2 Dulbecco 1987, 22. The draft sequence of the complete human genome published in February 2001 by two separate projects, the public Human Genome Project and the private Celera Genomics Corporation, revealed that the human genome has only about 30,000 protein-making genes. That's about twice as many as a fruit fly, making us humans "appear only five times as complex as a bacterium" (Claverie 2001). National Human Genome Research Institute director Francis Collins called the findings "a bit of an assault on our sensibilities" (Pennisi 2001b). But human genes do more work than do those of other organisms, the human genome having more sophisticated gene expression mechanisms, thus generating a larger number of proteins (Pennisi 2001b; Claverie 2001). For a commentary on the draft sequence, see Netting and Wang 2001.
In April 2003, the Human Genome Project announced that its work was completed, coinciding with the 50th anniversary of the discovery of DNA's structure (the double helix) by James Watson and the late Francis Crick. The work covered about 99 percent of the human genetic sequence (all that could be done with current technology), with an accuracy of 99.99 percent or about one error per 100,000 DNA bases (NIH News; Pennisi 2003c).
On the discovery of multiple copies of key genes as an explanation for much of the variation between people, see Redon et al. 2006 and Connor 2006. On so-called "junk DNA," which is not really useless junk but a "scrapyard" of "ready-to-use segments" in the genome for "nature's evolutionary experiments," see Makalowski 2003 and LevMaor et al. 2003. On genetics and behavior (or nature vs. nurture), see McGuffin et al. 2001; Hamer and Copeland 1998; and "The Philosopher's Tale," note 11. On genetics and metaphor (DNA as "information" that is "written" in "words" that are in "code"), see Kay 2000 and Lewontin 2001.
3 On cosmic rays, see Olinto 2007 and Clery 2004.
4 Futuyma 1982, 118.
5 Futuyma 1982, 143. The neutral theory of molecular evolution (Kimura 1968) holds that most genetic divergence between species is driven by mutation and genetic drift rather than by positive natural selection (Fay et al. 2002). Recent studies have shown that natural selection plays a larger role in molecular evolution than the neutral theory proposes (Smith and Eyre-Walker 2002; Fay et al. 2002; ScienceDaily; see also "The Paleoanthropologist's Tale," note 22).
6 The allusion is to the peppered moth (Biston betularia), whose protective coloring, beginning with a melanic or dark-colored mutant, made it hard to see by preying birds, and which has been a favorite textbook example of natural selection in action. See Majerus 1998, Cook 2003, and (for rebuttals of claims by Moonie biologist Jonathan Wells [2000] of evolutionist misrepresentation of the peppered-moth case in textbooks) Musgrave 2001, Padian and Gishlick 2002, and Scott 2001. (For lines on the peppered moth that appeared in this book's first two editions, click here.) On Majerus's and Kettlewell's work on the peppered moth, see Proffitt 2004 and Miller 1999b. For critical reviews of Judith Hooper's book Of Moths and Men, see Coyne 2002 and Grant 2002. For other examples of predation as an agent of natural selection, see Losos et al. 2006, Young et al. 2004, and Science 305:1909 (regarding the effect on lizards) and Zuk et al. 2006 (regarding the effect on crickets). On predator-driven evolution, see also Baumiller and Gahn 2004 and Stokstad 2004.
7 John Morris and other creationist leaders have acknowledged the reality of microevolution or small-scale changes as seen in varieties, adaptations, and genetic recombinations. These changes might not be trivial, Morris says, but they are "merely variations within a stable basic kind," and "do not lead to true evolution" (macroevolution) (1999b; see also Catchpoole and Wieland 2001; J. Morris 1996b and 1994a; Gish 1995a, 34; H. Morris 1985, 51-54; 1970, 33). Morris believes that "all genetic traits were originally shared among humankind," but that after the dispersal from the biblical tower of Babel (see "The Scholar's Tale," note 37) the "ethnic traits" of today's "races" arose because "natural selection would match traits to an environment" (J. Morris 2003). (On evidence that mutation of the gene SLC24A5, after the first human migration from Africa into colder climes, helped lead to the evolution of skin pigmentation differences between Europeans and Africans as late as 6,000 to 12,000 years ago, see Gibbons 2007c; Lamason et al. 2005; Balter 2005b; and Weiss 2005.) Morris has also suggested that Satan or his demons may have performed "selective breeding experiments" in the past both on humans (producing the "giants" of Genesis 6:4) and animals, and "maybe that's where some of the unthinkable features we see in the fossil record come from" (J. Morris 2002b).
Creationists also refer to a kind as a "baramin" (from the Hebrew words for create [bara] and kind [min]), which the Creation Wiki defines as "a group of organisms who share a genetic relationship through common descent from an organism originally created by God during the Creation Week." Thus species, say baraminologists, are variations descended within limits from created kinds.
8 Geographic isolation will lead to the evolution of traits resulting in reproductive isolation, which characterizes a species (Mayr 1988, 318). On the importance of geographic isolation to the theory of punctuated equilibrium, which sees small-scale or gradual changes alone as insufficient to produce new species (macroevolution), see "The Paleontologist's Tale," lines 212-246, note 33.
