HISTORY 598, FALL 2004

Professors Angela N.H. Creager and Michael S. Mahoney

Meeting Time: The seminar will meet Tuesday afternoons, 1:30-4:30, in Dickinson 211

Topics and Readings
(*Items added later for future offerings)

Week I (9/14)

Introduction: Questions and Themes

Jeremy Campbell, Grammatical Man
Evelyn Fox Keller, Refiguring Life: Metaphors of Twentieth-Century Biology
Week II (9/21)

The Discursive Rupture

Report: Philipp v. Hilgers

Lily E. Kay, "Cybernetics, Information, Life: The Emergence of Scriptural Representations of Heredity", Configurations 5(1997), 23-91 [PU online]; and "Who Wrote the Book of Life? Information and the Transformation of Molecular Biology," Science in Context 8 (1995): 609-34.
Michael S. Mahoney, "Cybernetics and Information Technology," in Companion to the History of Modern Science, ed. R. C. Olby et al., Chap.34 [online]
Karl L. Wildes and Nilo A. Lindgren, A Century of Electrical Engineering and Computer Science at MIT, 1882-1982, Parts III and IV (cf. treatment of some of the same developments in David Mindell, Between Humans and Machines)
James Phinney Baxter, Scientists Against Time

John M.Ellis, Against Deconstruction (Princeton, 1989), Chaps. 2-3
Daniel Chandler, "Semiotics for Beginners"
Week III (9/28)

Machines and Nervous Systems

Report:  Perrin Selcer

[read for overall structure before digging in to the extent you can]
Warren S. McCulloch and Walter Pitts, "A logical calculus of the ideas immanent in nervous activity", Bulletin of Mathematical Biophysics 5(1943), 115-33; repr. in Warren S. McCulloch, Embodiments of Mind (MIT, 1965), 19-39, and in Margaret A. Boden (ed.), The Philosophy of Artificial Intelligence (Oxford, 1990), 22-39.
Alan M. Turing, "On Computable Numbers, with an Application to the Entscheidungsproblem", Proceedings of the London Mathematical Society, ser. 2, vol. 42(1936-7), 230-265; corrections, ibid., vol. 43(1937), 544-46; repr. in Martin Davis (ed.), The Undecidable, 116-164  [online version, requires IE]
Stephen C. Kleene, "Representation of Events in Nerve Nets and Finite Automata", in C.E. Shannon and J. McCarthy (eds.), Automata Studies (Princeton, 1956), 3-41

Tara H. Abraham, "(Physio)logical circuits: The intellectual origins of the McCulloch-Pitts neural networks", Journal of the History of the Behavioral Sciences 38,1(2002), 3-25 [PU online]
Lily E. Kay, "From logical neurons to poetic embodiments of mind : Warren S. McCulloch's project in neuroscience", Science in Context 14,4(2001),591-614 [PU online]
Steven J. Heims, The Cybernetics Group, 1946-1953: Constructing a Social Science for Postwar America (Cambridge, MA: MIT Press, 1991, 1993), Chap. 3
Andrew Hodges, Alan Turing: The Enigma (NY: Simon & Schuster, 1983), pp. 78-159 (Hodges has composed a wonderful web page devoted to Turing's life and work; it includes a good account of Turing machines and a link to a Turing machine program for the Macintosh)
Martin Davis, "Mathematical Logic and the Origin of Modern Computers", in Esther R. Phillips (ed.), Studies in the History of Mathematics (Mathematical Assoc. of America, 1987), 137-165 

Warren S. McCulloch, "What is a Number, that a Man May Know It, and a Man, that He May Know a Number?", in Embodiments of Mind
Michael A. Arbib, Brains, Machines, and Mathematics (NY: McGraw-Hill, 1964; 2nd ed., NY: Springer Verlag, 1987), Chaps. 1, 2, 6; cf. his more recent article "Warren McCulloch's Search for the Logic of the Nervous System", Perspectives in Biology and Medicine 43,2(2000), 193-216 [pdf]
Neil R. Smalheiser, "Walter Pitts", Perspectives in Biology and Medicine 43,2(2000), 217-226 [pdf]
Rolf Herken, The Universal Turing Machine, a Half-Century Survey (1988); arts. by Andrew Hodges, Stephen C. Kleene, Robin Gandy
Martin Davis, The Universal Computer (NY: Norton, 2000)
James A. Anderson and Edward Rosenfeld, Talking Nets: An Oral History of Neural Networks (MIT Press, 1998)
Week IV (10/5)


