A Note on Web Sources

Where a book is cited, I have generally provided a link to the appropriate Amazon page. However, this may, on occasion, point to a different edition of the book to that cited in the text -- the original is held in the author's collection, and the link is provided as a service to the reader.

I also provide, where available, links to online versions of journal articles. Many journals prevent full text access without a subscription, so the full paper will not always be available.

Where a reference is cited on multiple occasions (eg. Artificial Life), only the first instance is linked.

Paperback Edition Notes

I have made a few minor changes to the references for the paperback edition (published, in the UK at least, on June 14 2007). These include updating web links, replacing "web-only" citations with rather more long-lived sources, and replacing all Wikipedia references with "traditional" (rather more rigorous) sources. Whilst Wikipedia might be a useful resource for initial research, I felt that using it as a primary source was perhaps inappropriate for a book with at least some scholarly aspirations.

Where a reference has changed, I have (for the time being) included the original after the new reference. These old citations will eventually be removed.

Prologue

  1. It was only after I'd written this prologue that I discovered a book that essentially shares the same title as this one. James P. Hogan's novel The Genesis Machine even opens with a remarkably similar scene, although any parallels observed here are completely unintentional, and, if anything, the creation of my fictional introduction owes more to Blood Music.
  2. Greg Bear. Blood Music. Arbor House, 1985.
  3. In a private email, Greg Bear confirmed my theory that the character was named in homage to Stanislaw Ulam, a stellar mathematician and one of the founders of the field of computational biology. He also pointed out that `Vergil I. Ulam' is an anagram of `I am Gulliver'. The double-helix derivation of `Neal Mendal' is left as an exercise to the reader.
  4. Nicholas Negroponte. Being Digital. Vintage, 1996.
  5. David Deutsch. The Fabric of Reality. Penguin, 1997.
  6. For a detailed list of current and completed genome sequence projects, see http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj.
  7. Nancy Forbes. Imitation of Life: How Biology is Inspiring Computing. MIT Press, 2004.

Chapter 1 - The Logic of Life

  1. http://news.com.com/Blue+GeneL+tops+its+own+supercomputer+record/2100-1006_3-5918025.html.
  2. For a discussion of the science of eggs, see http://www.exploratorium.edu/cooking/eggs/eggscience.html.
  3. Larry O'Hanlon. Honey bees recognize people. Discovery News, December 20 2005.
  4. Janine Benyus. Biomimicry: Innovation Inspired by Nature. HarperCollins, 2002.
  5. Richard Dawkins. The Selfish Gene. Oxford University Press, 1989.
  6. In fact, I originally suggested `Gene Machines' as the main title, but we found that this had already been (over)used as the headline for many popular articles on bioinformatics and biocomputing.
  7. Dennis Shasha and Cathy Lazere. Out of Their Minds: the Lives and Discoveries of 15 Great Computer Scientists. Copernicus, 1998.
  8. Sandeep Junnarkar. Researchers create logic gates with DNA reactions. New York Times, May 23 1997.
  9. Thomas Hobbes. Leviathan. Penguin, 1981. Edited by C.B. Macpherson.
  10. Erwin Schroedinger. What is Life? Cambridge University Press, 1992. With Mind and Matter and Autobiographical Sketches.
  11. Richard Gallagher and Tim Appenzeller. Beyond reductionism. Science, 284:79, 1999.
  12. James Watson. DNA: The Secret of Life. Arrow Books, 2004.
  13. Aristotle. On the Soul. 350 BC. Translated by J.A. Smith.
  14. Jessica Riskin, "The Defecating Duck, or, the Ambiguous Origins of Artificial Life". Critical Inquiry, Volume 29, Number 4, 2003. Available at http://criticalinquiry.uchicago.edu/issues/v29/v29n4.riskin.html.

    http://en.wikipedia.org/wiki/Digesting_Duck.

  15. Steven Levy. Artificial Life: The Quest for a New Creation. Pantheon Books, 1992.
  16. The British biologist Julian Huxley is reported to have pointed out the tautological nature of this definition by arguing that one may as well explain the motion of a steam train by `élan locomotif'.
  17. John von Neumann. The general and logical theory of automata. In A. H. Taub, editor, Collected Works of John von Neumann, Vol. 5, pages 289-326. John Wiley and Sons, 1951. Edited version of a talk presented at the Hixon Symposium on September 20, 1948.
  18. J. von Neumann. The Theory of Self-Reproducing Automata. University of Illinois Press, 1966. Edited by A. W. Burks.
  19. A. Turing. On computable numbers, with an application to the Entscheidungsproblem. Proceedings of the London Mathematical Society, Series 2, 42:230-265, 1936. Reprinted in M. Davis (ed.), The Undecidable, Hewlett, NY: Raven Press, 1965.
  20. The accepted lifetime of the Universe (13.7 billion years) translates to approximately 4.32 x 1016 seconds.
  21. Andrew Hodges. Alan Turing: the Enigma. Vintage, 1992.
  22. Andrew Hodges. Electronic spin. PC Pro magazine, 105, July 2003.
  23. You may actually be more familiar with the notion of an infinite loop than you think. When a computer crashes or freezes, this is often the result of the program spiralling downwards into an infinite loop. This may be caused by a hardware fault (for example, the computer repeatedly looking for a device that is not plugged in), user errors or sometimes just bad programming. The program is, for all intents and purposes, still running, which is why you often need to press CTRL-ALT-DELETE to interrupt its execution and restart the system.
  24. It is easy to simulate a Turing Machine on a standard computer (ignoring the requirement for unbounded memory). The mathematician Karl Scherrer actually built a Turing Machine in 1986, using construction kits and ball bearings to represent data. Its last known location was in the entrance to the Department of Computer Science at the University of Heidelberg, Germany.
  25. W. Wayt Gibbs. A digital slice of Pi. Scientific American, pages 23-24, May 2003.
  26. See, for example, http://driving.timesonline.co.uk/article/0,,19029-1448707,00.html. The claim was, I believe, first made by Sadie Plant, in her book Zeroes and Ones (Doubleday, 1997). However, this account has been disputed, with sources at Apple claiming that the rainbow is a reference to Isaac Newton's work on optics. A President of Apple Products, Jean-Louis Gassee, has commented: "One of the deep mysteries to me is our logo, the symbol of lust and knowledge, bitten into, all crossed with colors of the rainbow in the wrong order. You couldn't dream of a more appropriate logo: lust, knowledge, hope, and anarchy." (Apple Confidential: The Real Story of Apple Computer, Inc, Owen W. Linzmayer, No Starch Press, 1999). Regardless of the involvement of Apple, biographer Andrew Hodges said it best during his 1998 oration to Turing at the unveiling of a Blue Plaque on his birthplace; "...time has partly revealed his secret song of innocence and experience, and given significance to the veiled image of the poisoned apple.".
  27. L.Jeffress, editor. Cerebral Mechanisms of Behavior: The Hixon Symposium. Wiley, 1951.
  28. W.S. McCulloch and W. H. Pitts. A logical calculus of the ideas immanent in nervous activity. Bulletin of Mathematical Biophysics, 5:115-133, 1943.
  29. M. Mitchell Waldrop. Complexity: The Emerging Science at the Edge of Order and Chaos. Penguin, 1992.
  30. Norman Macrae. John von Neumann. Pantheon Books, 1992.
  31. John H. Holland. Adaptation in Natural and Artificial Systems. University of Michigan Press, 1975.

