Reasoning in Biological Discoveries Essays on Mechanisms, Interfield Relations, and Anomaly Resolution
Book contents
- Frontmatter
- Contents
- Long Contents
- List of Figures
- List of Tables
- Acknowledgments
- Introduction
- PART I BIOLOGICAL MECHANISMS
- PART II REASONING STRATEGIES: RELATING FIELDS, RESOLVING ANOMALIES
- 5 Interfield Theories with Nancy Maull
- 6 Theory Construction in Genetics
- 7 Relations Among Fields in the Evolutionary Synthesis
- 8 Selection Type Theories with Joseph A. Cain
- 9 Strategies for Anomaly Resolution: Diagnosis and Redesign
- 10 Exemplars, Abstractions, and Anomalies: Representations and Theory Change in Mendelian and Molecular Genetics
- 11 Strategies for Anomaly Resolution in the Case of Adaptive Mutation
- PART III DISCOVERING MECHANISMS: CONSTRUCTION, EVALUATION, REVISION
- Bibliography
- Index
- References
11 - Strategies for Anomaly Resolution in the Case of Adaptive Mutation
Published online by Cambridge University Press: 31 August 2009
Book contents
- Frontmatter
- Contents
- Long Contents
- List of Figures
- List of Tables
- Acknowledgments
- Introduction
- PART I BIOLOGICAL MECHANISMS
- PART II REASONING STRATEGIES: RELATING FIELDS, RESOLVING ANOMALIES
- 5 Interfield Theories with Nancy Maull
- 6 Theory Construction in Genetics
- 7 Relations Among Fields in the Evolutionary Synthesis
- 8 Selection Type Theories with Joseph A. Cain
- 9 Strategies for Anomaly Resolution: Diagnosis and Redesign
- 10 Exemplars, Abstractions, and Anomalies: Representations and Theory Change in Mendelian and Molecular Genetics
- 11 Strategies for Anomaly Resolution in the Case of Adaptive Mutation
- PART III DISCOVERING MECHANISMS: CONSTRUCTION, EVALUATION, REVISION
- Bibliography
- Index
- References
Summary
INTRODUCTION
Anomalies often challenge biological generalizations. Among the generalizations of widest scope in biology are natural selection and the central dogma of molecular biology. Because natural selection often produces novel variants, it might be expected that wide-scope generalizations would be infrequent (other than the theory of natural selection itself). Furthermore, biological regularities are evolutionarily contingent (Beatty 1995); whatever regularity has evolved can evolve away. Nonetheless, the central dogma of molecular biology is one of the most general findings in all of biology. It provides a schema for protein synthesis that involves unidirectional information flow from nucleic acids to proteins but not back. If information does not flow back into the genetic material, then there seems to be no mechanism for the inheritance of adaptive acquired characters. Although adaptive characters might be acquired during the life of one organism, their inheritance requires a change in the genetic material passed to the next generation. Because NeoLamarckian mechanisms require such inheritance, the lack of backwards flow of information strengthens the case for NeoDarwinian natural selection as the account of adaptations against any version of NeoLamarckism. The contemporary NeoDarwinian theory of natural selection claims that mutations arise spontaneously; that is, they are produced independently of their fitness in a given environment.
Anomalies challenging generalizations of such wide scope get attention. In a paper in 1988, John Cairns and colleagues claimed to find a new class of mutations in bacteria, called “directed mutations” and later “adaptive mutations.”