Report:  Chris Jones

John von Neumann, "First Draft of a Report on the Edvac" (1945), ed. Michael D. Godfrey (pdf)
John von Neumann, "On a logical and general theory of automata", in Cerebral Mechanisms in Behavior: The Hixon Symposium, ed. L.A. Jeffries (New York: Wiley, 1951), 1-31; repr. in Papers of John von Neumann on Computing and Computer Theory, ed. William Aspray and Arthur Burks (MIT, 1987), 391-431
Claude E. Shannon, "Computers and Automata", Proceedings Institute of Radio Engineers 41(1953), 1234-41; repr. in Methodos 6(1954), 115-30; and in Claude Elwood Shannon: Collected Papers (IEEE Press, 1993), 703-10
Christopher G. Langton, "Self-Reproduction in Cellular Automata", Cellular Automata, ed. D. Farmer et al. (North-Holland), 145-156
Christian Burks and Doyne Farmer, "Towards Modeling DNA Sequences as Automata", ibid., 157-67 

Arthur W. Burks, "Computation, Behavior and Structure in Fixed and Growing Automata", in Marshall C. Yovits and Scott Cameron (eds.), Self-Organizing Systems: Proceedings of an Interdisciplinary Conference, 5 and 6 May, 1959, (New York, 1960), 282-311
Burks, "Von Neumann's Self-Reproducing Automata", in Burks (ed.), Essays on Cellular Automata (U. Illinois Pr., 1970), Chap. 1. Look over the rest of the collection for a sense of how the field of cellular automata was taking shape during the 1960s.

M.D. Godfrey and D.F. Hendry, "The Computer as von Neumann Planned It", IEEE Annals of the History of Computing 15,1(1993) (pdf)
Ken Thompson, "Reflections on Trusting Trust", Communications of the ACM 27,8(1984), 761-63 [pdf]
Robert McNaughton, "The Theory of Automata, A Survey", Advances in Computing 2(1961), 379-421 

Week V (10/12)


Report: Matt Hersch

Arturo Rosenblueth, Norbert Wiener and Julian Bigelow, "Behavior, Purpose and Teleology," Philosophy of Science 10 (1943): 18-24 [JSTOR]
Norbert Wiener, Cybernetics, or Control and Communication in the Animal and the Machine (Cambridge: MIT, 1948; 2nd ed., 1961)
H. Kalmus, "A Cybernetical Aspect of Genetics," Journal of Heredity 41 (1950): 19-22
Jacques Monod and Francois Jacob, "General Conclusions: Teleonomic Mechanisms in Cellular Metabolism, Growth, and Differentiation," Cold Spring Harbor Symposium on Quantitative Biology, vol. 26 (1961): 389-401. 

Murray Eden, "Cybernetics", in Fritz Machlup and Una Mansfeld, The Study of Information: Interdisciplinary Messages (NY, 1983), 409-439; followed by commentaries by Peter Elias, Richard Mattessich, Manfred Kochen, Michael Arbib, and Eden in response, 441-471
Geof Bowker, "How to be Universal: Some Cybernetic Strategies, 1943-70," Soc. Stud. Sci. 23 (1993): 107-27 [JSTOR]
Peter Galison, "The Ontology of the Enemy: Norbert Wiener and the Cybernetic Vision," Critical Inquiry 21 (1994): 228-265
David A. Mindell, Between Human and Machine:  Feedback, Control, and Computing Before Cybernetics (Johns Hopkins, 2002), Chapters 11-12
Angela N.H. Creager and Jean-Paul Gaudillière, "Meanings in Search of Experiments and Vice-Versa: The Invention of Allosteric Regulation in Paris and Berkeley, 1959-1968," HSPS 27:1(1996): 1-89 (You only need to read 6-15, which focuses on what the authors called the "cell regulationists" and their agenda; 1-5 will give you an introduction to the whole paper if you want it.)
Robert Trappl, ed. Cybernetics: Theory and Application (Washington: Hemisphere, 1983); students should look at the range of fields covered under "Applications" 

Walter Cannon, The Wisdom of the Body (1932)
Donna Haraway, "A Cyborg Manifesto: Science, Technology, and Socialist-Feminism in the Late Twentieth Century," in Simian, Cyborgs, and Women (New York: Routledge, 1991)
Peter J. Taylor, "Technocratic Optimism, H. T. Odum, and the Partial Transformation of Ecological Metaphor after World War II," J. Hist. Biol. 21 (1988): 213-244