Chapter 2 - Birth of the Machines

  1. Andrew Hamilton. Brains that click. Popular Mechanics, 91(3):162-167,256,258, March 1949.
  2. Arthur W. Burks, Herman H. Goldstine, and John von Neumann. Preliminary discussion of the logical design of an electronic computing instrument. In A. H. Taub, editor, Collected Works of John von Neumann, Vol. 5, pages 34-79. John Wiley and Sons, 1951.
  3. Alternative architectures have been proposed and implemented, but the vast majority of computers in use today conform to the principles outlined by Burks, Goldstine and von Neumann.
  4. John von Neumann. The general and logical theory of automata. In A. H. Taub, editor, Collected Works of John von Neumann, Vol. 5, pages 289-326. John Wiley and Sons, 1951. Edited version of a talk presented at the Hixon Symposium on September 20, 1948.
  5. Georges Ifrah. The Computer and the Information Revolution. Harvill, 2000.
  6. http://www-groups.dcs.st-and.ac.uk/~history/HistTopics/Babylonian_numerals.html.
  7. A.K. Dewdney. On the spaghetti computer and other analog gadgets for problem solving. Scientific American, 250(6):19-26, June 1984.
  8. M. Mitchell Waldrop. Claude Shannon: Reluctant father of the digital age. MIT Technology Review, July/August 2001.
  9. G. Pascal Zachary, Endless Frontier: Vannevar Bush, Engineer of the American Century. MIT Press, 1999.

    http://en.wikipedia.org/wiki/Vannevar_Bush.

  10. Vannevar Bush. As we may think. The Atlantic Monthly, 176(1):101-108, July 1945.
  11. Arthur C. Clarke. Voice Across the Sea. HarperCollins, 1975.
  12. Claude E. Shannon. A Symbolic Analysis of Relay and Switching Circuits. MIT, 1937.
  13. http://web.mit.edu/newsoffice/2001/obitshannon-0228.html.
  14. C.E. Shannon. A mathematical theory of communication. Bell System Technical Journal, 27:379-423, 623-656, 1948.
  15. T.D. Schneider. Sequence logos, machine/channel capacity, Maxwell's demon, and molecular computers: a review of the theory of molecular machines. Nanotechnology, 5:1-18, 1994.
  16. Werner Gitt. Information, science and biology. TJ magazine, 10(2):181-187, August 1996. See also the detailed refutation of this paper.
  17. See, for example, the website at http://www.talkorigins.org/faqs/information/infotheory.html.
  18. Martin Campbell-Kelly and William Aspray, Computer: A History of the Information Machine, 2nd. ed., Westview Press, Colorado, 2004.

    EDSAC information at http://en.wikipedia.org/wiki/EDSAC.

  19. Notably, John William Mauchly and J. Presper Eckert with their work on ENIAC.
  20. Official Intel data at http://www.intel.com/pressroom/kits/quickreffam.htm.
  21. Gordon E. Moore. Cramming more components onto integrated circuits. Electronics, 38(8), 1965.
  22. Intel page on Moore's Law at http://www.intel.com/research/silicon/mooreslaw.htm.
  23. Transcript of interview with Moore at Stanford.
  24. News article at http://www.techweb.com/wire/30000176.
  25. For a biography of Shockley, see http://www.pbs.org/transistor/album1/shockley/.
  26. L.S. Hearnshaw. Cyril Burt, Psychologist. Cornell Univerisity Press, 1979.
  27. David Plotz. The Genius Factory: The Curious History of the Nobel Prize Sperm Bank. Random House, 2005.
  28. IEEE Spectrum, November 2004.
  29. The average chip contained 5.5 million components in 1995, a matrix of roughly 2.35 x 2.35 million. A standard postage stamp is roughly 2cm = 0.02m per side. 2.35 million (components) x 0.02m = 47,000m per side = 47km per side = 2,209 sq km. The area of Snowdonia National Park is 2,210 sq km, or roughly a tenth of the size of Wales (or a third of the size of Delaware, for readers in the USA).
  30. The average chip contains 256 million components (a conservative estimate), giving a matrix of 16 million by 16 million. Given 0.02m per stamp side, 16 million (components) x 0.02m = 320,000m per side = 320km per side = 102,400 sq km. According to the CIA Factbook at http://www.cia.gov/cia/publications/factbook/, the area of Iceland is roughly 103,000 sq km, or five times the size of Wales (or roughly the size of Virginia).
  31. http://www.intel.com/education/cleanroom/index2.htm.
  32. In reality, this process may be performed over 40 times, with the chip being constructed in three dimensions, layer-by-layer.
  33. Jim Turley. Silicon 101. http://www.embedded.com/showArticle.jhtml?articleID=17501489.
  34. Source: Lawrence Berkeley Laboratory, http://www.lbl.gov/MicroWorlds/ALSTool/EMSpec/EMSpec2.html.
  35. The real reason for the speed-up is that components are charged more quickly.
  36. http://www.cia.gov/cia/publications/factbook/geos/bd.html.
  37. http://news.com.com/Intel+scientists+find+wall+for+Moores+Law/2100-1008_3-5112061.html.
  38. Victor V. Zhirnov, Ralph K. Kavin, James A. Hutchby, and George I. Bourianoff. Limits to binary logic switch scaling - a Gedanken model. Proceedings of the IEEE, 91(11):1934-1939, 2003.
  39. BBC television Horizon programme, The Dark Secret of Hendrik Schon, February 5, 2004. Transcript available at http://www.bbc.co.uk/science/horizon/2004/hendrikshontrans.shtml.

    http://en.wikipedia.org/wiki/Jan_Hendrik_Sch\%F6n.

  40. Jan Hendrik Schoen, Hong Meng, and Zhenan Bao. Self-assembled monolayer organic field-effect transistors. Nature, 413:713-716, October 2001.
  41. Dan Vergano. Research advance could bring energy savings. USA Today, August 30 2001. http://www.usatoday.com/news/science/physics/2001-08-30-superconduct.htm.
  42. Lucent Annual Report, 2001.
  43. Lisa B. Song. Nanotech sparking surge in computer sciences: Degree demand up in engineering. Chicago Tribune, April 1 2002.
  44. http://www.dailyprincetonian.com/archives/2002/09/26/news/5462.shtml.
  45. Eugenie Samuel. Rising star of electronics found to have fabricated his ground-breaking results. New Scientist, page 4, October 5 2002.
  46. As physicist Doug Natelson has pointed out on his personal website at http://nanoscale.blogspot.com/, references to Schon (including, most importantly, the results of the case review) have recently been completely removed from the Lucent website. However, Natelson has made a copy of the review report available at http://www.ruf.rice.edu/~natelson/papers/researchreview.pdf.

    http://www.lucent.com/news_events/researchreview/.

  47. Doctor who? New Scientist, page 4, June 26 2004.
  48. Christine Hung, "Physics panel discusses Schon case", Yale Daily News, October 8, 2002. Available at http://www.yaledailynews.com/articles/view/5188.

    http://www.yaledailynews.com/article.asp?AID=20015.

