Advertisement

Minerva

, 46:463 | Cite as

Directed Evolution: A Historical Exploration into an Evolutionary Experimental System of Nanobiotechnology, 1965–2006

  • Eun-Sung KimEmail author
Article

Abstract

This study explores the history of nanotechnology from the perspective of protein engineering, which differs from the history of nanotechnology that has arisen from mechanical and materials engineering; it also demonstrates points of convergence between the two. Focusing on directed evolution—an experimental system of molecular biomimetics that mimics nature as an inspiration for material design—this study follows the emergence of an evolutionary experimental system from the 1960s to the present, by detailing the material culture, practices, and techniques involved. Directed evolution, as an aspect of nanobiotechnology, is also distinct from the dominant biotechnologies of the 20th century. The experimental systems of directed evolution produce new ways of thinking about molecular diversity that could affect concepts concerning both biology and life.

Keywords

Directed evolution RNA world Scanning probe microscopy Molecular biomimetics Nanotechnology Molecular diversity 

Notes

Acknowledgements

This study is largely indebted to Linda Hogle’s thoughtful advice. I also would like to thank Alan Porter and Alex Stephens for their bibliometric analysis, as well as Erich Schienke, Doogab Yi, Byoungyoon Kim, and Cyrus Mody for their careful and critical comments. I conducted this research at the Center for Nanotechnology in Society-Arizona State University, at the University of Wisconsin-Madison. This study is based upon work supported by the National Science Foundation, under grant #0531194. Any opinions, findings, and conclusions or recommendations expressed in this study are those of the author, and they do not necessarily reflect the views of the National Science Foundation.