Week VI (10/19)

Information Theory

Report: Corinna Schlombs

Claude E. Shannon, "The Mathematical Theory of Communication", Bell System Technical Journal 27(1948), 379-423, 623-656 (pdf)
Claude E. Shannon and Warren Weaver, The Mathematical Theory of Communication (Urbana, U. Illinois, 1949, rep. 1963)
Henry Quastler (ed.), Essays on the Use of Information Theory in Biology (Urbana: University of Illinois Press, 1953)
F. H. C. Crick, "On Protein Synthesis," Symposium of the Society for Experimental Biology 12 (1958): 138-63 
J.B.S. Haldane, "Data Needed for a Blueprint of the First Organism," in Sideney W. Fox, ed. The Origins of Prebiological Systems (Academic Press, 1965)

Mindell, Chapter 4
Sahotra Sarkar, "Biological Information: A Skeptical Look at Some Central Dogmas of Molecular Biology," The Philosophy and History of Molecular Biology: New Perspectives (Kluwer, 1996), pp. 187-231
Jean-Paul Gaudillière, "Regulation or Information: The Rhetoric and Practice of Molecular Biology in and out of the Pasteur Institute," unpublished manuscript. 
Evelyn Fox Keller, "The Body of a New Machine: Situating the Organism Between the Telegraph and the Computer," last essay in Refiguring Life: Metaphors of Twentieth-Century Biology (New York: Columbia University Press, 1995). 
Soraya de Chadarevian, "Sequences, Conformation, Information: Biochemists and Molecular Biologists in the 1960s," J. Hist. Biol. 29 (1996): 361-86

Lila L. Gatlin, Information Theory and the Living System (Columbia U.P., 1972), Chaps. 1,6,7
Francois Jacob, The Logic of Life: A History of Heredity (Pantheon, English translation 1973, French 1970)
John R. Pierce, An Introduction to Information Theory: Symbols, Signals and Noise (NY: Harper, 1961; 2nd. rev. ed., NY: Dover, 1980)
William Aspray, "The Scientific Conceptualization of Information: A Survey," Annals of the History of Computing 7:2 (1985): 117-140
Jérôme Segal, Le zéro et le un : histoire de la notion scientifique d'information au 20e siècle (Paris: Syllepse, 2003)

Week VII (11/2)

Entropy and Organization

Report:  Sultana Banalescu

Erwin Schrödinger, What is Life? (Cambridge University Press, 1944) [online Word version]
Max Delbrück, " What Is Life? And What is Truth?", Quarterly Review of Biology 20(1945): 370-372 (A review of What Is Life?) [JSTOR]
L. Brillouin, "Life, Thermodynamics, and Cybernetics," in Harvey S. Leff and Andrew Rex, Maxwell's Demon: Entropy, Information, Computing (Princeton: Princeton University Press, 1990).

Edward J. Yoxen, "Where Does Schrödinger's What Is Life? Belong in the History of Molecular Biology?," Hist. Sci. 17(1979): 17-52.
Robert C. Olby, "Schrödinger's Problem: What is Life?," Jour. Hist. Biol. 4 (1971): 119-148
Evelyn Fox Keller, "Molecules, Messages, and Memory: Life and the Second Law", in Refiguring Life
Robert Rosen, "The Schrödinger Question, What Is Life? Fifty-Five Years Later", in Essays on Life Itself, 5-32

Gatlin, Chap. 2 

Week VIII (11/9) 

Origins of the Genetic Code

Report:  Doogab Yi

Richard W. Hamming, "Error Detecting and Error Correcting Codes", Bell System Technical Journal 29(1950), 147-60; repr. in Key Papers in the Development of Coding Theory, ed. E.R. Berlekamp
George Gamow, "Possible Relation between Deoxyribonucleic Acid and Protein Structure"Nature 173(1954), 318
George Gamow, Alexander Rich, Martynas Ycas, "The Problem of Information Transfer from Nucleic Acids to Proteins", Advances in Biological and Medical Physics 4(1956), 41-51
F.H.C. Crick, J.S. Griffith, L.E. Orgel, "Codes Without Commas", Proc. Nat. Acad. Sci. 43,5(1957), 416-421 [JSTOR]
Sydney Brenner, "On the Impossibility of all Overlapping Triplet Codes in Information Transfer from Nucleic Acid to Proteins" Proceedings of the National Academy of Sciences 43,8(1957), 687-694 [JSTOR]
Robert Rosen, "The DNA-Protein Coding Problem", Bull. Math. Biophysics 21(1959), 71-95
Heinz Fraenkel-Conrat, "The Genetic Code of a Virus", Scientific American 211(1964)