  49. Paradise lost. New Scientist, page 5, December 21 2002.
  50. Matt Crenson. Fraud claims cast doubt on impressive results from Bell Labs' rising star. Portsmouth Herald, September 29 2002.
  51. Jan Hendrik Schoen, Hong Meng, and Zhenan Bao. Retraction: Self-assembled monolayer organic field-effect transistors. Nature, 422, March 6 2003.
  52. Valerie Jamieson. With hindsight, it was a hell of a lot of papers. New Scientist, October 5 2005.
  53. R. W. I. de Boer, M. E. Gershenson, A. F. Morpurgo, , and V. Podzorov. Organic single-crystal field-effect transistors. Phys. Stat. Sol. A, 201:1302-1331, 2004.
  54. Eugenie Samuel Reich. Crazy about crystals. New Scientist, pages 38-41, March 19 2005.
  55. John L. Casti and Cristian Calude. The jumble cruncher. New Scientist, pages 36-37, September 25 2004.
  56. Richard Jones. Soft Machines: Nanotechnology and Life. Oxford University Press, 2004.
  57. Michael Crichton. Prey. HarperCollins, 2002.
  58. Gary H. Anthes. Computation comes to life. Computerworld, February 28, 2005.
  59. Oliver Morton. Life, Reinvented. Wired, 13.01, January 2005.
  60. http://www.forbes.com/best/2001/0910/016_print.html.

Chapter 3 - There's Plenty of Room at the Bottom

  1. Richard P. Feynman. There's plenty of room at the bottom. In The Pleasure of Finding Things Out, pages 117-140. Allen Lane, 1999.
  2. Richard Jones. Soft Machines: Nanotechnology and Life. Oxford University Press, 2004.
  3. http://www.ostp.gov/NSTC/html/bioinformaticsreport.html.
  4. A.K. Dewdney. Computer recreations: Sharks and fish wage an ecological war on the toroidal planet wa-tor. Scientific American, pages 14-22, December 1984.
  5. A.K. Dewdney. Computer recreations: Exploring the field of genetic algorithms in a primordial computer sea full of flibs. Scientific American, pages 21-32, November 1985.
  6. Steven Levy. Artificial Life: The Quest for a New Creation. Pantheon Books, 1992.
  7. Leonard M. Adleman. Molecular computation of solutions to combinatorial problems. Science, 266:1021-1024, 1994.
  8. Gina Kolata. Novel kind of computing: Calculation with DNA. New York Times, November 22 1994.
  9. R. Rivest, A. Shamir, and L. Adleman. A method for obtaining digital signatures and public key cryptosystems. Comm. ACM, 21:120-126, 1978.
  10. Interview with Adleman in Networker, University of Southern California, Volume 7, Number 1, September/October 1996. Available at http://was.usc.edu/isd/publications/archives/networker/96-97/Sep_Oct_96/innerview-adleman.html.

    Interview with Adleman in USC Networker, September/October 1996.

  11. Gina Kolata. Hitting the high spots of computer theory: Leonard Adleman. New York Times, December 13 1994.
  12. Simon Singh. Fermat's Last Theorem. Fourth Estate, 2002.
  13. http://insight.zdnet.co.uk/internet/security/0,39020457,39118154,00.htm.
  14. http://www.usc.edu/dept/molecular-science/fm-adleman.htm.
  15. http://www.avert.org/usastaty.htm.
  16. Leonard M. Adleman. Computing with DNA. Scientific American, pages 34-41, August 1998.
  17. J. Rennie. Balanced immunity. Scientific American, pages 10-11, May 1993.
  18. Z. et al. Grossman. Conservation of total T-cell counts during HIV infection: alternative hypotheses and implications. Journal of Acquired Immune Deficiency Syndromes, 17(5):450-7, 1998.
  19. J.D. Watson, N.H. Hopkins, J.W. Roberts, J.A. Steitz, and A.M. Weiner. Molecular Biology of the Gene. BenjaminCummings, fourth edition, 1987.
  20. J.D. Watson and F.H.C. Crick. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature, 171:737-738, 1953.
  21. The closing line, also very coy, is perhaps rather more well-known in biological circles - "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.".
  22. http://my.webmd.com/content/article/26/1728_58756.
  23. http://www2.mrc-lmb.cam.ac.uk/dna2003/.
  24. John Sulston was awarded the Prize in 2002, but this fact was curiously omitted from his biography in the conference programme.
  25. Genesis, 30:30-33.
  26. Charles Darwin. On the Origin of Species. John Murray, 1859.
  27. Unfortunately for the people of the Soviet Union in the early 1930s, though, the notion of acquired characteristics appealed to Stalin, and was championed by the uneducated but ambitious Trofim Lysenko. His disastrous attempts to improve crop yields through the process of "vernalization", enthusiastically supported by the Soviet apparatchiks, led to widespread famine and set back Soviet biology by a generation.
  28. Available at http://www.mendelweb.org/Mendel.html.
  29. Robert Shapiro. The Human Blueprint: The Race to Unlock the Secrets of Our Genetic Script. Cassell, 1992.
  30. Hugo Iltis. Life of Mendel. Norton, 1932. Translated by Eden and Cedar Paul.
  31. Although there was some suspicion that Mendel had "smoothed" his data at the time, his basic hypothesis was shown to be correct.
  32. Richard Feynman made this point in typical fashion when describing his role as a school textbook reviewer for the California State Board of Education. `For example there was a book that started out with four pictures: first there was a wind-up toy; then there was an automobile; then there was a boy riding a bicycle; then there was something else. And underneath each picture it said `What makes it go?' ... I turned the page. The answer was, for the wind-up toy, `Energy makes it go.' ... Now that doesn't mean anything. Suppose it's `Wakalixes.' That's the general principle: `Wakalixes makes it go.' There's no knowledge coming in. The child doesn't learn anything; it's just a word!' (Richard P. Feynman, Surely You're Joking Mr. Feynman, Vintage, 1985, p. 297.
  33. James Watson. DNA: The Secret of Life. Arrow Books, 2004.
  34. James D. Watson. The Double Helix : A Personal Account of the Discovery of the Structure of DNA. Touchstone, 2001.
  35. Francis Crick. What Mad Pursuit: A Personal View of Scientific Discovery. Basic Books, 1990.
  36. Brenda Maddox. Rosalind Franklin : The Dark Lady of DNA. Harper Perennial, 2003.
  37. Thomas A. Bass. Gene genie. Wired, 3.08, August 1995.
  38. Adleman has emphasised that biocomputing is `...not the birth of a new science', and I completely agree with his assessment. The subtitle of this book was the subject of much editor-author discussion, after my publisher argued that, to the general reader, this research does seem like totally new science. I agreed to let it stand, on the condition that I was permitted to make my own position clear (that it isn't really a new science, and is more of a novel conjunction of existing scientific disciplines).
  39. C.H. Bennett. The thermodynamics of computation - a review. International Journal of Theoretical Physics, 21:905-940, 1982.
  40. Michael Conrad and E.A. Liberman. Molecular computing as a link between biological and physical theory. Journal of Theoretical Biology, 98:239-252, 1982.
  41. Dieter Oesterhelt, Christoph Brauchle, and Norbert Hampp. Bacteriorhodopsin: a biological material for information processing. Quarterly Reviews of Biophysics, 24(4):425-478, 1991.
  42. Robert R. Birge. Protein-based computers. Scientific American, pages 66-71, March 1995.
  43. Mark Buchanan. Small World: Uncovering Nature's Hidden Networks. Phoenix, 2002.
  44. See also the Oracle of Bacon .
  45. A version of the Kevin Bacon game also exists for mathematicians, replacing the actor with Paul Erdos, the late mathematician who was famously prolific in his collaborations. Erdos is assigned the value 0; if you co-authored a paper with Erdos before his death, you get the value 1. If you co-author with a co-author of Erdos you are assigned the value 2, and so on. A low number is considered prestigious by some mathematicians. See http://www.oakland.edu/enp/ for more details.

