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33. Private correspondence with Dr. Miller.
34. See for example D. Zheng and M. B. Gerstein, “The ambiguous boundary between
genes and pseudogenes: the dead rise up, or do they?,” Trends in Genetics, 23 (May,
2007): 219–24; S. Hirotsune et al., “An expressed pseudogene regulates the messenger-
RNA stability of its homologous coding gene,” Nature, 423 (May 1, 2003): 91– 96; O. H.
Tam et al., “Pseudogene-derived small interfering RNAs regulate gene expression in
mouse oocytes,” Nature, 453 (May 22, 2008): 534– 38; D. Pain et al., Multiple
Retropseudogenes from Pluripotent Cell-specific Gene Expression Indicates a Potential
Signature for
Novel Gene Identification,” The Journal of Biological Chemistry, 280 (February
25, 2005):6265–68; J. Zhang et al., “NANOGP8 is a retrogene expressed in cancers,”
FEBS Journal, 273 (2006): 1723– 30.
35. Evgeniy S. Balakirev and Francisco J. Ayala, “Pseudogenes, Are They ‘Junk’ or
Functional DNA?,” Annual Review of Genetics, 37 (2003): 123– 51.
36. Ryan Charles Pink, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura
Jacobs, and David Paul Francisco Carter, “Pseudogenes: Pseudo-functional or key
regulators in health and disease?,” RNA, 17 (2011): 792– 98.
37. Collins acknowledges that the caspase-12 gene produces a full-fledged protein
in chimps, so this is not a case where humans share a non-functional stretch of DNA
with another species. In fact, the gene is not always a pseudogene in humans.
According to a paper in The American Journal of Human Genetics,28% of people in sub-
Saharan Africa have a functioning copy of the caspase-12 gene, as do lower percentages
in some other human populations. Collins ignores the obvious possibility that caspase-
12 was originally designed to produce a functional protein in humans but was rendered
noncoding bya mutation in some human populations at some point the recent past. See
Yali Xue, Allan Daly, BryndisYngvadottir, Mengning Liu, Graham Coop, Yuseob Kim,
Pardis Sabeti, Yuan Chen, Jim Stalker, Elizabeth Huckle, John Burton, Steven Leonard,
Jane Rogers, and Chris Tyler-Smith, “Spread of an Inactive Form of Caspase-12 in
Humans Is Due to Recent Positive Selection,” The American Journal of Human Genetics,
78 (April, 2006): 659– 70.
38. M. Lamkanfi, M. Kalai, and P. Vandenabeele, “Caspase-12: an overview,” Cell
Death and Differentiation, 11: (2004)365–68.
39. Sug Hyung Lee, Christian Stehlik, and John C. Reed, “ COP, a Caspase
Recruitment Domain-containing Protein and Inhibitor of Caspase-1 Activation
Processing,” The Journal of Biological Chemistry, 276 (September 14, 2001): 34495– 500.
40. Lamkanfi, Kalai, and Vandenabeele, “ Caspase-12: an overview,” 365 –68.
41. Collins, quoted in Catherine Shaffer, “ One Scientist’s Junk Is a Creationist’s
Treasure,” Wired Magazine Blog (June 13, 2007), accessed March 6, 2012.