David Kahn, The Code-Breakers, Chaps. 1, 12, 14, 27
Lily Kay, Who Wrote the Book of Life? A History of the Genetic Code

Claude E. Shannon, "Communication Theory of Secrecy Systems" (1945), Collected Papers, 84-143
Thomas M. Thompson, From Error-Correcting Codes Through Sphere-Packings to Simple Groups, Chap. 1
Francis Y.C. Fung, "A Survey of the Theory of Error-Correcting Codes", Tangents Online, I,1 (Spring 1994)
Carl E. Woese, The Genetic Code: The Molecular Basis for Genetic Expression (1967)
Errol C. Friedberg, Correcting the Blueprint of Life: An Historical Account of the Discovery of DNA Repair Mechanisms (Cold Spring Harbor Laboratory Press, 1997)

Charles Petzold, Code: The Hidden Language of Computer Hardware and Software (Microsoft Press, 1999)

Week IX (11/16)


Report:  Joe November

Robert S. Ledley, "Digital Electronic Computers in Biomedical Science", Science 130(no. 3384), 1225-1234; cf his The Use of Computers in Biology and Medicine (NY, 1965)
Douglas Brutlag, "Conclusions and Recommendations" (of report to the NIH on biomedical modeling) [pdf]
Robert K. Lindsay, "DENDRAL: a case study of the first expert system for scientific hypothesis formation", Artificial Intelligence 61(1993), 209-61
Peter Friedland and Laurence H. Kedes, "Discovering the Secrets of DNA" Comm.ACM 28,11(1985), 1164-86 (pdf) (MOLGEN)
R. J. Spinrad, "Automation in the Laboratory", Science, 158: 55-60 (Oct 6, 1967) [online]
Lindsay, Robert K., Bruce G. Buchanan, and Edward A. Feigenbaum. DENDRAL: A Case Study of the First Expert System for Scientific Hypothesis Formation. Artificial Intelligence 61 (1993): 209-261. [pdf] {NOT PERMANENT}
James Shreeve, The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World,  2004.
Joe November, "LINC: Biology's Revolutionary Little Computer" Endeavour 28,3 (September 2004): 125-131 [pdf]

Timothy Lenoir, " Shaping Biomedicine as an Information Science"
Evelyn Fox Keller, "Models of and Models For: Theory and Practice in Contemporary Biology" [pdf]
Eric S. Lander, Robert Langridge, Damian M Saccocio, "Computing in Molecular Biology: Mapping and Interpreting Biological Information, Computer 24,11(1991), 6-13; another version in Communications of the ACM 34,11(1991), 32-39
Joshua Lederberg, "How DENDRAL Was Conceived and Born", A History of Medical Informatics (NY: ACM Press, 1987), 14-44; appendix (37-44) is memo of 4/5/65 by E.A. Feigenbaum and R.W. Watson, "An Initial Research Statement for a Machine Induction Research Project" (pdf version)
Temple F. Smith, "The History of Genetic Sequence Databases", Genomics 6(1990): 701-707

History of Bioinformatics is the subject of an extensive online collection of primary and secondary sources compiled as a collaboration between historians of science and the scientists involved.  As an introduction to the subject and to the resources, see Lenoir, above. Use the site to get a sense of the nature and structure of the major early projects, DENDRAL, MYCIN, AND MOLGEN (current version online)

Week X (11/23)

Evolution and Communication

Report:  Dan Bouk

Eigen, Manfred et al., "The Origin of genetic information" Scientific American (1981)
Herbert Simon, "The Architecture of Complexity", in The Sciences of the Artificial 1962
Rupert Riedl, Order in Living Organisms, 1975 (1978), Chapters 1 2 and 8
C.H. Waddington, "The basic ideas of biology", in Towards a Theoretical Biology 1967
C.H. Waddington, "Form and Information", in Towards a Theoretical Biology 1968
H.H. Pattee, "The physical basis of coding and reliability in biological evolution", in Towards a Theoretical Biology
Michael A. Arbib, , "Self-reproducing Automata - Some implications for Theoretical Biology", in Towards a Theoretical Biology

Walter Fontana, et al., "Beyond Digital Naturalism", Artificial Life 1(1994), 211-227 [ps]
Walter Fontana and Leo Buss, "What would be conserved if 'the tape were played twice?", Proc. NAS  91,2(1994),  757-761. [JSTOR]

