Rendering Life Molecular: Models, Modelers, and Excitable Matter

Rendering Life Molecular: Models, Modelers, and Excitable Matter

by Natasha Myers

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Overview

What are living bodies made of? Protein modelers tell us that our cells are composed of millions of proteins, intricately folded molecular structures on the scale of nanoparticles. Proteins twist and wriggle as they carry out the activities that keep cells alive. Figuring out how to make these unruly substances visible, tangible, and workable is a challenging task, one that is not readily automated, even by the fastest computers. Natasha Myers explores what protein modelers must do to render three-dimensional, atomic-resolution models of these lively materials. Rendering Life Molecular shows that protein models are not just informed by scientific data: model building entangles a modeler’s entire sensorium, and modelers must learn to feel their way through the data in order to interpret molecular forms. Myers takes us into protein modeling laboratories and classrooms, tracking how gesture, affect, imagination, and intuition shape practices of objectivity. Asking, ‘What is life becoming in modelers' hands?’ she tunes into the ways they animate molecules through their moving bodies and other media. In the process she amplifies an otherwise muted liveliness inflecting mechanistic accounts of the stuff of life.

Product Details

ISBN-13: 9780822375630
Publisher: Duke University Press
Publication date: 08/27/2015
Series: Experimental Futures
Sold by: Barnes & Noble
Format: NOOK Book
Pages: 344
File size: 9 MB

About the Author

Natasha Myers is Associate Professor of Anthropology at York University.

Read an Excerpt

Rendering Life Molecular

Models, Modelers, and Excitable Matter


By Natasha Myers

Duke University Press

Copyright © 2015 Natasha Myers
All rights reserved.
ISBN: 978-0-8223-7563-0



CHAPTER 1

ONE | CRYSTALLOGRAPHIC RENDERINGS


Diane is the head of a protein crystallography laboratory. She is a tenured faculty member based in the departments of chemistry and biology at research institute on the East Coast of the United States. Her laboratory hums with activity. It takes up a number of rooms on the fourth floor of a large building that also houses chemistry laboratories and several other academic units, including the anthropology department. The groups' dozen graduate students and postdocs occupy a large open space lined with laboratory benches. Stacks of used petri dishes, test tubes, Styrofoam containers, used pipette tips, and beakers are scattered across the surfaces of their black laboratory benches. Some benches have apparatuses to purify proteins or automated PCR (polymerase chain reaction) machines for amplifying specific strands of DNA. Microscopes, water baths, hot plates, and shakers take up the remaining surfaces. Shelves lining the walls are stacked high with darkened glass jars full of chemicals, fresh supplies wrapped in plastic, and gleaming glassware. The fume hoods that line the walls are filled with instruments that must be carefully calibrated. Personal workspaces are decorated with pictures of family, friends, comic strips and cartoons, and one or two of the desks sport glamour shots of celebrities.

The machines scattered through the lab are part of a larger assemblage of attendant refrigerators, incubators, and centrifuges that take up space in the halls and adjoining rooms. Vapors billow forth from liquid nitrogen canisters and -80°C freezers. A massive X-ray diffraction machine is housed in its own set of rooms. A protective glass wall separates this machine and its radiation from users and the computers they use to process diffraction data. Down the hall a darkened computer room equipped with several workstations feels like a quiet sanctuary. It is here that lab members render their long-sought-after crystallographic data into three-dimensional computer graphic models.

Just down the hall from the computer lab is Diane's office. When I arrived for our first interview, her aging dog, Max, greeted me with sweet, mournful eyes. His arthritic gait told me he wasn't long for this world. He was Diane's constant companion in the lab, and her grad students would come by throughout the day to take him out for walks. His presence sometimes made the lab seem like a family, especially when he came to the weekly lab meetings. These group meetings gave Diane and her students opportunities to present their progress on current research projects, as well as seek support to navigate difficult problems. At the same time this was also their opportunity to negotiate who was going to take on routine chores, tasks that involved cleaning communal workspaces and maintaining equipment. If some took up these tasks with a sense of collegial duty, others had to mute their disdain for washing glassware or cleaning out the refrigerators.