Chapter 4 - The TT-100

  1. http://www.sigma-genosys.eu.com/oligo_pricelist.asp.
  2. http://biotech.biology.arizona.edu/labs/DNA_extraction_onion_teach.html.
  3. Leonard M. Adleman. Computing with DNA. Scientific American, pages 34-41, August 1998.
  4. James Gleick. Genius: Richard Feynman and Modern Physics. Abacus, 1992.
  5. Paul Rabinow. Making PCR: A Story of Biotechnology. University of Chicago Press, 1996.
  6. Alexander Still. New mission for DNA: preservation. New York Times, February 12, 2000.
  7. Robert Simpson. Deciphering DNA. Research/Penn State, 20(2), May 1999.
  8. Kary B. Mullis. The unusual origin of the polymerase chain reaction. Scientific American, pages 36-43, April 1990.
  9. Tabitha M. Powledge. The polymerase chain reaction. Advances in Physiology Education, 28:44-50, 2004.
  10. Richard P. Feynman. Surely You're Joking, Mr. Feynman! Vintage, 1985.
  11. Celia Farber. AIDS; words from the front. Spin, July 1994.
  12. http://nobelprize.org/chemistry/laureates/1993/mullis-lecture.html.
  13. Kary Mullis. The cosmological significance of time reversal. Nature, 218:663, 1968.
  14. John Morkes. Untamed genius. Georgia Tech Alumni Magazine, 67(3), 1992.
  15. Jeremy Cherfas. Genes unlimited. New Scientist, (1712), April 14 1990.
  16. Randall K. Saiki, Stephen Scharf, Fred Faloona, Kary B. Mullis, Glenn T. Horn, Henry A. Erlich, and Norman Arnheim. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sick cell anemia. Science, 230:1350-1354, 1985.
  17. R. Saiki, D. Gelfland, S. Stoffel, S. Scharf, R. Higuchi, G Horn, K. Mullis, and H. Erlich. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science, 239:487-491, 1988.
  18. Loh E.Y., J.F. Elliott, S Cwirla, L.L Lanier, and M.M. Davis. Polymerase chain reaction with single-sided specificity: analysis of T cell receptor delta chain. Science, 243:217-220, 1989.
  19. H. Ochman, A.S. Gerber, and D.L. Hartl. Genetic applications of an inverse polymerase chain reaction. Genetics, 120:621-623, 1988.
  20. US patent number 4683202, see http://www.uspto.gov/patft/index.html.
  21. H. Gobind Khorana. A life in science. Science, 287:810, 2000.
  22. Arthur Kornberg. For the Love of Enzymes: the Odyssey of a Biochemist. Harvard University Press, 1989.
  23. An even greater stir was caused by a related 1989 patent, taken out on the heat-resistant polymerase enzyme, but the legal details are outside the scope of this book.
  24. Ruth Levy Guyer and Daniel E. Koshland. The molecule of the year. Science, 246:1543-1546, 1989.
  25. http://www.bio-ned.nl/BioHistory.htm.
  26. Andy Coghlan. The food scare the world forgot. New Scientist, pages 8-10, April 22 2006.
  27. http://www.neb.com/nebecomm/products/productN0468.asp.
  28. Anders Holmberg, Anna Blomstergren, Olof Nord, Morten Lukacs, Joakim Lundeberg, and Mathias Uhlén. The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures. Electrophoresis, 26(3):501-510, 2005.
  29. Leonard M. Adleman. Molecular computation of solutions to combinatorial problems. Science, 266:1021-1024, 1994.
  30. Thomas A. Bass. Gene genie. Wired, 3.08, August 1995.
  31. Interview with Adleman in Networker, University of Southern California, Volume 7, Number 1, September/October 1996. Available at http://was.usc.edu/isd/publications/archives/networker/96-97/Sep_Oct_96/innerview-adleman.html.

    http://www.usc.edu/isd/pubarchives/networker/96-97/Sep_Oct_96/innerview-adleman.html.