Alan M. Turing, "The Chemical Basis of Morphogenesis" Philosophical Transactions B,237(1952), 37-72
Karl Sigmund, Games of Life
J.B.S. Haldane, "The Mechanical Chess-Player," Brit. J. Phil. Sci.3 (1952): 190
Alex Rich, "On the Problems of Evolution and Biochemical Information Transfer," Horizons in Biochemistry (1962)

Week XI (11/30)

Automata, Languages, Development

Report: Alicia Imperiale

Noam Chomsky, "Three models of language", IRE Transactions in Information Theory 2,3(1956), 113-24, and "On certain formal properties of grammars", Information and Control 2,2(1959), 137-167
Noam Chomsky and George A. Miller, "Introduction to the Formal Analysis of Natural Languages", in Handbook of Mathematical Psychology [1963-5], ed. R.D. Luce, R.R. Bush, E. Galanter, Vol. 2, Chap. 11
Aristide Lindenmayer, "Mathematical models for cellular interactions in development", J. Theor. Biol. 18(1968), 280-99, 300-15 Cf. his L-systems (also An L-system Tutorial, another tutorialL-system java applet)

David B. Searls, "The language of genes", Nature 420(2002), 211-217 [html, pdf (PU only)]
Noam Chomsky, The Logical Structure of Linguistic Theory, 1-53 ("Introduction 1973")
Robert Friedin, "Conceptual Shifts in the Science of Grammar: 1951-1992", in Carlos P. Otero (ed.), Noam Chomsky: Critical Assessments
Sheila A. Greibach, "Formal languages: Origins and directions", Annals of the History of Computing 3,1(1981), 14-41

Gary William Flake, The Computational Beauty of Nature
Przemyslaw Prusinkiewicz and Aristid Lindenmayer, The Algorithmic Beauty of Plants (Springer Verlag, 1990), esp. Chap.1
Przemyslaw Prusinkiewicz, Mark Hall, and Radomir Mech, Visual Models of Morphogenesis: A Guided Tour (online text with illustrations)
Week XII (12/7)

Synthetic Biology

Report: Lydia Kallipoliti

Christopher Langton, "Artificial Life", in Margaret A. Boden (ed.) The Philosophy of Artificial Life, Chap. 1
Thomas S. Ray, "An Approach to the Synthesis of Life", ibid., Chap. 3; see the Tierra home page and get a copy of the software
John Maynard Smith, "Evolution -- Natural and Artificial" ibid., Chap. 5
Elliott Sober, "Learning from Functionalism -- Prospects for Strong Artificial Life", ibid., Chap. 14
John L. Casti, "Newton, Aristotle and the Modeling of Living Systems", in John Casti and Anders Karlqvist (eds.), Newton to Aristotle: Toward a Theory of Models for Living Systems, 47-89
Carlo C. Maley, "Models in Evolutionary Ecology and the Validation Problem", Artificial Life VI
*Mark A. Bedau, "Can Unrealistic Computer Models Illuminate Theoretical Biology?" , Proc. 1999 Genetic and Evolutionary Computation Conference Workshop Program, Orlando, FL, July 13, 1999, ed. Annie S. Wu, 20-23 [pdf]
*Mark A. Bedau, et al., "Open Problems in Artificial Life", Artificial Life 6,4(2000),  363-376 [preprint pdf]

Claus Emmeche, The Garden in the Machine: The Emerging Science of Artificial Life
Stefan Helmreich, Silicon Second Nature: Culturing Artificial Life in a Digital World

John H. Holland, Hidden Order: How Adaptation Builds Complexity
Richard Doyle, On Beyond Living: Rhetorical Transformations of the Life Sciences, Chap. 7, "Emergent Power: Vitality and Theology in Artificial Life" 
John L. Casti, Alternate Realities: Mathematical Models of Nature and Man, Chap. 2 

Genetic Algorithms
John H. Holland, "Outline for a Logical Theory of Adaptive Systems", J. ACM 9,3(1962), 297-314 [pdf (PU only)] and Adaptation in Natural and Artificial Systems: An Introductory Intelligence (Ann Arbor, 1975)
Stephanie Forrest, "Genetic Algorithms: Principles of Natural Selection Applied to Computation", Science 261, no. 5123 (Aug. 13, 1993), 872-878
Melanie Mitchell, An Introduction to Genetic Algorithms (MIT, 1998) [online PU only]