9 Ronshaugen et al. 2002; ScienceDaily. On Hox genes, see also Davidson 2001; Carroll et al. 2001; Wray 2001; and "The Biologist's Tale," note 9. On the search for regulatory DNA and enhancers that control gene expression including Hox genes, see Pennisi 2004d. On macroevolution, see Theobald 1999-2004 and Wilkins 2006. On evolutionary developmental biology ("evo-devo"), see "The Biologist's Tale," note 6. On genetic drift, see Moran 1993-1997b and note 5 above.
10 See H. Morris 1985, 117-120, 252; Ham 2003; and "The Geologist's Tale," 87-112.
11 Mayr 1988, 318.
12 On the origin of the domestic dog from wolves, see Savolainen et al. 2002; Leonard et al. 2002; Hare et al. 2002; Pennisi 2002c; Milius 2002a. On cat evolution, see Wade 2007 and Johnson et al. 2006. On domesticated cats in Cyprus as early as 9,500 years ago, see Vigne et al. 2004.
13 According to John Morris (1989), there was "plenty of room" on the ark for the "younger" dinosaurs.
14 In their creationist classic The Genesis Flood, John Whitcomb and Henry Morris (1961, 69) conclude that Noah had to get no more than 35,000 animals aboard the ark. On kinds, see note 6 above. For a review of a creationist "feasibility study" on Noah's ark (Woodmorappe 1996), see Morton 2003. See also Mark Isaak's Problems with a Global Flood, and "The Geologist's Tale," note 21. For the biblically based argument for a global flood, see J. Morris 1999a. For a good history of Noah's flood in Western thought, see Cohn 1996.
On "arkeology" expeditions to Turkey, see J. Morris 2002a and Ecker 1990, 29-30, 118. The ICR believes the ark is still somewhere high on Mount Ararat, "apparently awaiting God's timing for conclusive revelation of its preservation and testimony" (Acts & Facts 25[11]:5).
In April 1997 in Australia, a trial was held in a lawsuit brought by University of Melbourne geologist Ian Plimer against fundamentalist Allen Roberts, who promoted a site in Turkey as the remains of Noah's ark. Plimer claimed that Roberts's lectures and fundraising for research on the site (geologically identified as an ophiolite, or piece of ancient sea floor) violated Australian fair-trade laws. Plimer hoped the trial would draw attention to creationist pseudoscience in education, and had to sell his home to cover the legal expense (Finkel 1997a). In late May the case was dismissed, the court holding that Roberts was not engaged in trade and commerce. Judge Ronald Sackville wrote, "Some issues--no matter how great the passions they arouse--are more appropriately dealt with outside the courtroom." (See Finkel 1997b.)
Plimer is also famous (or, some would say, infamous) for a 1988 debate with the ICR's Duane Gish. In the debate Plimer, after assailing creationism as well as the personal integrity of some of its leaders, "donned insulating gloves, took a live electric wire and offered Dr. Gish the opportunity to electrocute himself" (Creation/Evolution Newsletter 8[5]:10). Plimer's point was that creationists accept electrical science as based on theory, yet will not so accept evolutionary science. Gish called Plimer's presentation "the most disgusting performance" he had ever witnessed.
15 See "General Prologue," note 15.
16 On the classic Miller-Urey experiment, see Miller 1953; Bada and Lazcano 2003; Miller and Orgel 1974, 83-85; Orgel 1994. See also note 20 below, and the Miller-Urey Experiment.
17 On origin-of-life research, see Cook 2005; Schopf 2002; Darling 2001; Morell 1997; Deamer and Fleischaker 1994; de Duve 1995a and 1995b; Orgel 1994; Chang et al. 1983; Miller and Orgel 1974; Lipkin 1995b; Robertson and Miller 1995; Nash 1993. See also notes 29, 30, 32, and 35 below.
18 On the more recent experiments, see Rode 1999. On the early atmosphere, see note 27 below.
19 Other energy sources such as ultraviolet light have also been used in origin-of-life experiments (Miller and Orgel 1974, 86).
20 One may indeed overrate the particulars, though not the overall significance, of Miller's achievement. The late biophysicist Thomas H. Jukes noted, for example, that glycine and alanine--two amino acids yielded by the experiment--"are far, far from life--almost as far as water is" (Jukes 1992). Nobel laureate Christian de Duve (1995b, 19) states that "Miller's experiment alerted organic chemists to the origin of life as a chemical problem," and "remains a paradigm," though often the conditions of such experiments are "somewhat more contrived than one would like for a truly abiotic process." See also note 30 below.
21 S. Fox 1988, 21-22; Scott 1986, 107-109.
22 McKean 1983, 42.
23 Creationists (e.g., Johnson 1995) tend wrongfully to assume that science's methodological naturalism (the search for natural causes) makes all scientists philosophical naturalists (those who believe nature is all that there is) (Scott 1996a, 25). See "The Philosopher's Tale," 137-145.