Chapter 5 - The Gold Rush

  1. Gina Kolata. A vat of DNA may become the fast computer of the future. New York Times, April 11, 1995.
  2. Robert Pool. A boom in plans for DNA computing. Science, 268:498-499, 1995.
  3. Warren D. Smith. An opinionated, but reasonably short, summary of the mini DIMACS workshop on DNA based computers, held at Princeton University on April 4 1995.
  4. Richard J. Lipton. DNA solution of hard computational problems. Science, 268:542-545, 1995.
  5. Benjamin H. Yandell. The Honors Class: Hilbert's Problems and Their Solvers. A.K. Peters, 2003.
  6. John Derbyshire. Prime Obsession: Bernhard Riemann and the Greatest Unsolved Problem in Mathematics. Joseph Henry Press, 2003.
  7. Martin Davis. Computability and Unsolvability. Dover Publications, 1982.
  8. Simon Singh. Fermat's Last Theorem. Fourth Estate, 2002.
  9. Values of the abstract. Nature, 405:379, 2000.
  10. Ivars Peterson. Searching for new mathematics. SIAM Review, 33(1):37-42, 1991.
  11. J. Robert Oppenheimer. The encouragement of science. In I. Gordin and S. Sorkin, editors, The Armchair Science Reader. Simon and Schuster, 1959.
  12. http://mathforum.org/social/math.perception.html.
  13. J. Hartmanis and R. Stearns. On the computational complexity of algorithms. Transactions of the American Mathematical Society, 117:285-306, 1965.
  14. L. Fortnow and S. Homer. A Short History of computational complexity, 2002.
  15. A. Cobham. The intrinsic computational difficulty of functions. In Proceedings of the 1964 International Congress for Logic, Methodology and Philosophy of Science, pages 24-30, 1964.
  16. Ian P. Gent and Toby Walsh. The search for satisfaction, April 27 1999.
  17. For lots of weblinks dealing with SAT, see http://www.satlive.org/.
  18. Martyn Amos. Theoretical and Experimental DNA Computation. Springer, 2005.
  19. Dennis Shasha and Cathy Lazere. Out of Their Minds: the Lives and Discoveries of 15 Great Computer Scientists. Copernicus, 1998.
  20. Michael S. Mahoney. Computer science: the search for a mathematical theory. In J. Echeverria, A. Ibarra, and T. Mormann, editors, The Space of Mathematics, pages 347-361. De Gruyter, 1992.
  21. S. A. Cook. The complexity of theorem proving procedures. In Proceedings of the 3rd Annual ACM Symposium on Theory of Computing, pages 151-158, 1971.
  22. Richard M. Karp. Reducibility among combinatorial problems. In Complexity of Computer Computations, pages 85-103. Plenum, 1972.
  23. M.R. Garey and D.S. Johnson. Computers and Intractability: A Guide to the Theory of NP-Completeness. W.H. Freeman, 1979.
  24. http://arxiv.org/abs/cs.CC/0210020.
  25. Richard Kaye. Minesweeper is NP-complete! Mathematical Intelligencer, 22(2):9-15, 2000. See also http://for.mat.bham.ac.uk/R.W.Kaye/minesw/ordmsw.htm.
  26. http://www.sciencenews.org/articles/20050618/mathtrek.asp.
  27. http://www.cs.umd.edu/~gasarch/papers/poll.ps.
  28. James Glanz. Computer scientists rethink their discipline's foundations. Science, 269:1363-1364, 1995.
  29. M. L. Minsky. Size and structure of universal Turing machines using tag systems. Proc. Sympos. Pure Math., 5:229-238, 1962.
  30. P.W.K. Rothemund. A DNA and restriction enzyme implementation of turing machines. In R.J. Lipton and E.B. Baum, editors, DNA Based Computers: Proceedings of the DIMACS Workshop, April 4, 1995, Princeton University, pages 75 - 119. American Mathematical Society, 1996.
  31. Rothemund, Paul W.K. US Patent 5,843,661, issued December 1, 1998. `Method for construction universal DNA based molecular Turing machine'. Available at http://patft.uspto.gov/.
  32. Dan Boneh, Christopher Dunworth, and Richard J. Lipton. Breaking DES using a molecular computer. In R.J. Lipton and E.B. Baum, editors, DNA Based Computers: Proceedings of the DIMACS Workshop, April 4, 1995, Princeton University, pages 37-66. American Mathematical Society, 1996.
  33. Steven Levy. Crypto: Secrecy and Privacy in the New Cold War. Penguin, 2002.
  34. Matt Curtin. Brute Force: Cracking the Data Encryption Standard. Springer-Verlag, 2005.
  35. http://www.iaik.tu-graz.ac.at/research/krypto/AES/.
  36. Dan Boneh, Christopher Dunworth, Richard J. Lipton, and Jirí Sgall. Making DNA computers error resistant. In Laura F. Landweber and Eric B. Baum, editors, Proceedings of the Second Annual Meeting on DNA Based Computers, pages 163-170. American Mathematical Society, 1996.
  37. Martyn Amos, Alan Gibbons, and David Hodgson. Error-resistant implementation of DNA computations. In Laura F. Landweber and Eric B. Baum, editors, Proceedings of the Second Annual Meeting on DNA Based Computers, pages 151-162. American Mathematical Society, 1996.
  38. Mitsunori Ogihara and Animesh Ray. DNA computing on a chip. Nature, 403:143-144, 2000.
  39. Sir Arthur Conan Doyle. The Sign of Four. Penguin, 2001.
  40. George Orwell. Coming Up for Air. Penguin, 2001.
  41. S.E. Luria and M. Human. A nonhereditary, host-induced variation of bacterial viruses. J. Bact., 64:557-569, 1952.
  42. John Whitfield. Origins of DNA: base invaders. Nature, 439:130-131, 2006.
  43. http://nobelprize.org/medicine/laureates/1978/.
  44. Sam Roweis, Erik Winfree, Richard Burgoyne, Nickolas Chelyapoc, Myron F. Goodman, Paul W.K. Rothemund, and Leonard M. Adleman. A sticker based model for DNA computation. In Laura F. Landweber and Eric B. Baum, editors, Proceedings of the Second Annual Meeting on DNA Based Computers, pages 1-29. American Mathematical Society, 1996.
  45. Qinghua Liu, Zhen Guo, Zhengdong Fei, Anne E. Condon, Robert M. Corn, Max G. Lagally, and Lloyd M. Smith. A surface-based approach to DNA computation. In Laura F. Landweber and Eric B. Baum, editors, Proceedings of the Second Annual Meeting on DNA Based Computers, pages 123-132. American Mathematical Society, 1996.
  46. Martyn Amos, Steve Wilson, David A. Hodgson, Gerald Owenson, and Alan Gibbons. Practical implementation of DNA computations. In C.S. Calude, J. Casti, and M.J. Dinneen, editors, Unconventional Models of Computation, Discrete Mathematics and Theoretical Computer Science, pages 1-18. Springer, Singapore, 1998.
  47. Martyn Amos. DNA Computation. PhD thesis, Department of Computer Science, University of Warwick, UK, September 1997.
  48. Historical information from the creators of VisiCalc available at http://www.bricklin.com/visicalc.htm.

    http://en.wikipedia.org/wiki/VisiCalc.

  49. Ivars Peterson. DNA, computers and killer apps, June 17, 1996.
  50. Harvey Rubin. Looking for the DNA killer app. Nature Structural Biology, 3(8):656-658, August 1996. Editorial.
  51. L.F. Landweber and R.J. Lipton. DNA2DNA: A potential `killer app'? In 24th International Colloquium on Automata, Languages and Programming (ICALP), Lecture Notes in Computer Science, pages 672-683. Springer, 1997.
  52. Jennier Kahn. It's alive! Wired, 10.03, March 2002.
  53. Eric B. Baum. Building an associative memory vastly larger than the brain. Science, 268:583-585, April 28, 1995.