- Type
- Chapter
- Information
- Reasoning in Biological DiscoveriesEssays on Mechanisms, Interfield Relations, and Anomaly Resolution, pp. 248 - 268Publisher: Cambridge University PressPrint publication year: 2006
References
, , and (1998), “Evidence that Gene Amplification Underlies Adaptive Mutability of the Bacterial lac Operon,” Science 282: 1133–1135.CrossRefGoogle ScholarPubMed
Beatty, John (1995), “The Evolutionary Contingency Thesis,” in and (eds.), Concepts, Theories, and Rationality in the Biological Sciences. Pittsburgh, PA: University of Pittsburgh Press, pp. 45–81.Google Scholar
(1997), “Why Do Biologists Argue Like They Do?” Philosophy of Science 64 (Proceedings): S432–S443.CrossRefGoogle Scholar
, , , , , , , and (2003), “Stress-Induced Mutagenesis in Bacteria,” Science 300: 1404–1409.CrossRefGoogle ScholarPubMed
(1995), “Sexual Potency and Adaptive Mutation in Bacteria,” Trends in Microbiology 3: 291–292.CrossRefGoogle ScholarPubMed
(2003), “The Directed Mutation Controversy in an Evolutionary Context,” Critical Reviews in Microbiology 29: 25–35.CrossRefGoogle Scholar
(1997), Matters of Life and Death: Perspectives on Public Health, Molecular Biology, Cancer, and the Prospects for the Human Race. Princeton, NJ: Princeton University Press.Google Scholar
(1998), “Mutation and Cancer: The Antecedents to Our Studies of Adaptive Mutation,” Genetics 148: 1433–1440.Google ScholarPubMed
and (1991), “Adaptive Reversion of a Frameshift Mutation in Escherichia coli,” Genetics 128: 695–701.Google ScholarPubMed
and (2003), “Letter to the Editor: The Risk of Lethals for Hypermutating Bacteria in Stationary Phase,” Genetics 165: 2317–2318.Google Scholar
(1958), “On Protein Synthesis,” Symposium of the Society of Experimental Biology 12: 138–163.Google ScholarPubMed
(1988), What Mad Pursuit: A Personal View of Scientific Discovery. New York: Basic Books.Google Scholar
(1987), “Viewing the History of Science as Compiled Hindsight,” AI Magazine 8(2): 33–41.Google Scholar
Darden, Lindley (1990), “Diagnosing and Fixing Faults in Theories,” in and (eds.), Computational Models of Scientific Discovery and Theory Formation. San Mateo, CA: Morgan Kaufmann, pp. 319–346.Google Scholar
(1991), Theory Change in Science: Strategies from Mendelian Genetics. New York: Oxford University Press.Google Scholar
Darden, Lindley (1992), “Strategies for Anomaly Resolution,” in (ed.), Cognitive Models of Science, Minnesota Studies in the Philosophy of Science, v. 15. Minneapolis, MN: University of Minnesota Press, pp. 251–273.Google Scholar
Darden, Lindley (1995), “Exemplars, Abstractions, and Anomalies: Representations and Theory Change in Mendelian and Molecular Genetics,” in and (eds.), Concepts, Theories, and Rationality in the Biological Sciences. Pittsburgh, PA: University of Pittsburgh Press, pp. 137–158.Google Scholar
(1996), “Generalizations in Biology,” Essay Review of K. Schaffner's Discovery and Explanation in Biology and Medicine. Studies in History and Philosophy of Science 27: 409–419.CrossRefGoogle Scholar
(2002), “Strategies for Discovering Mechanisms: Schema Instantiation, Modular Subassembly, Forward/Backward Chaining,” Philosophy of Science (Supplement) 69: S354–S365.Google Scholar
Darden, Lindley and Michael Cook (1994), “Reasoning Strategies in Molecular Biology: Abstractions, Scans and Anomalies,” in , , and (eds.), PSA 1994, v. 2. East Lansing, MI: Philosophy of Science Association, pp. 179–191.Google Scholar
(1997), “Nonadaptive Mutations Occur on the F' Episome During Adaptive Mutation Conditions in Escherichia coli,” Journal of Bacteriology 179: 1550–1554.CrossRefGoogle ScholarPubMed
(2000), “Adaptive Mutation: Implications for Evolution,” BioEssays 22: 1067–1074.3.0.CO;2-Q>CrossRefGoogle ScholarPubMed
