Science without Laws: Model Systems, Cases, Exemplary Narratives

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Overview

Physicists regularly invoke universal laws, such as those of motion and electromagnetism, to explain events. Biological and medical scientists have no such laws. How then do they acquire a reliable body of knowledge about biological organisms and human disease? One way is by repeatedly returning to, manipulating, observing, interpreting, and reinterpreting certain subjects—such as flies, mice, worms, or microbes—or, as they are known in biology, “model systems.” Across the natural and social sciences, other disciplinary fields have developed canonical examples that have played a role comparable to that of biology’s model systems, serving not only as points of reference and illustrations of general principles or values but also as sites of continued investigation and reinterpretation. The essays in this collection assess the scope and function of model objects in domains as diverse as biology, geology, and history, attending to differences between fields as well as to epistemological commonalities.

Contributors examine the role of the fruit fly Drosophila and nematode worms in biology, troops of baboons in primatology, box and digital simulations of the movement of the earth’s crust in geology, and meteorological models in climatology. They analyze the intensive study of the prisoner’s dilemma in game theory, ritual in anthropology, the individual case in psychoanalytic research, and Athenian democracy in political theory. The contributors illuminate the processes through which particular organisms, cases, materials, or narratives become foundational to their fields, and they examine how these foundational exemplars—from the fruit fly to Freud’s Dora—shape the knowledge produced within their disciplines.

Contributors Rachel A. Ankeny Angela N. H. Creager Amy Dahan Dalmedico John Forrester Clifford Geertz Carlo Ginzburg E. Jane Albert Hubbard Elizabeth Lunbeck Mary S. Morgan Josiah Ober Naomi Oreskes Susan Sperling Marcel Weber M. Norton Wise

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Editorial Reviews

From the Publisher
Science without Laws inspires with its breathtaking scope. Delving from ethology to economics, molecular biology to microhistory, the authors illuminate crucial congruences in the way experts make their cases. Generations of scholars have taken physics as their model for right thinking, in science and beyond. This volume demonstrates that we are all biologists now.”—David Kaiser, author of Drawing Theories Apart: The Dispersion of Feynman Diagrams in Postwar Physics

Science without Laws is a superb book. It is a very strong collection, sharply defined yet impressive in scope and reach, rich in substance and deep in analysis.”—Arkady Plotnitsky, author of Complementarity: Anti-Epistemology after Bohr and Derrida

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Product Details

  • ISBN-13: 9780822340683
  • Publisher: Duke University Press
  • Publication date: 10/28/2007
  • Series: Science and Cultural Theory Series
  • Edition description: New Edition
  • Pages: 296
  • Sales rank: 1,153,164
  • Product dimensions: 6.00 (w) x 9.20 (h) x 0.80 (d)

Meet the Author

Angela N. H. Creager is Professor of History at Princeton University. She is the author of The Life of a Virus: Tobacco Mosaic Virus as an Experimental Model, 1930–1965.

Elizabeth Lunbeck is the Nelson Tyrone Jr. Professor of American History at Vanderbilt University. Her books include The Psychiatric Persuasion: Knowledge, Gender, and Power in Modern America.

M. Norton Wise is Professor of History and Co-Director of the Center for Society and Genetics at the University of California, Los Angeles. He is the editor of Growing Explanations: Historical Perspectives on Recent Science, also published by Duke University Press.

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Read an Excerpt

SCIENCE WITHOUT LAWS

MODEL SYSTEMS, CASES, EXEMPLARY NARRATIVES

Duke University Press

Copyright © 2007 Duke University Press
All right reserved.

ISBN: 978-0-8223-4068-3


Chapter One

Redesigning the Fruit Fly: The Molecularization of Drosophila

MARCEL WEBER

Laboratory organisms such as the fruit fly Drosophila melanogaster, the soil nematode Caenorhabditis elegans, or the budding yeast Saccharomyces cerevisiae are often described as model systems or model organisms. These terms suggest that biologists cultivate and study these organisms because they provide a basis for extrapolating theoretical knowledge to other organisms, in particular Homo sapiens. While this is clearly one of the roles that such organisms play in research, this fact alone can hardly explain the widespread distribution of just a few of these organisms in laboratories all around the world. Taking an ecological perspective, we can ask what makes certain organisms so well adapted or, perhaps, adaptable to certain types of laboratories. Robert Kohler has shown for the case of Drosophila that this species entered the laboratory mostly for contingent reasons, but then turned out to be extremely well adapted and adaptable for laboratory life. In addition, there now exists an impressive body of scholarship documenting how such organisms, once they have successfully colonized a few laboratories, start to affect the investigative pathways followed by the scientists.

