Analysis of the Discovery Institute's Bibliography: Appendix

Appendix A

The publications listed in the Bibliography

Respondents to NCSE's questionnaire are in boldface.

1. Ying Cao, Axel Janke, Peter J. Waddell, Michael Westerman, Osamu Takenaka, Shigenori Murata, Norihiro Okada, Svante P bo, and Masami Hasegawa, "Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders," Journal of Molecular Evolution 47 (1998): 307 32

2. Simon Conway Morris, "Evolution: Bringing Molecules into the Fold," Cell 100 (2000): 1 11.

3. W. Ford Doolittle, "Tempo, Mode, the Progenote, and the Universal Root," in W. Fitch and F. Ayala, eds., Tempo and Mode in Evolution (Washington, DC: National Academy Press, 1995), pp. 3 24.

4. W. Ford Doolittle, "At the core of the Archaea," Proceedings of the National Academy of Sciences USA 93 (1996): 8797 8799.

5. W. Ford Doolittle, "Uprooting the Tree of Life," Scientific American, February 2000, pp. 90 95.

6. W. Ford Doolittle, "Phylogenetic Classification and the Universal Tree," Science 284 (1999) :2124 2128.

7. W. Ford Doolittle, "The nature of the universal ancestor and the evolution of the proteome," Current Opinion in Structural Biology 10 (2000): 355 358.

8. Douglas H. Erwin, "Early introduction of major morphological innovations," Acta Palaeontologica Polonica 38 (1994): 281 294.

9. Trisha Gura, "Bones, molecules...or both?" Nature 406 (2000): 230 233.

10. Michael S. Y. Lee, "Molecular Clock Calibrations and Metazoan Divergence Dates," Journal of Molecular Evolution 49 (1999): 385 391.

11. Michael S. Y. Lee, "Molecular phylogenies become functional," Trends in Ecology and Evolution 14 (1999): 177 178.

12. Detlef D. Leipe, L. Aravind, and Eugene V. Koonin, "Did DNA replication evolve twice independently?" Nucleic Acids Research 27 (1999): 3389 3401.

13. Peter J. Lockhart and Sydney A. Cameron, "Trees for bees," Trends in Ecology and Evolution 16 (2001): 84 88.

14. David P. Mindell, Michael D. Sorenson, and Derek E. Dimcheff, "Multiple independent origins of mitochondrial gene order in birds," Proceedings of the National Academy of Sciences USA 95 (1998): 10693 10697.

15. Paul Morris and Emily CoBabe, "Cuvier meets Watson and Crick: the utility of molecules as classical homologies," Biological Journal of the Linnean Society 44 (1991): 307 324.

16. Arcady R. Mushegian, James R. Garey, Jason Martin, and Leo X. Liu, "Large Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes," Genome Research 8 (1998): 590 598.

17. Gavin J. P. Naylor and Wesley M. Brown, "Amphioxus Mitochondrial DNA, Chordate Phylogeny, and the Limits of Inference Based on Comparisons of Sequences," Systematic Biology 47 (1998): 61 76.

18. Colin Patterson, David M. Williams, and Christopher J. Humphries, "Congruence Between Molecular and Morphological Phylogenies," Annual Review of Ecology and Systematics 24 (1993): 153 188.

19. Michael K. Richardson et al., "There is no highly conserved stage in the vertebrates: implications for current theories of evolution and development," Anatomy and Embryology 196 (1997): 91 106.

20. Kensal E. van Holde, "Respiratory proteins of invertebrates: Structure, function and evolution," Zoology: Analysis of Complex Systems 100 (1998): 287 297.

21. Kenneth Weiss, "We Hold These Truths to Be Self Evident," Evolutionary Anthropology 10 (2001): 199 203.

22. Carl Woese, "The universal ancestor," Proceedings of the National Academy of Sciences USA 95 (1998): 6854 6859.

23. Robert L. Carroll, "Towards a new evolutionary synthesis," Trends in Ecology and Evolution 15 (2000):27 32.

24. Douglas Erwin, "Macroevolution is more than repeated rounds of microevolution," Evolution & Development 2 (2000): 78 84.

25. Scott F. Gilbert, Grace A. Loredo, Alla Brukman, and Ann C. Burke, "Morphogenesis of the turtle shell: the development of a novel structure in tetrapod evolution," Evolution & Development 3 (2001): 47 58.

26. Olivier Rieppel, "Turtles as Hopeful Monsters," BioEssays 23 (2001): 987 991.

27. Scott F. Gilbert, John M. Opitz, and Rudolf A. Raff, "Resynthesizing Evolutionary and Developmental Biology," Developmental Biology 173 (1996): 357 372.

28. George L. Gabor Miklos, "Emergence of organizational complexities during metazoan evolution: perspectives from molecular biology, palaeontology and neo Darwinism," Mem. Ass. Australas. Palaeontols. 15 (1993): 7 41.

29. Neil H. Shubin and Charles R. Marshall, "Fossils, genes, and the origin of novelty," in Deep Time (2000, The Paleontological Society), pp. 324 340.

30. Keith Stewart Thomson, "Macroevolution: The Morphological Problem," American Zoologist 32 (1992): 106 112.

31. B rbel M. R. Stadler, Peter F. Stadler, G nther P. Wagner, and Walter Fontana, "The Topology of the Possible: Formal Spaces Underlying Patterns of Evolutionary Change," Journal of Theoretical Biology 213 (2001): 241 274.