References

  1. Arnold, Frances H. 1998. Design by directed evolution. Accounts of Chemical Research 31(3): 125–131.CrossRefGoogle Scholar
  2. Arnold, Frances H. 2001. Combinatorial and computational challenges for biocatalyst design. Nature 409(6817): 253–257.CrossRefGoogle Scholar
  3. Ashcroft, Robert G., and Peter A. Lopez. 2000. Commercial high speed machines open new opportunities in High Throughput Flow Cytometry. Journal of Immunological Methods 243(1–2): 13–24.CrossRefGoogle Scholar
  4. Baird, Davis, and Ashley Shew. 2004. Probing the history of scanning tunneling microscopy. In Discovering the nanoscale, ed. Davis Baird, Alfred Nordmann, and Joachim Schummer, 145–156. Amsterdam: IOS Press.Google Scholar
  5. Bartel, David P., and Jack W. Szostak. 1993. Isolation of new Ribozymes from a large pool of random sequences. Science 261(5127): 1411–1418.CrossRefGoogle Scholar
  6. Bartlett, Paul A., and Gerald F. Joyce. 1999. Combinatorial chemistry: the search continues—editorial overview. Current Opinion in Chemical Biology 3(3): 253–255.CrossRefGoogle Scholar
  7. Battye, Francis L., Amanda Light, and David M. Tarlinton. 2000. Single cell sorting and cloning. Journal of Immunological Methods 243(1–2): 25–32.CrossRefGoogle Scholar
  8. Boder, Eric T., and K. Dane Wittrup. 1997. Yeast surface display for screening combinatorial polypeptide libraries. Nature Biotechnology 15(6): 553–557.CrossRefGoogle Scholar
  9. Brown, Stanley. 1997. Metal-recognition by repeating polypeptides. Nature Biotechnology 15(3): 269–272.CrossRefGoogle Scholar
  10. Cadwell, R.Craig, and G.F. Joyce. 1994. Mutagenic PCR. PCR-Methods and Applications 3(6): S136–S140.Google Scholar
  11. Cech, Thomas R. 1987. The chemistry of self-splicing RNA and RNA enzymes. Science 236(4808): 1532–1539.CrossRefGoogle Scholar
  12. Cech, Thomas R., Arthur J. Zaug, and Paula J. Grabowski. 1981. In vitro splicing of the ribosomal-RNA precursor of tetrahymena—involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 27(3): 487–496.CrossRefGoogle Scholar
  13. Chapman, Graeme V. 2000. Instrumentation for flow cytometry. Journal of Immunological Methods 243(1–2): 3–12.CrossRefGoogle Scholar
  14. Choi, Hyungsub, and Cyrus C. M. Mody (forthcoming). The long history of molecular electronics: microelectronics origins of nanotechnology. Social Studies of Science.Google Scholar
  15. Crameri, Andreas, Sun-Ai Raillard, Ericka Bermudez, and Willem P.C. Stemmer. 1998. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391(6664): 288–291.CrossRefGoogle Scholar
  16. Crandall, B.C. (ed.). 1996. Nanotechnology: Molecular speculations on global abundance. Cambridge, MA: The MIT Press.Google Scholar
  17. Crick, Francis. 1968. The origin of the genetic code. Journal of Molecular Biology 38: 367–379.CrossRefGoogle Scholar
  18. Crick, Francis. 1993. Foreword. In The RNA world: The nature of modern RNA suggests a prebiotic RNA world, ed. R. Gesteland, and J.F. Atkins, xi–xiv. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.Google Scholar
  19. Daugherty, Patrick S., Brent L. Iverson, and George Georgiou. 2000. Flow cytometric screening of cell-based libraries. Journal of Immunological Methods 243(1–2): 211–227.CrossRefGoogle Scholar
  20. Davis, Jason J., H.Allen O. Hill, and Alan M. Bond. 2000. The application of electrochemical scanning probe microscopy to the interpretation of metalloprotein voltammetry. Coordination Chemistry Reviews 200: 411–442.CrossRefGoogle Scholar
  21. Drexler, K.Eric. 1986. Engines of creation: The coming era of nanotechnology. Garden City, NY: Anchor Press/Doubleday.Google Scholar
  22. Eigen, Manfred, and William Gardiner. 1984. Evolutionary molecular engineering based on RNA replication. Pure and Applied Chemistry 56(8): 967–978.CrossRefGoogle Scholar
  23. Fisher, Michael M.J. 1999. Emergent forms of life: Anthropologies of late or post modernities. Annual Review of Anthropology 28: 455–478.CrossRefGoogle Scholar
  24. Fleck, Ludwik. 1979. Genesis and development of a scientific fact. Chicago, IL: University of Chicago Press.Google Scholar