While Drosophila proved instrumental for the rise of genetics during the first decades of the twentieth century, the molecularization of genetics in the 1950s and 1960s largely resulted from research on microorganisms, especially Escherichia coli and bacteriophage. The latter organisms offered the advantage that they could be handled in the laboratory in vast numbers, thus allowing the detection of extremely rare genetic events (e.g., mutation or recombination events). Even tiny Drosophila was much too bulky for this task. Furthermore, most of its genes are far too complex in terms of their phenotypic effects for fine-structure mapping. Even though Drosophila did not vanish into complete obscurity during the so-called molecular revolution, it clearly lost some of its scientific glamour. However, the fly made a spectacular comeback in the 1980s. One of the favorite experimental animals of developmental biologists today, the fruit fly even closed the race as only the second multicellular organism for which the full genomic DNA sequence became available. Indeed, the fly has come a very long way since T. H. Morgan found the first mutant white eyes in 1910.

There are probably several factors that contributed to Drosophila's comeback. Developmental biologists had kept an interest in the fly because it offered certain possibilities for the genetic analysis of development. For example, Drosophila can produce genetic mosaics, that is, individuals in which some lineages of somatic cells have mutated. This allowed developmental biologists to determine the fate of certain embryonic cell lineages. Furthermore, the old "breeder-reactor" (Kohler's term) proved useful for a systematic screen for mutants that affect embryonic development. Initially, there was little reason to believe that Drosophila would turn out to be a good model system for understanding the molecular basis of development in other organisms, perhaps even humans. Flies show quite a special developmental mechanism, one not only characterized by the phenomenon of metamorphosis but also by other unusual features like the syncytial stage, in which the embryo contains thousands of nuclei but no cells. Drosophila's success as an experimental organism cannot be explained by its being typical or characteristic in terms of development. In fact, it is unclear in what sense Drosophila is really a model for other organisms, especially mammals.

In this article, I want to show that the main advantage responsible for Drosophila's reproductive success in molecular laboratories lies in the enormous experimental resources associated with this organism. Drosophila became a powerful research tool for molecular biology because geneticists were able to mobilize these resources for molecular cloning, which gave them access to genes and gene products not confined to Drosophila. I also show that a hybrid technology was instrumental for this mobilization. The experimental resources include, first, classical genetic and cytological mapping techniques; second, highly detailed genetic maps; and third, research materials such as thousands of mutants and genetically well-characterized fly strains.

In addition, I will show that the successful deployment of these experimental resources for molecular studies depended on certain theoretical concepts from classical genetics, in particular, the classical gene concept itself. I am hoping that this will shed new light on the old philosophical problem of the relationship between classical and molecular genetics.

In the following section, I will examine how the first Drosophila genes were isolated and characterized at the molecular level in the later 1970s and early 1980s. Then I examine the relationship between the classical genes that had already been studied by the pioneers of Drosophila genetics and the new molecular entities. In the section thereafter, I will examine what this case reveals about the dynamics of model system-based research. The final section of my essay draws together the main conclusions from this study of experimental practice in biology.

HOW THE FIRST DROSOPHILA GENES WERE CLONED

Our story begins in the midst of the cloning revolution, which originated in the Stanford University biochemistry department, where the first in vitro recombined DNA molecules were produced in 1972. The scientific and technological promises, as well as ethical concerns, that the first genetically engineered organisms generated need no recounting here. In the present context, the term cloning designates a set of methods by which DNA fragments from any organism are inserted in vitro into a vector, that is, a small replicating unit (typically a bacterial plasmid or a bacteriophage) for amplification and subsequent molecular analysis, experimental intervention, and gene transfer. It did not take long until the new so-called recombinant DNA technology-originally developed on bacteria, bacteriophage, and animal viruses-was applied to Drosophila, the genetically best understood multicellular organism.

In fact, some of the standard methods of gene cloning were developed using DNA isolated from Drosophila. For example, the laboratory of David Hogness at Stanford developed a method called "colony hybridization" that allows the isolation of any DNA fragments complementary to a given RNA molecule. Michael Grunstein and Hogness used the method to clone the genes for the Drosophila 18S and 28S ribosomal RNA (rRNA). Recombinant plasmids containing these genes were isolated from a so-called genomic library (a set of random fragments of the entire genomic DNA of an organism inserted into a cloning vector) by hybridizing radioactively labeled RNA probes to a filter paper to which the DNA of bacterial colonies had been attached.