In our first interview, I learned a lot from Diane about what motivated her to pursue a career in the field of protein crystallography. Diane studied chemistry as an undergraduate student. One of the questions that fascinated her was how enzymes and their substrates interacted to catalyze biochemical processes. She explained: "I really liked the idea of trying to understand enzymes. What did they do? How did they catalyze this reaction? What was the detailed mechanism involved?" She wanted to be able to "see" biochemical reactions unfold: "I figured out that I couldn't think of working on a project if I didn't understand what it looked like. I needed that first.... You have to have some kind of concrete thing to start with, even if it's just one picture. At least there is something more tangible involved there. It was just that it seemed to me that that was the starting place for science. The first thing you ask is, 'What does it look like?'" This desire to see what proteins "look like" is evocative of the efforts of nineteenth-century natural historians' efforts to describe "nature's panopoly" through drawings, images, and models. It is only once they could see what proteins "look like," that modelers could begin to compare and contrast these remarkably diverse forms. What Diane was proposing seemed at first like a high-tech, high-resolution natural history of enzymes.

Protein crystallography was the technique that could give her visual access to these unseen dimensions of cellular life. Yet, this was more than a descriptive project. It was only with a three-dimensional model of the precise atomic configuration of a molecule that she would be able to discern the fine details of a protein's "active site," the area in the molecule that reacts chemically with other molecules. This was crucial knowledge if she was going to be able to figure out how that protein interacted with other molecules and how it catalyzed chemical reactions in the cell. Crystallographic models were "tangible" objects that could give her "concrete" access to these molecular interactions. The models she built would enable her to design experiments to intervene in an enzymatic reaction, and these interventions would help her interpret what particular proteins were up to inside the cell.

When Diane was ready to begin her graduate work in the 1990s, however, many of her mentors saw protein crystallography as a dead-end discipline. This was a time when rapid advancements in molecular genetic techniques and recombinant DNA technologies were shaping the direction of research questions and funding. Researchers in the biological sciences had already diverted their interest and investments from atomic-scale models of proteins to the automation of genetic sequence analysis. Informatic models of the genetic determinants of life held sway and molecular genetic studies dominated the life sciences. Diane was warned not to pursue training in protein crystallography. In some ways, she was getting sound advice. It was hard to build models of protein structure. It took Nobel Prize laureate Max Perutz twenty-two years to solve an atomic resolution crystallographic structure of just one protein molecule. His crystallographic model of hemoglobin, published in 1967, was at that time only the second high-resolution protein structure to be determined. Twenty years later faster computers and better equipment helped to speed things up. But by 1990 the Protein Data Bank housed just 486 protein structures determined by this technique. The future of the field did not look bright.

Yet, Diane's desire to gain visual access to the molecular realm was so strong that she ignored the sage advice, and began graduate work in protein crystallography. Her perseverance, it seems, paid off. By the time she began her tenure-track academic position in 1999, techniques had improved so much that contributions to the field had grown exponentially. That year alone nearly two thousand novel structures were determined by crystallographic methods, bringing the total to over nine thousand unique crystal structures archived in the Protein Data Bank. By 2004 she was tenured and head of a thriving lab at a prestigious research university.

This chapter offers a detailed examination of the techniques and practices protein crystallographers must learn in the course of their training. While it focuses primarily on the experiences of graduate students in Diane's laboratory, it also explores how graduate student life is rendered in the documentary Naturally Obsessed. In ways similar to the documentary, this chapter describes the practical and conceptual hurdles graduate students, postdocs, and their mentors encounter while attempting to build their first models. Alongside stories of scientists-in-training struggling to figure out how to comport themselves in the lab, this chapter traces the early history of X-ray diffraction and offers an overview of the suite of techniques that make up crystallographic vision. It foregrounds the limitations of X-ray diffraction methods and pays special attention to the contributions modelers must make at every step in the process to fill in the gaps between what is perceptible and what remains unseen. And as a step-by-step guide to help readers understand the technical challenges crystallographers encounter, it details the peculiar sequence of crystallographic techniques, from protein purification and modification methods to techniques for protein crystallization and diffraction. It offers an account of both the pleasures and the perils students face in their attempts to simultaneously master crystallographic techniques and learn to fashion themselves as scientists.