Chapter 6 - Flying Fish and Feynman

  1. http://nobelprize.org/chemistry/laureates/1962/press.html.
  2. http://www.virtualgenomics.org/vcgb/biopics/seeman.htm.
  3. Unfortunately, the cost of reproducing the image prohibits us from showing it here, but versions of it are easy enough to find on the web.
  4. N.C. Seeman. Nucleic acid junctions: building blocks for genetic engineering in three dimensions. In R.H. Sarma, editor, Biomolecular Stereodynamics, pages 269-277. Adenine, 1981.
  5. Bruce H. Robinson and Nadrian C. Seeman. The design of a biochip: a self-assembling molecular-scale memory device. Protein Engineering, 1(4):295-300, 1987.
  6. George M. Whitesides and Bartosz Grzybowski. Self-assembly at all scales. Science, 295(5564):2418-2421, 2002.
  7. Philip Ball. The Self-made Tapestry: Pattern Formation in Nature. Oxford University Press, 2001.
  8. Self Assembly in Cereal.
  9. Paul W.K. Rothemund. Using lateral capillary forces to compute by self-assembly. Proceedings of the National Academy of Sciences of the USA (PNAS), 97(3):984-989, 2000.
  10. Xiaoping Yang et al. Nadrian C. Seeman, Hui Wang. New motifs in DNA nanotechnology. Nanotechnology, 9:257-273, 1998.
  11. J. J. Hopfield. Neural networks and physical systems with emergent collective computational abilities. Proceedings of the National Academy of Sciences of the USA (PNAS), 79(8):2554-2558, 1982.
  12. Antonio Regalado. DNA computing. MIT Technology Review, January 11, 2002.
  13. Erik Winfree. DNA computing by self-assembly. National Academy of Engineering: The Bridge, 33(4), 2003.
  14. H. Wang. Proving theorems by pattern recognition. Bell System Technical Journal, 40:1-42, 1961.
  15. Erik Winfree, Xiaoping Yang, and Nadrian C. Seeman. Universal computation via self-assembly of DNA: some theory and experiments. In Laura F. Landweber and Eric B. Baum, editors, Proceedings of the Second Annual Meeting on DNA Based Computers, pages 191-213. American Mathematical Society, 1996.
  16. Erik Winfree. Algorithmic self-assembly of DNA. PhD thesis, California Institute of Technology, May 1998.
  17. E. Winfree, F. Liu, L. Wenzler, and N.C. Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, 394:539-544, 1998.
  18. Paul W.K. Rothemund and Erik Winfree. The program-size complexity of self-assembled squares (extended abstract). In Proceedings of the Thirty-Second Annual ACM Symposium on Theory of Computing, pages 459-468. ACM Press, 1999.
  19. Erik Winfree. On the computational power of DNA annealing and ligation. In R.J. Lipton and E.B. Baum, editors, DNA Based Computers: Proceedings of the DIMACS Workshop, April 4, 1995, Princeton University, pages 199-210. American Mathematical Society, 1996.
  20. Chengde Mao, Thomas H. LaBean, John H. Reif, and Nadrian C. Seeman. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature, 407:493-496, 2000.
  21. Duke University Press Release, September 29, 2000.
  22. Rothemund P.W.K., N. Papadakis, and E. Winfree. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biology, 2(12):e424, 2004.
  23. Paul W.K. Rothemund. Folding DNA to create nanoscale patterns. Nature, 440:297-302, 2006.
  24. Lloyd M. Smith. Nanostructures: The manifold faces of DNA. Nature, 440:283-284, 2006.
  25. Nell Boyce. Fun with DNA, March 15 2006.
  26. Caltech press release, March 15 2006.
  27. Hao Yan, Sung Ha Park, Gleb Finkelstein, John H. Reif, and Thomas H. LaBean. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science, 301:1882-1884, 2003.
  28. A.T. Winfree. The Geometry of Biological Time. Springer, 2001.
  29. Qinghua Liu, Liman Wang, Anthony G. Frutos, Anne E. Condon, Robert M. Corn, and Lloyd M. Smith. DNA computing on surfaces. Nature, 403:175-179, 2000.
  30. Dirk Faulhammer, Anthony R. Cukras, Richard J. Lipton, and Laura F. Landweber. Molecular computation: RNA solutions to chess problems. Proceedings of the National Academies of Science, 97(4):1385-1389, 2000.
  31. Dirk Faulhammer, Anthony R. Cukras, Richard J. Lipton, and Laura F. Landweber. When the Knight falls: on constructing an RNA computer. In Erik Winfree and David K. Gifford, editors, DNA Based Computers V, pages 1-8. Americal Mathematical Society, 1999.
  32. Martyn Amos. Theoretical and Experimental DNA Computation. Springer, 2005.
  33. http://mathworld.wolfram.com/KnightsProblem.html.
  34. http://mathworld.wolfram.com/KnightsTour.html.
  35. John J. Watkins. Across the Board: The Mathematics of Chess Problems. Princeton University Press, 2004.
  36. R. Colin Johnson. RNA computer clears 10-bit hurdle, EE Times, February 1, 2000.
  37. Ravinderjit S. Braich, Nickolas Chelyapov, Cliff Johnson, Paul W.K. Rothemund, and Leonard Adleman. Solution of a 20-variable 3-SAT problem on a DNA computer. Science, 296:499-502, 2002.
  38. Philip Ball. Gene machine. Nature, 10 August 2000.
  39. B. Yurke, A.J. Turberfield, A.P. Mills, F.C. Simmel, and J.L. Neumann. A DNA-fuelled molecular machine made of DNA. Nature, 406:605-609, 2000.
  40. Jonathan Amos. DNA makes tiny tweezers, 9 August 2000. BBC news online.
  41. http://www.guinnessworldrecords.com.
  42. Yaakov Benenson, Tamar Paz-Elizur, Rivka Adar, Ehud Keinan, Zvi Livneh, and Ehud Shapiro. Programmable and autonomous computing machine made of biomolecules. Nature, 414:430-434, 2001.
  43. Guinness World Record number 58383, "World's Smallest Biological Computing Device".
  44. http://www.content-wire.com/lateral/lateral.cfm?ccs=107&cs=1100.
  45. Yaakov Benenson, Rivka Adar, Tamar Paz-Elizur, Zvi Livneh, and Ehud Shapiro. DNA molecule provides a computing machine with both data and fuel. Proceedings of the National Academies of Science, 100(5):2191-2196, 2003.
  46. Ivars Peterson. Computers by the trillions. Science News, 161(3), January 19, 2002.
  47. Yaakov Benenson, Binyamin Gil, Uri Ben-Dor, Rivka Adar, and Ehud Shapiro. An autonomous molecular computer for logical control of gene expression. Nature, 429:423-429, 2004.
  48. Richard Jones. Soft Machines: Nanotechnology and Life. Oxford University Press, 2004.
  49. http://www.wisdom.weizmann.ac.il/~udi/PressRoom/new_pages/press_eng.html.
  50. Alexandra Goho. Injectable medibots: programmable DNA could diagnose and treat cancer. Science News, 165(18):275, May 1, 2004.
  51. Milan N. Stojanovic and Darko Stefanovic. A deoxribozyme-based molecular automaton. Nature Biotechnology, 21(9):1069-1074, 2003.
  52. Jenny Hogan. DNA computer is the champion of tic-tac-toe. New Scientist, 23 August 2003.
  53. Juris Hartmanis. On the weight of computations. Bulletin of the European Association for Theoretical Computer Science, 55:136-138, 1995.
  54. Eric Smalley. Transcript of interview with Ned Seeman. Technology Research News, May 4, 2005.
  55. Max Glaskin. Bringing computers to life. Tomorrow's World Magazine, pages 52-54, May 1998.
  56. In fact, Microsoft are actually valuable supporters of and participants in research into biocomputing and other `wacky' models. See, for example, http://research.microsoft.com/towards2020science/.

    In fact, Microsoft are actually valuable supporters of and participants in research into biocomputing and other `wacky' models. See Luca Cardelli's web page, for example.

  57. Warren D. Smith. An opinionated, but reasonably short, summary of the mini DIMACS workshop on DNA based computers, held at Princeton University on April 4 1995.
  58. Mitsunori Ogihara and Animesh Ray. DNA computing on a chip. Nature, 403:143-144, 2000.
  59. Richard Powers. The Gold Bug Variations, page 369. HarperPerennial, 1991.