Hogness was originally not a Drosophila geneticist (although he quickly became one); he was a classical molecular geneticist who had previously worked with E. coli and bacteriophage. However, several established Drosophila labs became interested in doing molecular work on the fly. One such lab was Walter Gehring's at the University of Basel, which was working on embryonic development in Drosophila. They established a "gene bank" (the Swiss equivalent of a genomic library) by inserting DNA fragments produced by mechanical shearing of total nuclear DNA into a bacterial plasmid. Then they used the colony hybridization technique on this gene bank to isolate the Drosophila 5S rRNA genes. Gehring's laboratory later turned to the heat shock genes. Like most cells, Drosophila expresses a number of specific proteins after a heat shock and shuts down the expression of most other genes. Thus mRNA isolated from heat-shocked cells, together with the colony hybridization technique, provided an easy way to isolate the genes encoding the heat shock proteins. The colony hybridization method requires a purified RNA molecule complementary to the gene to be cloned. In the case of the rRNA and heat shock genes, abundant RNA species were available for this task. However, not all genes that interested the geneticists offered such ready access. A much more difficult cloning task involved the white gene-the oldest Drosophila gene known, as the first white mutation was described and localized to the X-chromosome by T. H. Morgan in 1910. This gene, characterized by mutations with a variety of phenotypic effects, had eluded all attempts to determine its physiological function. Therefore Gerald Rubin's laboratory at the Carnegie Institution used a trick called "transposon tagging" to clone the white locus. They made use of a particular white allele (white-apricot or [w.sup.a]), which had been shown to result from an insertion of the transposable element copia into the white locus. Since copia DNA was easy to isolate (it produces an abundant mRNA species that contaminated many cloning experiments and was thus accidentally isolated as a false positive in many colony hybridization screens), Rubin's laboratory was able to use copia as a molecular probe to isolate cloned DNA fragments containing sequences from the white locus. Gehring's lab used a different strategy to clone the white locus. They made use of the existence of a Drosophila strain in which the white locus had moved with a large transposon from the X-chromosome to a new location on chromosome 3, which happened to be in the vicinity of the already cloned heat shock genes. They then used a technique called "chromosomal walking" (see below) to isolate sequences from the white locus. This was possible because they had already cloned the heat shock genes, which served as a starting point for their chromosomal walk. In order to confirm the identity of the cloned DNA, they showed that it hybridized in situ to the known cytological location of the white locus. This technique of in situ hybridization proves important for our story and I therefore briefly describe it here.

The salivary glands of Drosophila larvae contain giant chromosomes composed of thousands of copies of nuclear DNA. These so-called polytene chromosomes have been used for cytological mapping since the 1930s. Cytological maps based on the specific banding patterns of polytene chromosomes were shown to be colinear with linkage maps in the 1930s. The method of in situ hybridization allows the localization of specific DNA fragments on polytene chromosome preparations. In this method, the DNA fragment to be localized is radioactively labeled and subsequently hybridized to polytene chromosomes. The chromosomal locations in which the DNA probe hybridized can then be visualized using autoradiography.

Direct evidence that these cloned DNA fragments really contain the white gene was only obtained two years later: Using a transposable element (P-element) as a vector for germ-line transformation that was developed in Gerald Rubin's laboratory, Gehring and his coworkers demonstrated that the putative white-locus sequences are capable of rescuing the white-minus phenotype, that is, white-mutants transformed with the cloned DNA showed the red eye color of the wild type.

The cloning strategies used for the rRNA and heat shock genes relied on the availability of the gene products of these genes (rRNA and heat shock protein mRNA, respectively). The Rubin lab's strategy to clone the white gene made use of the fact that one of the white alleles was the result of a transposable element insertion, so that cloned DNA containing this transposable element could be used to "fish" for DNA fragments containing the white gene. Since these are rather serendipitous circumstances that may not obtain in the case of other genes of interest, Hogness's laboratory developed an ingenious method to clone Drosophila DNA sequences about which nothing is known save their chromosomal location. This method came to be known as the chromosomal walking mentioned earlier.