  25. Flynn, Christine E., Seung-Wuk Lee, Beau R. Peelle, and Angela M. Belcher. 2003. Viruses as vehicles for growth, organization and assembly of materials. Acta Materialia 51(19): 5867–5880.CrossRefGoogle Scholar
  26. Georgiou, George, Christos Stathopoulos, Patrick S. Daugherty, Amiya R. Nayak, Brent L. Iverson, and Roy Curtiss III. 1997. Display of heterologous proteins on the surface of microorganisms: From the screening of combinatorial libraries to live recombinant vaccines. Nature Biotechnology 15(1): 29–34.CrossRefGoogle Scholar
  27. Gesteland, Raymond, Thomas R. Cech, and John F. Atkins (eds.). 1993. The RNA world: The nature of modern RNA suggests a prebiotic RNA world. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.Google Scholar
  28. Gilardi, Gianfranco, and Andrea Fantuzzi. 2001. Manipulating redox systems: Application to nanotechnology. Trends in Biotechnology 19(11): 468–476.CrossRefGoogle Scholar
  29. Gilbert, Walter. 1986. Origin of life—the RNA world. Nature 319(6055): 618.CrossRefGoogle Scholar
  30. Hacking, Ian. 1983. Representing and intervening: Introductory topics in the philosophy of natural science. Cambridge: Cambridge University Press.Google Scholar
  31. Hall, Barry G. 1978. Regulation of newly evolved enzymes. Directed evolution of ebg repressor. Genetics 90(4): 673–681.Google Scholar
  32. Joy, Bill. 2000. Why the future doesn’t need us. Wired (April 2000):37–51.Google Scholar
  33. Joyce, Gerald F. 1991. The rise and fall of the RNA world. New Biologist 3(4): 399–407Google Scholar
  34. Joyce, Gerald F. 2006. Plenary lecture: Evolution in an RNA world. Origins of Life and Evolution of the Biosphere 36(3): 202–204.Google Scholar
  35. Kauffman, Stuart, and Andrew D. Ellington. 1999. Thinking combinatorially. Current Opinion in Chemical Biology 3(3): 256–259.CrossRefGoogle Scholar
  36. Keating, Peter, and Alberto Cambrosio. 1994. Ours is an engineering approach: Flow cytometry and the constitution of human t-cell subsets. Journal of the History of Biology 27(3): 449–479.CrossRefGoogle Scholar
  37. Keller, Evelyn F. 2002. Making sense of life: Explaining biological development with models, metaphors, and machines. Cambridge, MA: Harvard University Press.Google Scholar
  38. Kohler, Robert E. 1994. Lords of the fly: Drosophila genetics and the experimental life. Chicago: University of Chicago Press.Google Scholar
  39. Kriplani, Ushma, and Brian K. Kay. 2005. Selecting peptides for use in nanoscale materials using phagedisplayed combinatorial peptide libraries. Current Opinion in Biotechnology 16(4): 470–475.CrossRefGoogle Scholar
  40. Lenoir, Tim, and Eric Giannella. 2006. The emergence and diffusion of DNA microarray technology. Journal of Biomedical Discovery and Collaboration 1(11). doi:  10.1186/1747-5333-1-11.
  41. Leung, David W., Ellson Y. Chen, and David V. Goeddel. 1989. A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Journal of Methods in Cell and Molecular Biology 1(1): 11–15.Google Scholar
  42. Lewis, Ricki. 1997. Scientists debate RNA’s role at beginning of life on earth. Scientist 11(7): 11.Google Scholar
  43. McCray, Patrick. 2007. MBE deserves a place in the history books. Nature Nanotechnology 2: 259–261.CrossRefGoogle Scholar
  44. Merzlyak, Anna, and Seung-Wuk Lee. 2006. Phage as templates for hybrid materials and mediators for nanomaterial synthesis. Current Opinion in Chemical Biology 10(3): 246–252.CrossRefGoogle Scholar
  45. Mills, D.R., R.L. Peterson, and S. Spiegelman. 1967. An extracellular Darwinian experiment with a self-duplication nucleic acid molecule. Proceedings of the National Academy of Sciences of the United States of America 58: 217–223.CrossRefGoogle Scholar
  46. Mody, Cyrus C.M. 2004. How probe microscopists became nanotechnologists. In Discovering the nanoscale, ed. D. Baird, A. Nordmann, and J. Schummer, 119–156. Amsterdam: IOS Press.Google Scholar
