological Motion, Berlin, Heidelberg and New York: Springer, 1989 ; Vicente-Manzanares, Miguel and Horwitz, Alan Rick, ‘Cell migration: developmental methods and protocols’, in Wells, Claire M. and Parsons, Maddy (eds.), Methods in Molecular Biology, New York: Humana Press, 2011, pp. 77106 .

54 See Wellmann, Janina, The Form of Becoming: Embryology and the Epistemology of Rhythm, 1760–1830, New York: Zone Books, 2017 .

55 Wellmann, Janina, ‘Wie das Formlose Formen schafft: Bilder in der Haller–Wolff–Debatte und die Anfänge der Embryologie um 1800’, Bildwelten des Wissens: Kunsthistorisches Jahrbuch für Bildkritik (2003) 1(2), pp. 105115 .

56 Wellmann, Janina, ‘Folding into being: early embryology and the epistemology of rhythm’, History and Philosophy of the Life Sciences (2015) 37(1), pp. 1733 .

57 The quotation is taken from Megason's website at, last accessed 8 August 2016.

The research for this article was funded by DFG-Kollegforschergruppe Medienkulturen der Computersimulation (KFOR 1927), Leuphana Universität Lüneburg. I would also like to thank the two anonymous reviewers for their valuable comments.

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