32. G nther P. Wagner, "What is the Promise of Developmental Evolution? Part II: A Causal Explanation of Evolutionary Innovations May Be Impossible," Journal of Experimental Zoology (Mol Dev Evol) 291 (2001): 305 309.

33. Philip Ball, "Life's lessons in design," Nature 409 (2001): 413 416.

34. Rodney Brooks, "The relationship between matter and life," Nature 409 (2001): 409 411.

35. David W. Deamer, "The First Living Systems: a Bioenergetic Perspective," Microbiology and Molecular Biology Reviews 61 (1997): 239 261.

36. Michael J. Katz, Templets and the explanation of complex patterns, Cambridge: Cambridge University Press, 1986.

37. Claire M. Fraser et al., "The Minimal Gene Complement of Mycoplasma genitalium," Science 270 (1995): 397 403.

38. Clyde A. Hutchison et al., "Global Transposon Mutagenesis and a Minimal Mycoplasma Genome," Science 286 (1999): 2165 2169.

39. Eugene V. Koonin, "How Many Genes Can Make a Cell: The Minimal Gene Set Concept," Annual Review of Genomics and Human Genetics 1 (2000): 99 116.

40. Jack Maniloff, "The minimal cell genome: 'On being the right size,'" Proceedings of the National Academy of Sciences USA 93 (1996): 1004 1006.

41. Arcady R. Mushegian and Eugene V. Koonin, "A minimal gene set for cellular life derived by comparison of complete bacterial genomes," Proceedings of the National Academy of Sciences USA 93 (1996): 10268 10273.

42. Scott N. Peterson and Claire M. Fraser, "The complexity of simplicity," Genome Biology 2 (2001): 1 7.

43. Leslie E. Orgel, "Self organizing biochemical cycles," Proceedings of the National Academy of Sciences 97 (2000): 12503 12507.

44. E rs Szathm ry, "The evolution of replicators," Philosophical Transactions of the Royal Society of London B 335 (2000): 1669 1676.

Appendix B

NCSE's questionnaire

Text in [brackets] is explanatory and was not part of the questionnaire.

Dear [addressee],

I'm writing from the National Center for Science Education, a nonprofit organization that works to defend the teaching of evolution in the public schools. We are an affiliate of the American Association for the Advancement of Science.

An article [or "a book" or "several articles" as appropriate] written [or "co-authored" as appropriate] by you [citation of publication or publications] has [or "have" as appropriate] been cited in a "Bibliography of Supplementary Resources for Ohio Science Instruction" prepared by the staff of the Discovery Institute (DI), a Seattle-based public policy organization. According to the DI, the publications cited in this bibliography

represent dissenting viewpoints that challenge one or another aspect of neo-Darwinism (the prevailing theory of evolution taught in biology textbooks), discuss problems that evolutionary theory faces, or suggest important new lines of evidence that biology must consider when explaining origins.
The DI prepared the bibliography to give to the Ohio Board of Education, which is presently being lobbied by several organizations either to weaken the newly-proposed state science standards' coverage of evolution or to include material on "alternative theories" in their coverage of evolution. The DI, for its part, is the institutional home of the so-called intelligent design movement, spearheaded by Phillip Johnson (author of Darwin on Trial) and having William Dembski (author of Intelligent Design: The Bridge Between Science and Theology), Michael Behe (author of Darwin's Black Box), and Jonathan Wells (author of Icons of Evolution) among its Senior Fellows.

We would appreciate your reviewing the information about your work included in the DI's bibliography and answering a few questions. Please feel free either to answer just yes or no, or to expand as you see fit.

1. The DI describes your work as follows:

[The Discovery Institute's summary of the publications, taken from the Bibliography.]

Do you consider this accurate?

2. The DI seeks to promote "intelligent design," which it describes on one of its web sites as follows:

"Intelligent design" refers to a scientific research program as well as a community of scientists, philosophers and other scholars who seek evidence of design in nature. Through the study and analysis of a system's components, a design theorist is able to determine whether various natural structures are the product of chance, natural law, intelligent design, or some combination thereof. In nature, design theorists cite information rich systems like the genetic code, irreducibly complex systems like the bacterial flagellum, and the fine-tuning of the laws of physics as evidence of intelligent design. [See n. 1 above for the source of the description.]
Do you consider your work to provide scientific evidence for intelligent design?

3. Do you consider your work to provide scientific evidence against evolution?

[In questionnaires sent after the Bibliography appeared on the Discovery Institute's web site with the disclaimer, the sentence "Please note that (perhaps having gotten wind of our questionnaire) the DI now disclaims any intention to portray your work either as supportive of intelligent design or as providing evidence against evolution: see id=1127&program=CRSC%20Responses." appeared here. The same information was sent separately to those respondents to whom questionnaires were sent before the Bibliography appeared on the web site.]

4. Do you consider your work to be appropriate for use (e.g., as a supplement to a textbook) in high school biology classes?

5. May we have your permission to publish or otherwise disseminate your responses to this questionnaire?

Thanks very much for your time. We would appreciate hearing from you as soon as possible. If you have any questions about NCSE or this questionnaire, please feel free to get in touch with us.