Molecular Embodiments and the Body-work of Modeling in Protein Crystallography

Protein molecules, those objects of increasing interest and investment in post-genomics research, are complex, three-dimensional structures made up of thousands of atoms. Protein crystallographers build atomic-resolution models of proteins using the techniques of X-ray diffraction. This ethnographic study of protein crystallography shows that becoming an expert crystallographer, and so making sense of such intricate objects, requires researchers to draw on their bodies as a resource to learn about, work with, and communicate precise molecular configurations. Contemporary crystallographic modeling relies intensively on interactive computer graphics technology, and requires active and prolonged handling and manipulation of the model onscreen throughout the often arduous process of model-building. This paper builds on both ethnographic observations of contemporary protein crystallographers and historical accounts of early molecular modeling techniques to examine the body-work of crystallographic modeling, in particular the corporeal practices through which modelers learn the intricate structures of protein molecules. Ethnographic observations suggest that, in the process of building and manipulating protein models, crystallographers also sculpt embodied models alongside the digital renderings they craft onscreen. Crystallographic modeling at the computer interface is thus not only a means of producing representations of proteins; it is also a means of training novice crystallographers' bodies and imaginations. Protein crystallographers' molecular embodiments thus offer a site for posing a new range of questions for studies of the visual cultures and knowledge practices in the computer-mediated life sciences.

[1]  Maurice Merleau-Ponty Phenomenology of Perception , 1964 .

[2]  W. Bean Personal Knowledge: Towards a Post-Critical Philosophy , 1961 .

[3]  J. Kendrew Myoglobin and the structure of proteins. , 1963, Science.

[4]  M. Perutz THE HEMOGLOBIN MOLECULE. , 1964, Scientific American.

[5]  D. Hodgkin The x-ray analysis of complicated molecules. , 1965, Science.

[6]  C. Levinthal Molecular model-building by computer. , 1966, Scientific American.

[7]  M. Polanyi The Logic of Tacit Inference , 1966, Philosophy.

[8]  G. Stent That was the molecular biology that was. , 1968, Science.

[9]  H. Bassow Construction and Use of Atomic and Molecular Models , 1968 .

[10]  W. R. Roderick The double helix. A personal account of the discovery of the structure of DNA (Watson, James D.) , 1968 .

[11]  Maurice Merleau-Ponty,et al.  The Visible And The Invisible , 1968 .

[12]  J. Glusker,et al.  Crystal Structure Analysis: A Primer , 1972 .

[13]  P. Klingenberg The Molecular Basis of Life. An Introduction to Molecular Biology. Readings from Scientific American, herausgegeben und eingeführt von Robert H. Haynes und Philip C. Hanawalt. 368 Seiten, zahlreiche Abb. W. H. Freeman and Company, San Francisco 1968. Preis: 4,95 $ , 1972 .

[14]  John Law,et al.  The Development of Specialties in Science: the Case of X-ray Protein Crystallography , 1973 .

[15]  C. Geertz,et al.  The Interpretation of Cultures , 1973 .

[16]  C. D. Barry,et al.  Evolving macromodular molecular modeling system. , 1974, Federation proceedings.

[17]  Donald A. B. Lindberg,et al.  Computers in life science research , 1974 .

[18]  R Langridge,et al.  Interactive three-dimensional computer graphics in molecular biology. , 1974, Federation proceedings.

[19]  D. Collins,et al.  Protein crystal structures: quicker, cheaper approaches , 1975, Science.

[20]  G. Petsko,et al.  Molecular graphics: application to the structure determination of a snake venom neurotoxin. , 1977, Science.

[21]  James L. McClelland,et al.  Phenomenology of perception. , 1978, Science.

[22]  R Langridge,et al.  Real-time color graphics in studies of molecular interactions. , 1981, Science.

[23]  J. Glusker Structural crystallography in chemistry and biology , 1981 .

[24]  Ian Hacking,et al.  Representing and Intervening: Introductory Topics in the Philosophy of Natural Science , 1983 .

[25]  Susan Leigh Star,et al.  Changing Order: Replication and Induction in Scientific Practice by H. M. Collins (review) , 1988, Technology and Culture.

[26]  E. Keller,et al.  A feeling for the organism : the life and work of Barbara McClintock , 1985 .

[27]  D. Boersema Representing and Intervening: Introductory Topics in the Philosophy of Natural Science , 1985 .

[28]  D. Haraway Simians, Cyborgs, and Women: The Reinvention of Nature , 1990 .

[29]  S. L. Star,et al.  9. Craft vs. Commodity, Mess vs. Transcendence: How the Right Tool Became the Wrong One in the Case of Taxidermy and Natural History , 1992 .

[30]  L. Daston,et al.  The Image of Objectivity , 1992 .

[31]  Lily E. Kay,et al.  The molecular vision of life : Caltech, the Rockefeller Foundation, and the rise of the new biology , 1994 .

