PRINCETON UNIVERSITY
DEPARTMENT OF HISTORY

HISTORY 598, FALL 1997 
COMPUTERS AND ORGANISMS

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

Meeting Time:

The seminar will meet Tuesday afternoons, 1:30-4:30, in the Latin American Studies Study Room in Firestone

Topics and Readings
(Subject to Change as Seminar Proceeds)

Week I (9/16)

Introduction: Questions and Themes

Jeremy Campbell, Grammatical Man
Week II (9/23)

The Discursive Rupture

Report: Jay Turner 

Lily E. Kay, "Cybernetics, Information, Life: The Emergence of Scriptural Representations of Heredity", Configurations 5(1997), 23-91; 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
Karl L. Wildes and Nilo A. Lindgren, A Century of Electrical Engineering and Computer Science at MIT, 1882-1982, Parts III and IV
James Phinney Baxter, Scientists Against Time
Week III (9/30)

Machines and Nervous Systems

Report: Tom Haigh 

Primary
[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 
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 

Secondary
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 

Supplementary
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
Rolf Herken, The Universal Turing Machine, a Half-Century Survey (1988); arts. by Andrew Hodges, Stephen C. Kleene, Robin Gandy 

Week IV (10/7)

Automata

Report: Joakim Marner 

Primary
John von Neumann, "First Draft of a Report on the Edvac" (1945), ed. Michael D. Godfrey
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 

Secondary
Arthur W. 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. 

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

Week V (10/14)

Cybernetics

Report: Guenter Schmidt 

Primary
Arturo Rosenblueth, Norbert Wiener and Julian Bigelow, "Behavior, Purpose and Teleology," Philosophy of Science 10 (1943): 18-24
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. 

Secondary
Geof Bowker, "How to be Universal: Some Cybernetic Strategies, 1943-70," Soc. Stud. Sci. 23 (1993): 107-27. 
Peter Galison, "The Ontology of the Enemy: Norbert Wiener and the Cybernetic Vision," Critical Inquiry 21 (1994): 228-265
David A. Mindell, "'Datum for it Own Annihilation:' Feedback, Contol, and Computing, 1916-1945" (Ph.D., MIT, 1996), Chapter 9
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" 

Supplementary
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 (10/21)

Information Theory

Report: Nathan Ensmenger 

Primary
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)

Secondary
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

Supplementary
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

Week VII (11/4)

Entropy and Organization

Report: David Berol

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

 Secondary
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

 Supplementary
Gatlin, Chap. 2 

Week VIII (11/11) 

Codes and Ciphers

Report: Adam Thornton 

Primary
Claude E. Shannon, "Communication Theory of Secrecy Systems" (1945), Collected Papers, 84-143
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

 Secondary
David Kahn, The Code-Breakers, Chaps. 1, 12, 14, 27
Lily Kay, Who Wrote the Book of Life? A History of the Genetic Code (forthcoming), Chap. 4
George Gamow, Mr. Tompkins Learns the Facts of Life and 1,2,3, ..., Infinity, Chaps. 8-9

 Supplementary
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) 

Week IX (11/18)

Origins of the Genetic Code

Report: Gail Schmitt 

Primary
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
Sidney 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(1957), 687-694
F. H. C. Crick, "On Protein Synthesis," Symposium of the Society for Experimental Biology 12 (1958): 138-63
Heinz Fraenkel-Conrat, "The Genetic Code of a Virus", Scientific American 211(1964)

 Secondary
Lily Kay, Who Wrote the Book of Life? A History of the Genetic Code (Stanford University Press, forthcoming, 1998)

 Supplementary
Carl E. Woese, The Genetic Code: The Molecular Basis for Genetic Expression (1967) 

Week X (11/25)

Evolution and Communication

Report: Manfred Laubichler 

Primary

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 TheoreticalBiology1967
C.H. Waddington, "Form and Information", in Towards a TheoreticalBiology 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

Secondary
Walter Fontana, et al., "Beyond Digital Naturalism", Artificial Life 1(1994), 211-227
Walter Fontana and Leo Buss, "What would be conserved if 'the tape were played twice'"?, PNAS 1994.
Richard Semon, Mnemic Psychology, Chapters to be announced

Supplementary
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 (12/2)

Automata, Languages, Development

Report: Jamie Cohen-Cole 

Primary
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(An L-system Tutorial)

Secondary
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
Michael S. Mahoney, The Structures of Computation, Chapter 4 (draft) 

Supplementary
Przemyslaw Prusinkiewicz and Aristid Lindenmayer, The Algorithmic Beauty of Plants (Springer Verlag, 1990), esp. Chap.1 

Week XII (12/9)

Synthetic Biology

Report: Ruth Michaels 

Primary
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 

Secondary
Claus Emmeche, The Garden in the Machine: The Emerging Science of Artificial Life

Supplementary
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 

Working Bibliography

General background:

Robert Olby, "The Molecular Revolution in Biology," Companion to the History of Modern Science, ed. R. C. Olby, G. N. Cantor, J.R.R. Christie, and M.J.S. Hodge (New York: Routledge, 1990).
Evelyn Fox Keller, Refiguring Life: Metaphors in Twentieth-Century Biology (Columbia University Press, 1995)
Fritz Machlup and Una Mansfeld, The Study of Information: Interdisciplinary Messages (NY: Wiley, 1983)
Donald M. MacKay, Information, Mechanism and Meaning (Cambridge: MIT Press, 1969)
Jagjit Singh, Great Ideas in Information Theory, Language and Cybernetics (NY: Dover, 1966)
Colin Cherry, On Human Communication (Cambridge: MIT Press and John Wiley & Sons, 1957).

Cybernetics and the Problem of Feedback:

Norbert Wiener, "Cybernetics," Scientific American 179 (1948): 14-19
H. Kalmus, "A Cybernetical Aspect of Genetics," Journal of Heredity41 (1950): 19-22.

Secondary:

William C. Wimsatt, "Some Problems with the Concept of Feedback," Boston Studies in the Philosophy of Science8 (1971): 241-256
Andrew Pickering, "WWII regime," Perspectives in Science

Mathematical and Biological Information:

Larry Owens, "Mathematicians at War: Warren Weaver and the Applied Mathematics Panel, 1942-45," The History of Modern Mathematics, eds. David E. Rowe and John McLeary (Boston: Academic Press, 1989), vol. 2, pp.l 287-305

Coding:

F. H. Hinsley and Alan Stripp, eds., Code Breakers: The Inside Story of Bletchley Park (Oxford University Press, 1993)
David Kahn, The Code Breakers (New York: MacMillan, 1967).

Entropy Considerations/Maxwell's Demon:

E. E. Daub, "Maxwell's Demon," in Harvey S. Leff and Andrew Rex, Maxwell's Demon: Entropy, Information, Computing (Princeton: Princeton University Press, 1990).