and (1994), “Adaptive Reversion of a Frameshift Mutation in Escherichia coli by Simple Base Deletions in Homopolymeric Runs,” Science 265: 407–409.CrossRefGoogle ScholarPubMed
(1997), Correcting the Blueprint of Life: An Historical Account of the Discovery of DNA Repair Mechanisms. Plainview, NY: Cold Spring Harbor Laboratory Press.Google Scholar
and (1996), “A Search for a General Phenomenon of Adaptive Mutability,” Genetics 143: 645–659.Google ScholarPubMed
(1990), “Spontaneous Point Mutations That Occur More Often When Advantageous Then When Neutral,” Genetics 126: 5–16.Google ScholarPubMed
, , and (1994), “Recombination in Adaptive Mutation,” Science 264: 258–260.CrossRefGoogle ScholarPubMed
, , , , and (2002), “Amplification Mutagenesis: Evidence that ‘Directed’ Adaptive Mutation and General Hypermutability Result from Growth With a Selected Gene Amplification,” Proceedings of the National Academy of Sciences 99: 2164–2169.CrossRefGoogle ScholarPubMed
and (1995), Epigenetic Inheritance and Evolution: The Lamarckian Dimension. New York: Oxford University Press.Google Scholar
(1996), The Eighth Day of Creation: The Makers of the Revolution in Biology. Expanded Edition. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.Google Scholar
(1962), The Structure of Scientific Revolutions. Chicago, IL: University of Chicago Press.Google Scholar
Lakatos, Imre (1976), Proofs and Refutations: The Logic of Mathematical Discovery. and (eds.). Cambridge: Cambridge University Press.Google Scholar
(1991), “The Inheritance of Acquired Characteristics,” Annual Review of Genetics 25: 1–20.CrossRefGoogle ScholarPubMed
and (2003), “Error-prone DNA Polymerase IV is Controlled by the Stress-response Sigma Factor, RpoS, in Escherichia coli,” Molecular Microbiology 50: 549–561.CrossRefGoogle ScholarPubMed
(1989), “Replica Plating and Indirect Selection of Bacterial Mutants: Isolation of Preadaptive Mutants in Bacteria by Sib Selection,” Genetics 121: 395–399.Google ScholarPubMed
and (1990a), “New Data on Excisions of Mu from E. coli MCS2 Cast Doubt on Directed Mutation Hypothesis,” Nature 344: 173–175.CrossRefGoogle Scholar
(1995), “Philosophy in the Laboratory: The Debate Over Evidence for E. J. Steele's Lamarckian Hypothesis,” Studies in History and Philosophy of Science 26: 469–492.CrossRefGoogle Scholar
(1994), “In Pursuit of a Molecular Mechanism for Adaptive Mutation,” Genome 37: 893–899.CrossRefGoogle ScholarPubMed
and (2003), “Modulating Mutation Rates in the Wild,” Science 300: 1382–1384.CrossRefGoogle ScholarPubMed
, , , and (1994), “Adaptive Mutation by Deletions in Small Mononucleotide Repeats,” Science 265: 405–407.CrossRefGoogle ScholarPubMed
, , , , , and (2003a), “Regulating General Mutation Rates: Examination of the Hypermutable State Model for Cairnsian Adaptive Mutation,” Genetics 163: 1483–1496.Google Scholar
, , , , , and (2003b), “Letter to the Editor: Adaptive Mutation Requires No Mutagenesis – Only Growth Under Selection: A Response,” Genetics 165: 2319–2321.Google Scholar
Sarkar, Sahotra (1991), “Lamarck Contre Darwin, Reduction Versus Statistics: Conceptual Issues in the Controversy Over Directed Mutagenesis in Bacteria,” in (ed.), Organism and the Origins of Self. Dordrecht: Kluwer, pp. 235–271.CrossRefGoogle Scholar
Sarkar, Sahotra (1996), “Biological Information: A Skeptical Look at Some Central Dogmas of Molecular Biology,” in (ed.) The Philosophy and History of Molecular Biology: New Perspectives. Dordrecht: Kluwer, pp. 187–231.CrossRefGoogle Scholar
(1995), “Adaptive Mutation: Who's Really in the Garden?” Science 268: 373–374.CrossRefGoogle ScholarPubMed
(1981), Somatic Selection and Adaptive Evolution: On the Inheritance of Acquired Characters. 2nd ed. Chicago, IL: University of Chicago Press.Google Scholar