Naturally Obsessed is particularly generative to think within the context of this study, as it helps to keep in view the broader social, political, and economic forces that shape scientific lives. This chapter takes a close look at how audiences responded to Naturally Obsessed in various discussion forums. The documentary has spurred numerous conversations and debates on such issues as the naturalization of science as a competitive game, what counts as success, and who succeeds in science. These issues are crucial to keep in the foreground as this chapter hones attention on forms of affective labor that shape modelers' intimate relationships with the molecules, materials, and machines that populate their laboratories. It is by turning close ethnographic attention to the affective entanglements of laboratory practice, without losing sight of the political economy in which laboratory labor gains its traction, that it is possible to hear practitioners' accounts of their encounters with the affectivity of matter. This chapter shows how, in their hands, the stuff of life comes to matter as a lively, wily, and excitable substance. What becomes clear is that the forms of life that materialize in the intimate spaces of these laboratories are not so readily captured by any technique or industrial enterprise.


ENROLLING NEW SCIENTISTS

In the fall of 2006, during one of her lab's weekly group meetings, Diane practiced a talk she was about to give at an upcoming symposium that featured researchers at the forefront of the field. A group of graduate students, undergraduates, and postdocs were seated around the long table. Standing, she gestured across the room to a half-finished PowerPoint slide. As she walked through the points she would make in her talk, she laid out her approach to the "incredible" chemical structures that "nature has tailored" in living cells. Undeterred by the serious technical challenges protein crystallographers like her face in visualizing molecular forms, she told members of her lab that she wanted to "think bigger about what we can accomplish": "Instead of solving the structure of one enzyme from a [biochemical] pathway, we [want to] solve the structures of all the enzymes in the pathway, alone and in complexes. Instead of solving the structure of one protein from a superfamily, [we want to] solve structures of multiple members of that family — because in the comparison you can often figure out what is truly important in those molecules.... [We want to] solve many structures of one enzyme and capture states as it proceeds through its reaction cycle."

What Diane wanted her audience to consider were the dynamic properties of proteins: proteins move and change shape as they participate in chemical reactions in the cell. For the most part, protein crystallography is a static visualization technology, producing three-dimensional structures. Diane's ambitious proposal reimagines protein crystallography as a time-lapse imaging technology for playing through the sequence of structural changes that a protein undergoes as it encounters other molecules in a given biochemical reaction pathway.

Protein crystallography requires "resolving" differences in each region of the molecule; a crystallographer must be able distinguish between each atom at high resolution. Yet, note Diane's use of the verb "to solve" here. Where natural historians claim to "discover" new species in nature, Diane relates to protein crystallography as a puzzle-solving exercise, or what she describes as "detective story." Recall that one of the meanings of the verb "to render" is "to decipher" (see introduction). This is an apt description of the kind of work involved in making crystallographic data visible in the form of molecular models. If solving a single protein structure requires arduous labor, generating multiple models of a molecule at each step in its reaction cycle would be a monumental task. Diane's lab has been exceptionally productive, and she has built up an international reputation for solving the structures of significant proteins, yet this vision still seemed ambitious.

As she and the other practitioners documented in this book have taught me, the determination of a protein structure is a remarkable achievement. It takes serious work to model the atomic configuration of a protein. Practitioners require intensive training to cultivate the technical expertise they will need to accomplish this feat. According to Diane, to succeed as a protein crystallographer you must simultaneously be "a molecular biologist and a protein biochemist." Additionally, "you have to be a little bit of a physicist, you have to be a computer jock, and you have to be an artist." The wide range of dexterities and competencies bound up together in this "bricolage of expertise" means there is a steep learning curve for students in training. Many students arrive in Diane's lab with an undergraduate degree in either biochemistry, inorganic chemistry, or molecular biology. Some have never worked directly with computer codes; others have never worked with proteins or living organisms; most have no experience doing laboratory research.