[32]  A. Cambrosio,et al.  Ehrlich's "Beautiful Pictures" and the Controversial Beginnings of Immunological Imagery , 1993, Isis.

[33]  M. Perutz Linus Pauling , 1994, Nature Structural Biology.

[34]  H. Rheinberger Toward a History of Epistemic Things: Synthesizing Proteins in the Test Tube , 1997 .

[35]  M. Trumpler Converging Images: Techniques of Intervention and Forms of Representation of Sodium-Channel Proteins in Nerve Cell Membranes , 1997, Journal of the history of biology.

[36]  D. Haraway,et al.  Modest_Witness@Second_Millennium. FemaleMan_Meets_OncoMouse , 1997 .

[37]  Eric Francoeur,et al.  The Forgotten Tool: The Design and Use of Molecular Models , 1997 .

[38]  R. Doyle On Beyond Living: Rhetorical Transformations of the Life Sciences , 1997 .

[39]  J. Tambling How We Became Posthuman: Virtual Bodies in Cybernetics, Literature and Informatics by N. Katherine Hayles (review) , 2001, Modern Language Review.

[40]  N. Hopwood "Giving Body" to Embryos: Modeling, Mechanism, and the Microtome in Late Nineteenth-Century Anatomy , 1999, Isis.

[41]  Meredith Wadman US plans giant effort on protein structure , 1999, Nature.

[42]  A. Abbott Structures by numbers , 2000, Nature.

[43]  P. Smaglik Genomics initiative to decipher 10,000 protein structures , 2000, Nature.

[44]  Lily E. Kay,et al.  Who Wrote the Book of Life?: A History of the Genetic Code , 2000 .

[45]  C. Waldby The Visible Human Project , 2003 .

[46]  Eric Francoeur,et al.  Does the materiality of molecular models really matter , 2000 .

[47]  C. Waldby The Visible Human Project : Informatic Bodies and Posthuman Medicine , 2000 .

[48]  Evelyn Fox Keller,et al.  Models of and Models for: Theory and Practice in Contemporary Biology , 2000, Philosophy of Science.

[49]  James Brouwer How We Became Posthuman: Virtual Bodies in Cybernetics, Literature, and Informatics , 2001 .

[50]  É. Francoeur Molecular models and the articulation of structural constraints in chemistry , 2001 .

[51]  M. Nye Paper Tools and Molecular Architecture in the Chemistry of Linus Pauling , 2001 .

[52]  C. Tanford,et al.  Nature's Robots: A History of Proteins , 2001 .

[53]  É. Francoeur Cyrus Levinthal, the Kluge and the origins of interactive molecular graphics. , 2002, Endeavour.

[54]  Evelyn Fox Keller,et al.  Making sense of life : explanation in developmental biology , 1999 .

[55]  P. Griffiths Making Sense of Life: Explaining Biological Development With Models, Metaphors, and Machines , 2002 .

[56]  M. Zaitlin The Life of a Virus: Tobacco Mosaic Virus as an Experimental Model, 19301965 , 2002 .

[57]  Karen Barad Posthumanist Performativity: Toward an Understanding of How Matter Comes to Matter , 2003, Signs: Journal of Women in Culture and Society.

[58]  David T. Jones Learning to Speak the Language of Proteins , 2003, Science.

[59]  A. Mol The Body Multiple: Ontology in Medical Practice , 2003 .

[60]  Theresa M. Senft Haraway, Donna J. , 2003 .

[61]  J. Griesemer CHAPTER FIFTEEN. Three-Dimensional Models in Philosophical Perspective , 2004, Models.

[62]  C. Meinel Molecules and Croquet Balls , 2004 .

[63]  Eric Francoeur,et al.  From model kits to interactive computer graphics , 2004 .

[64]  B. Latour How to Talk About the Body? the Normative Dimension of Science Studies , 2004 .

[65]  M. Cobb Making sense of life: explaining biological development with models, metaphors and machines , 2004, Heredity.

[66]  L. Daston The glass flowers , 2004 .

[67]  David Kaiser Drawing Theories Apart: The Dispersion of Feynman Diagrams in Postwar Physics , 2005 .

[68]  Albena Yaneva,et al.  Citations (this article cites 5 articles hosted on the SAGE Journals Online and HighWire Press platforms): , 2022 .

[69]  I. Löwy Models: The Third Dimension of Science , 2006 .

[70]  Natasha Myers,et al.  Animating Mechanism: Animations and the Propagation of Affect in the Lively Arts of Protein Modelling , 2006 .

[71]  Victor Braitberg Picturing Personhood: Brain Scans and Biomedical Identity , 2007 .

[72]  Natasha Myers Modeling proteins, making scientists : an ethnography of pedagogy and visual cultures in contemporary structural biology , 2007 .

[73]  R. Dubos,et al.  The body multiple: Ontology in medical practice , 2007 .