Chapter 7 - Scrapheap Challenge

  1. James Gleick. Genius: Richard Feynman and Modern Physics. Abacus, 1992.
  2. Hasan Zillur Rahim. `Transcript' of imagined conversation between Bill Gates and Richard Feynman.
  3. Richard P. Feynman. Feynman Lectures on Computation. Addison-Wesley, 1996. Edited by Anthony J.G. Hey and Robin W. Allen.
  4. Karen Hopkin. Life: The next generation. The Scientist, 18(19):56, October 11, 2004. Available online at http://www.the-scientist.com/2004/10/11/56/1/.
  5. Oliver Morton. Life, Reinvented. Wired, 13.01, January 2005.
  6. Andrew Pollack. Custom-made microbes, at your service. New York Times, January 17, 2006.
  7. Chappell Brown. BioBricks to help reverse-engineer life. EE Times, June 11, 2004.
  8. B. Hobom. Surgery of genes. at the doorstep of synthetic biology. Medizin. Klinik., 75:14-21, 1980.
  9. Steven A. Benner and Michael Sismour. Synthetic biology. Nature Reviews Genetics, 6:533-543, 2005.
  10. http://www.syntheticbiology.org.
  11. Richard Dawkins. The Blind Watchmaker. Penguin, 1986.
  12. Steven A. Benner. Synthetic biology: Act natural. Nature, 421:118, 2003.
  13. C.R. Geyer, T.R. Battersby, and S.A. Benner. Nucleobase pairing in expanded Watson-Crick-like genetic information systems. Structure, 11:1485-1498, 2003.
  14. Francis Crick. Central dogma of molecular biology. Nature, 227:561-563, 1970.
  15. Feynman's take on the use of such terms was this: `There are 1011 stars in the galaxy. That used to be a huge number. But it's only a hundred billion. It's less than the national deficit! We used to call them astronomical numbers. Now we should call them economical numbers.'.
  16. Matt Ridley. Genome: The Autobiography of a Species in 23 Chapters. Fourth Estate, 1999.
  17. Or, if you prefer, `soccer' ball. A typical eukaryotic cell might be 20 micrometers in diameter. The nucleus is roughly 6 micrometers across. A standard football is 22 cm in diameter. If we round this down to 20 cm, we can see that a football is 10,000 times the size of a cell. Scaling the nucleus up by the same factor, we arrive at a diameter of 6 cm, which is roughly the size of a satsuma.
  18. Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. Molecular Biology of the Cell. Garland Publishing, fourth edition, 2002. Freely (and legally) available online.
  19. T. A. Brown. Genomes. BIOS Scientific Publishers, 2nd edition, 2002. Freely (and legally) available online.
  20. James Watson. DNA: The Secret of Life. Arrow Books, 2004.
  21. C.R. Woese. The Genetic Code: the Molecular Basis for Genetic Expression. Harper and Row, 1967.
  22. F.H.C. Crick. The origin of the genetic code. Journal of Molecular Biology, 38(3):367-379, 1968.
  23. R.D. Knight, S.J. Freeland, and L.F. Landweber. Selection, history and chemistry: the 3 faces of the genetic code. Trends in the Biochemical Sciences, 24(6):241-247, 1999.
  24. David Brown. Deciphering the message of life's assembly. Washington Post, April 6, 2001.
  25. http://folding.stanford.edu.
  26. http://www.nature.com/nature/focus/humangenome/index.html.
  27. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature, 420:520-562, 2002.
  28. Nature special on the chimp genome.
  29. http://www.wellcome.ac.uk/doc_WTD002944.html.
  30. Jean-Michel Claverie. Gene number. what if there are only 30,000 human genes? Science, 291(5507):1255-1257, 2001.
  31. Jacques Monod. Chance and Necessity. Penguin, 1970.
  32. F. Jacob and J. Monod. Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology, 3:318-356, 1961.
  33. When a newly-sequenced gene sequence is lodged in the public databases, it is given a `name' by which it may be referred in the literature. These names are often informal - one gene, for example, when knocked out in fruitflies, caused them to develop pointy projections on their body, so the gene was named hedgehog. A similar gene was subsequently found and named Sonic hedgehog, after the game character, and this name now regularly appears in the titles and abstracts of serious scientific papers. Recently, the manufacturers of the Pokemon toy took out legal action to prevent gene researchers infringing their trademark with a gene name. Other, more serious problems may arise - as Ken Maclean points out in a letter to Nature, the innocent `humour' of gene names may be lost in translation to patients, when `people facing serious illness are told that they or their child have a mutation in a gene such as Sonic hedgehog, Slug or Pokemon' (Nature 439, 266, January 19, 2006).
  34. Tracy Kidder. The Soul of a New Machine. Back Bay Books, 2000.
  35. Johnjoe McFadden. The unselfish gene. The Guardian, May 6, 2005.
  36. Alok Jha. From the cells up. The Guardian, March 10, 2005.
  37. Institute for Systems Biology.
  38. Dan Ferber. Synthetic biology: Microbes made to order. Science, 303(5655):158-161, 2004.
  39. Richard Jones. Soft Machines: Nanotechnology and Life. Oxford University Press, 2004.
  40. Steven Levy. Hackers: Heroes of the Computer Revolution. Penguin, 2001.
  41. Simson L. Garfinkel. Biological computing. MIT Technology Review, May/June 2000.
  42. http://www.time.com/time/innovators/science/profile_arkin.html.
  43. Audrey M. Huang. Adam Arkin: Life, in theory. Berkeley Science Review, 4(1):43-46, 2004. http://sciencereview.berkeley.edu/.
  44. Harley H. McAdams and Adam Arkin. Simulation of prokaryotic genetic circuits. Annu. Rev. Biophys. Biomol. Struct., 27:199-224, 1998.
  45. Mark Ptashne. A Genetic Switch. Cell Press and Blackwell Scientific, 1987.
  46. Harley H. McAdams and Lucy Shapiro. Circuit simulation of genetic networks. Science, 269(5224):650-656, 1995.
  47. http://www.biomed-singapore.com/bms/sg/en_uk/index/career_centre/inspirations/year_2005/_prof_lucy_shapiro1.html.
  48. Paul Preuss. Circuits of a cell. Berkeley Lab Research Review, Winter 2000.
  49. H. McAdams and A. Arkin. Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA, 94:814-819, 1997.
  50. H.H. McAdams and A. Arkin. Genetic regulatory circuits: Advances toward a genetic circuit engineering discipline. Current Biology, 10:318-320, 2000.
  51. The DARPA programme is now closed, but details are still available at http://www.darpa.mil/ipto/solicitations/closed/01-26_CBD.htm.

    http://www.darpa.mil/ipto/programs/biocomp/index.htm.

  52. http://biospice.org.
  53. M. Elowitz and S. Leibler. A synthetic oscillatory network of transcriptional regulators. Nature, 403:335-338, January 2000.
  54. Steven Strogatz. Sync: The Emerging Science of Spontaneous Order. Penguin, 2003.
  55. Naama Barkai and Stanislas Leibler. Circadian clocks limited by noise. Nature, 403:267-268, 2000.
  56. Christopher Dickey. I love my glow bunny. Wired, 9.04, April 2001.
  57. Emma Young. Mutant bunny. New Scientist, September 22, 2000.
  58. D.C. Schwartz and C.R. Cantor. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell, 37:67-75, 1984.
  59. T. Gardner, R. Cantor, and J. Collins. Construction of a genetic toggle switch in Escherichia coli. Nature, 403:339-342, January 2000.
  60. Anne Eisenberg. Unlike viruses, bacteria find a welcome in the world of computing. New York Times, June 1, 2000.
  61. Official Sun Java applets information available at http://java.sun.com/applets/.

    Information on applets, and links to examples at http://en.wikipedia.org/wiki/Java_applet.

  62. Much of this discussion of natural genetic engineering is taken from `Going Back to Our Roots': Second Generation Biocomputing. Jon Timmis, Martyn Amos, Wolfgang Banzhaf and Andy Tyrrell; in press. Preprint available at http://arxiv.org/cs.AI/0512071.
  63. James A. Shapiro. Thinking about evolution in terms of cellular computing. Natural Computing, 4(4):297-324, 2005.
  64. Howard A. Shuman. Just toothpicks and logic: How some labs succeed at solving complex problems. Journal of Bacteriology, 185(2):387-390, 2003.
  65. J.A. Shapiro. Genome organization, natural genetic engineering and adaptive mutation. Trends in Genetics, 13(3):98-104, 1997.
  66. http://news.bbc.co.uk/1/hi/sci/tech/1535945.stm.
  67. Laura F. Landweber, Tai-Chih Kuo, and Edward A. Curtis. Evolution and assembly of an extremely scrambled gene. Proc. Natl. Acad. Sci. USA, 97(7):3298-3303, 2000.
  68. Kathy Sawyer. With DNA, `simple' cells perform acrobatic feats of computation. Washington Post, December 15, 1997.
  69. Laura F. Landweber and Lila Kari. The evolution of cellular computing: nature's solution to a computational problem. BioSystems, 52:3-13, 1999.
  70. A. Ehrenfeucht, T. Harju, I. Petre, D.M. Prescott, and G. Rozenberg. Computation in Living Cells: Gene Assembly in Ciliates. Springer, 2004.
  71. David M. Prescott. Invention and mystery in hypotrich DNA. Journal of Eukaryotic Microbiology, 45(6):575-581, 1998.
  72. The original source has been removed, but it is cached at Google.
  73. Joe Woodard. Design or Darwin? Calgary Herald, August 28, 2005. Copy online at http://www.christianity.ca/faith/faith-and-thought/2005/09.000.html.
  74. James A. Shapiro. A third way. Boston Review, February/March 1997. Available at http://www.bostonreview.net/BR22.1/shapiro.html.