The field is changing with innovations in technology and new investments, and as researchers like Diane refine their techniques they are taking on more challenging questions. Faster computers, automated laboratory techniques, powerful software, interactive computer graphics interfaces, and synchrotron X-ray sources now make it possible to solve protein structures on the timescale of a PhD student's tenure in the lab. Some labs are involved in large-scale collaborations to build models of massive protein complexes. Yet, crystallographic techniques today are far from foolproof, and almost every project is plagued by setbacks, failures, and detours. Novice modelers need to cultivate patience to weather the slow, painstaking work required to isolate and crystallize proteins, collect their data, and build models. Each step in the process is time-consuming, and physically, intellectually, and emotionally demanding. Even today it might take five years to determine a high-resolution structure of a large molecular assemblage. This is often too long for students who must complete a structure in time to graduate. Some students get lucky, or have the skills to make quick progress. When I first met Dehlia, a third-year student in Diane's lab, she was just putting the final touches on a paper forthcoming in Nature. Some projects present too many obstacles. Things were not moving so quickly for Amy. Already in her fifth year, she was still struggling to get usable crystallographic data.

In this sense, Diane's message wasn't just geared to impress the audience at the following week's symposium; her practice talk also served as a rallying call to her graduate students and postdocs. Indeed, the weight of these ambitious goals would fall on their shoulders. They would each spend at least five years apprenticing with her and learning from the other students and postdocs in the lab. They wouldn't graduate until they had successfully modeled their own proteins. In order to produce such fine-tuned, high-resolution visions of molecular life, Diane would have to invest her energies in training this new generation of scientists. Thus, while her laboratory is dedicated to the work of producing scientific facts, it is also a site geared to the task of making newscientists. So while lab directors like Diane are keen to solve protein structures and publish their results, they are also explicitly invested the training and continual retraining of graduate students and postdoctoral researchers. It is in the process of learning how to craft molecular facts that novices begin to fashion themselves as scientists. But what is the model for a good scientist? What does success in science look like?


(Continues...)

Excerpted from Rendering Life Molecular by Natasha Myers. Copyright © 2015 Natasha Myers. Excerpted by permission of Duke University Press.
All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.
Excerpts are provided by Dial-A-Book Inc. solely for the personal use of visitors to this web site.

Table of Contents

Preface  ix

Acknowledgments  xiii

Introduction  1

Part One. Laboratory Entanglements

1. Crystallographic Renderings  35

2. Tangible Media  74

3. Molecular Embodiments  99

Part Two. Ontics and Epistemics

4. Rending Representation  121

5. Remodeling Objectivity  136

Part Three. Forms of Life

6. Machinic Life  159

7. Lively Machines  182

8. Molecular Calisthenics  204

Conclusion: What Is Life Becoming?  230

Appendix: A Protein Primer  239

Notes  243

Bibliography  277

Index  299

What People are Saying About This

When Species Meet - Donna Haraway

"Bodies in motion—bodies of all kinds and at all scales—dance together in the act of coming to palpable, knowable attention. Further, mindful bodies think best and build richer worlds of knowledge and practice when play infuses work in the symbiosis called science. In this astute and beautifully written book, it is protein models and their people and machines that dance together, tuned to the visceral sensibilities, vital affections, and kinesthetic energies that make the sciences of molecular biology work. Rendering Life Molecular shows in just how many ways biology is a full-bodied practice. Readers will be excited in all the best ways."

Human-Machine Reconfigurations - Lucy Suchman

"With a lively and engaging style, a commitment to a feminist and phenomenological analysis, and an extraordinary attention to the specificity of scientists' embodied, material, and affective engagement in the creation of knowledge, Natasha Myers takes the study of the biosciences in a new direction. Rendering Life Molecular expands the laboratory studies canon as it re-animates our sense of the dynamic contingencies and relationalities of all biological entities."

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