Chromosomal walking makes full use of the powerful resources of Drosophila cytogenetics. A chromosomal walk can start with any fragment of previously cloned Drosophila DNA located not too far from the region to be cloned. In a first step, the cytological location of the cloned DNA sequence is determined by in situ hybridization to polytene chromosomes. In the following step, the starting DNA fragment is used to screen a genomic library for random fragments overlapping the starting fragment. The new fragments are mapped by in situ hybridization. Then they can be aligned to the starting fragment by restriction endonuclease mapping in order to determine the fragment farthest from the starting point in the direction of the walk. This second step is repeated many times and generates overlapping cloned DNA fragments that lie farther and farther from the starting point. The end point of a chromosomal walk is the region of interest, that is, the known or assumed location of a gene or gene complex of interest (as determined by classical cytogenetic mapping). In order to save time, it is possible (step 3) to "jump" large distances on the chromosome by using chromosomal rearrangements such as inversions. Rearrangements such as small deletions can also be used to narrow down the position of any cloned DNA fragment. For instance, if such a fragment fails to hybridize to a polytene chromosome carrying a deletion, this indicates that the cloned sequence lies within the break points of the deletion.

To my knowledge, the technique of using in situ hybridization in order to clone DNA sequences about which only their cytological location is known was unique to Drosophila. Hogness's laboratory first used it to clone the rosy and Ace genes. As Welcome Bender, Pierre Spierer, and Hogness report in their paper, while their "walk" was in progress, they learned from E. B. Lewis of inversions with end points in the Bithorax complex and in the region in which they were walking and used these to jump into the Bithorax region. Thus, rather accidentally, the first homeotic gene complex was cloned.

One of the next genes to be cloned by chromosomal walking was Antennapedia (Antp), another homeotic gene responsible for bizarre mutations, such as flies with legs on their heads. Two (competing) laboratories were involved in this strenuous effort, which, in the case of the Gehring group, took more than three years to complete. They cloned the Antp gene by a long chromosomal walk that made use of the chromosomal inversion Humeral, used to jump from a previously cloned region into the Antp region. It is the availability of mutants such as Humeral, which had previously been characterized by classical genetic methods, that made Drosophila such a powerful system for molecular research.

The laboratory of Thomas Kaufman at Indiana University used a somewhat different strategy, which also involved much chromosomal walking, to isolate clones spanning the Antp region. Both laboratories were able to use their chromosomal walk in the Antp region to clone another gene located in close vicinity (in fact, it is part of the Antennapedia gene complex): fushi tarazu or ftz. The Basel and Indiana groups independently found a sequence homology between Antp, ftz, and Ultrabithorax (one of the genes of the Bithorax gene complex, which had also been cloned). The homologous sequence turned out to be a highly conserved sequence element of 180 base pairs length. It was named the "homeobox" and had a great impact on molecular studies of development. Using cloned Drosophila sequences containing the homeobox as hybridization probes, homeobox genes from a great range of organisms including humans and plants have been isolated in a very short time. (Continues...)



Excerpted from SCIENCE WITHOUT LAWS Copyright © 2007 by Duke University Press. Excerpted by permission.
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.

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Table of Contents


Introduction   Angela N. H. Creager   Elizabeth Lunbeck   M. Norton Wise     1
Biology
Redesigning the Fruit Fly: The Molecularization of Drosophila   Marcel Weber     23
Wormy Logic: Model Organisms as Case-Based Reasoning   Rachel A. Ankeny     46
Model Organisms as Powerful Tools for Biomedical Research   E. Jane Albert Hubbard     59
The Troop Trope: Baboon Behavior as a Model System in the Postwar Period   Susan Sperling     73
Simulations
From Scaling to Simulation: Changing Meanings and Ambitions of Models in Geology   Naomi Oreskes     93
Models and Simulations in Climate Change: Historical, Epistemological, Anthropological, and Political Aspects   Amy Dahan Dalmedico     125
The Curious Case of the Prisoner's Dilemma: Model Situation? Exemplary Narrative?   Mary S. Morgan     157
Human Sciences
The Psychoanalytic Case: Voyeurism, Ethics, and Epistemology in Robert Stoller's Sexual Excitement   John Forrester     189
"To Exist Is to Have Confidence in One's Way of Being": Rituals as Model Systems   Clifford Geertz     212
Democratic Athens as an Experimental System: History and the Project of Political Theory   Josiah Ober     225
Latitude, Slaves, and the Bible: An Experimentin Microhistory   Carlo Ginzburg     243
Afterword: Reflections on Exemplary Narratives, Cases, and Model Organisms   Mary S. Morgan     264
Contributors     275
Index     279
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