    James A. Shapiro. A third way. Boston Review, February/March 1997. Online at http://www.bostonreview.net/br22.1/shapiro.html.

  75. Stuart Kauffman. At Home in the Universe: The Search for Laws of Complexity. Viking, 1995.
  76. H. Allen Orr. Response. Boston Review, February/March 1997. Available at http://www.bostonreview.net/BR22.1/orr.html.

    H. Allen Orr. Response. Boston Review, February/March 1997.

  77. James A. Shapiro and Martin Dworkin, editors. Bacteria as Multicellular Organisms. Oxford University Press, 1997. Reviewed at http://www.sciencemag.org/cgi/content/full/279/5359/2062.
  78. Ronald Kotulak. The cosmic conversation. Chicago Tribune, January 8, 2006.
  79. Gary H. Anthes. Computation comes to life. Computerworld, February 28, 2005. Available online at http://www.computerworld.com/hardwaretopics/hardware/story/0,10801,99996,00.html.
  80. MIT Biological Engineering Division.
  81. Drew Endy, Deyu Kong, and John Yin. Intracellular kinetics of a growing virus: a genetically structured simulation for bacteriophage T7. Biotechnology and Bioengineering, 55(2):375-389, 1997.
  82. Drew Endy, Lingchong You, John Yin, and Ian J. Molineux. Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. Proc. Natl. Acad. Sci. USA (PNAS), 97(10):5375-5380, 2000.
  83. W. Wayt Gibbs. Synthetic life. Scientific American, April 26, 2004.
  84. http://parts.mit.edu/.
  85. http://openwetware.org/.
  86. Nathanael Johnson. Steal this genome! East Bay Express, March 30, 2005.
  87. Lauren Gravitz. 10 emerging technologies that will change your world. MIT Technology Review, February 2004.
  88. Ron Weiss and Thomas F. Knight. Engineered communications for microbial robotics. In Anne Condon and Grzegor Rozenberg, editors, DNA Computing: Sixth International Workshop, pages 1-16. Springer, 2001.
  89. Mark Ward. BT ponders bacterial intelligence. BBC News Online, September 14, 2001.
  90. A.M. Turing. The chemical basis of morphogenesis. Philosophical Transactions of the Royal Society B (London), 237:37-72, 1952.
  91. Yohei Yokobayashi, Ron Weiss, and Frances H. Arnold. Directed evolution of a genetic circuit. Proc. Natl. Acad. Sci. USA (PNAS), 99(26):16587-16591, 2002.
  92. Jeff Hasty. Design then mutate. Proc. Natl. Acad. Sci. USA (PNAS), 99(26):16516-16518, 2002.
  93. Lingchong You, Robert Sidney Cox III, Ron Weiss, and Frances H. Arnold. Programmed population control by cell-cell communication and regulated killing. Nature, 428:868-871, 2004.
  94. Philip Ball. Starting from scratch. Nature, 431:624-626, 2004.
  95. Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold, and Ron Weiss. A synthetic multicellular system for programmed pattern formation. Nature, 434:1130-1134, 2005.
  96. Robert Roy Britt. Scientists make bacteria behave like computers. Live Science, April 28, 2005.
  97. Anselm Levskaya, Aaron A. Chevalier, Jeffrey J. Tabor, Zachary Booth Simpson, Laura A. Lavery, Matthew Levy, Eric A. Davidson, Alexander Scouras, Andrew D. Ellington, Edward M. Marcotte, and Christopher A. Voight. Engineering Escherichia coli to see light. Nature, 438:441-442, 2005.
  98. Sarah Boxer, "But is there intelligent spaghetti out there?", New York Times, August 29, 2005.

    http://en.wikipedia.org/wiki/Flying_Spaghetti_Monster.

  99. Paul Marks. Living camera uses bacteria to capture image. New Scientist, November 23, 2005.
  100. Susan Brown. Command performances. San Diego Union-Tribune, December 14, 2005.
  101. Maggie Fox. Scientists on the verge of building artificial life. , January 1999. Source: Reuters News Service.
  102. James Shreeve. The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World. Alfred A. Knopf, 2004.
  103. John Sulston and Georgina Ferry. The Common Thread: Science, Politics, Ethics and the Human Genome. Corgi, 2003.
  104. http://www.sciencewatch.com/sept-oct97/.
  105. Clyde A. Hutchison III, Scott N. Peterson, Steven R. Gill, Robin T. Cline, Owen White, Claire M. Fraser, Hamilton O. Smith, and J. Craig Venter. Global transposon mutagenesis and a minimal Mycoplasma genome. Science, 286(5447):2165-2169, 1999.
  106. Andrew Luck-Baker. Creating artificial bugs. BBC News, January 25, 1999.
  107. Justin Gillis. Scientists planning to make new form of life. Washington Post, November 21, 2002.
  108. Eliot Marshall. Venter gets down to life's basics. Science, 298(5599):1701, 2002.
  109. John I. Glass, Nacrya Assad-Garcia, Nina Alperovich, Shibu Yooseph, Matthew R. Lewis, Mahid Maruf, Clyde A. Hutchison III, Hamilton O. Smith, and J. Craig Venter. Essential genes of a minimal bacterium. Proc. Natl. Acad. Sci. USA (PNAS), 103(2):424-430, 2006.

Epilogue

  1. Philip Ball. Starting from scratch. Nature, 431:624-626, 2004.
  2. John W. Milor. Aliens in the Bible. Xlibris, 2000. Also see the website at http://www.aliensinthebible.com.
  3. Jonathon Porritt and Yorick Blumenfeld. Playing Safe: Science and the Environment. Thames and Hudson, 2000.
  4. Mary Warnock. We need have no fear of interference with nature. The Guardian, May 15, 2001.
  5. Terrence M. Tumpey, Christopher F. Basler, Patricia V. Aguilar, Hui Zeng, Alicia Solórzano, David E. Swayne, Nancy J. Cox, Jacqueline M. Katz, Jeffery K. Taubenberger, Peter Palese, and Adolfo García-Sastre. Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science, 310(5745):77-80, 2005.
  6. Jeronimo Cello, Aniko V. Paul, and Eckard Wimmer. Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template. Science, 297(5583):1016-1018, 2002.
  7. Eliot Marshall. Venter gets down to life's basics. Science, 298(5599):1701, 2002.
  8. George Church. Let us go forth and safely multiply. Nature, 438:423, 2005.
  9. Karen Hopkin. Life: The next generation. The Scientist, 18(19):56, October 11, 2004.
  10. Susan Brown. Command performances. San Diego Union-Tribune, December 14, 2005.
  11. Drew Endy. Foundations for engineering biology. Nature, 436:449-453, 2005.


    12. File translated from TEX by TTH, version 3.74.
    On 11 Jul 2006, 11:13.