  47. Mody, Cyrus C.M. 2006. Corporations, universities, and instrumental communities—commercializing probe microscopy, 1981–1996. Technology and Culture 47(1): 56–80.CrossRefGoogle Scholar
  48. Mody, Cyrus. C. M. (forthcoming). Why history matters in understanding the social issues of nanotechnology. Nanoethics.Google Scholar
  49. O’Connell, Philip J., and George G. Guilbault. 2001. Future trends in biosensor research. Analytical Letters 34(7): 1063–1078.CrossRefGoogle Scholar
  50. Olsen, Mark J., Daren Stephens, Devin Griffiths, Patrick Daugherty, George Georgiou, and Brent L. Iverson. 2000. Function-based isolation of novel enzymes from a large library. Nature Biotechnology 18(10): 1071–1074.CrossRefGoogle Scholar
  51. Orgel, Leslie E. 1968. Evolution of the genetic apparatus. Journal of Molecular Biology 38: 381–393.CrossRefGoogle Scholar
  52. Rabinow, Paul. 1996. Making PCR: A story of biotechnology. Chicago, IL: University of Chicago Press.Google Scholar
  53. Rheinberger, Hans-Jorg. 1997. Toward a history of epistemic things: Synthesizing proteins in the test tube. Stanford, CA: Stanford University Press.Google Scholar
  54. Roco, Mihail C. 2003. Nanotechnology: Convergence with modern biology and medicine. Current Opinion in Biotechnology 14(3): 337–346.CrossRefGoogle Scholar
  55. Rose, Nicholas. 2007. The politics of life itself: Biomedicine, power, and subjectivity in the twenty-first century. Princeton, NJ: Princeton University Press.Google Scholar
  56. Saffhill, R., H. Schneider-Bernloehr, L.E. Orgel, and S. Spiegelman. 1970. In vitro selection of Qß ribonucleic acid variants resistant to ethidium bromide. Journal of Molecular Biology 51: 531–539.CrossRefGoogle Scholar
  57. Sarikaya, Mehmet, Candan Tamerler, Alex K.Y. Jen, Klaus Schulten, and Francois Baneyx. 2003. Molecular biomimetics: Nanotechnology through biology. Nature Materials 2(9): 577–585.CrossRefGoogle Scholar
  58. Seeman, Nadrian C., and Angela M. Belcher. 2002. Emulating biology: Building nanostructures from the bottom up. Proceedings of the National Academy of Sciences of the United States of America 99: 6451–6455.CrossRefGoogle Scholar
  59. Smalley, Richard 2002. Nanotechnology: The wet/dry frontier. Paper presented at the Small Wonders Workshop, Washington, DC.Google Scholar
  60. Smith, George P. 1985. Filamentous fusion phage—novel expression vectors that display cloned antigens on the Virion surface. Science 228(4705): 1315–1317.CrossRefGoogle Scholar
  61. Smith, George P., and Valery A. Petrenko. 1997. Phage display. Chemical Reviews 97(2): 391–410.CrossRefGoogle Scholar
  62. Spiegelman, Sol. 1971. An approach to the experimental analysis of precellular evolution. Quarterly Reviews of Biophysics 4(2&3): 213–253.CrossRefGoogle Scholar
  63. Spiegelman, S., I. Haruna, I.B. Holland, G. Beaudreau, and D. Mills. 1965. The synthesis of a self-propagating and infectious nucleic acid with a purified enzyme. Proceedings of the National Academy of Sciences of the United States of America 54(3): 919–927.CrossRefGoogle Scholar
  64. Stemmer, Willem P.C. 1994a. DNA shuffling by random fragmentation and reassembly—in vitro recombination for molecular evolution. Proceedings of the National Academy of Sciences of the United States of America 91(22): 10747–10751.CrossRefGoogle Scholar
  65. Stemmer, Willem P.C. 1994b. Rapid evolution of a protein in-vitro by DNA shuffling. Nature 370(6488): 389–391.CrossRefGoogle Scholar
  66. Tobin, Matthew B., Claes Gustafsson, and Gjalt W. Huisman. 2000. Directed evolution: The ‘rational’ basis for ‘irrational’ design. Current Opinion in Structural Biology 10(4): 421–427.CrossRefGoogle Scholar
  67. Wells, James A., Mark Vasser, and David B. Powers. 1985. Cassette mutagenesis—an efficient method for generation of multiple mutations at defined sites. Gene 34(2–3): 315–323.CrossRefGoogle Scholar
  68. Woese, Carl R. 1967. The genetic code. New York: Harper and Row.Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Korea Research Institute of Bioscience and Biotechnology, Biotechnology Policy Research CenterDaejeonSouth Korea

Personalised recommendations