24 This is a paraphrase of H. Morris 1984a, 234.
25 Futuyma 1982, 184, 204.
26 On life as chemically inevitable, as "a cosmic imperative," see de Duve 1995a and 1995b. See also biochemist David Deamer's discussion of the self-assembly of organic molecules and the origin of life, and "The Physicist's Tale," note 19.
27 On the early atmosphere, see Tian et al. 2005; Chyba 2005; Weichert 2003; Bekker et al. 2004; and Holland 1984. On the evolution of atmospheric oxygen, see Kerr 2005a; Perkins 2005b; Bekker et al. 2004; Kasting and Siefert 2002; Catling et al. 2001; Kasting 2001; Towe 2002; Farquhar et al. 2000; and ScienceDaily. On the evolution of oxygenic photosynthesis, see Des Marais 2000. On increase in oxygen levels, adaptation to oxygen, and the rise of multicellular life, see Hedges et al. 2004; Kennedy et al. 2006; and Raymond and Segre 2006. On evidence of an approximate doubling of atmospheric oxygen over the past 205 million years as a critical factor in the evolution and increase in average size of placental mammals, see Falkowski et al. 2005.
28 Asimov 1984, 639; McGowan 1984, 48; Van Andel 1985, 225.
29 On the ancient, hypothetical "RNA world," in which RNA molecules performed functions in synthesis that are carried out today by DNA and proteins, see Gesteland et al. 1999; Robertson and Scott 2007; Netting 2001; de Duve 1995a and 1995b, 22-27, passim; Johnston et al. 2001; Davenport 2001; Unrau and Bartel 1998; Lipkin 1995a; Orgel 1994; Bohler et al. 1995; Piccirilli 1995; Waldrop 1989 and 1992a; Schimmel and Alexander 1998; Gilbert 1986. (On creating life in the laboratory, see also note 34 below.) On "molecular midwives," simple molecules that may have acted as templates for the first RNA-like molecules, see SpaceDaily. "We will never be able to prove the existence of the RNA world because we can't go back in time," says researcher David Bartel, "but we can examine the basic properties of RNA and see if these are compatible with the RNA world scenario" (ScienceDaily). On evidence suggesting that proteins evolved after RNA but before DNA, see Freeland et al. 1999.
In April 2000, Stanley L. Miller (who died in May 2007) and two colleagues published evidence, based on an experiment reminiscent of Miller�s famous 1953 synthesis of amino acids and other organic molecules, that peptide nucleic acid (PNA) may have been the first genetic material (Nelson et al. 2000; Travis 2000a).
On an alternative "metabolist" theory, according to which life began as "a self-sustaining chain of chemical reactions associated with mineral surfaces, with no requirement for genetic information" (a case of "life as we don�t know it" [Wachtershauser 2000]), see Bada and Lascano 2002.
30 Hanczyc et al. 2003; Russell 2003; Powell 2003; Goho 2003a; Cairns-Smith 1985.
31 Huber and Wachtershauser 2006; Bada et al. 2006; Simpson 1999; Lollar 2004; Imai et al. 1999; Vogel 1998; Holm 1992; Bada 1995. On the Lost City hydrothermal vent system (named for its mineral towers up to 60 meters high), see Proskurowsky et al. 2008; Kelley et al. 2005; Boetius 2005; and Fruh-Green et al. 2003. Some studies suggest, however, that heat-loving microbes did not originate in such a hot environment, but rather "descended from less hardy species and evolved new defenses against heat" (Zimmer 2005b).
32 On speculation that organic molecules important for life's origin came to Earth through asteroid, comet, or meteorite impacts, see Goho 2004a and 2004c; Gorman 2001; Cowen 2001j; Cooper et al. 2001; ScienceDaily; Bernstein et al. 2002; Munoz Caro et al. 2002; Chyba et al. 1990; Nash 1996; Cowen 1997e; and notes 36 and 37 below.
33 Crick 1981.
34 H. Morris 1985, 49. A study published in 1999 suggests that 265 to 350 genes (out of 480 protein-coding genes sequenced in the bacterium Mycoplasma genitalium) comprise the minimum genome or set of genes essential to create cellular life under laboratory growth conditions (Hutchison et al. 1999). While the ability to create a novel organism, a new species, based on a minimal genome is still a long way off, there are ethical considerations that need to be addressed before the technology advances further (Cho et al. 1999; see also Whitehouse 1999).
On efforts to synthesize life in the laboratory, see Barry 2008. The late biologist Sidney W. Fox demonstrated how amino acids can be heated under Earth conditions to form proteinoids or "thermal proteins," which when placed in water self-organize into microspheres or protocells, possible precursors of the contemporary living cell. Fox argued that RNA or DNA need not date back to the origin of life, and he showed that proteinoid microspheres exhibit growth, metabolism, reproduction (by budding), and responsiveness to stimuli--all properties of life. Still, the microspheres lack a genetic system, and thus do not qualify as life defined in genomic terms. See S. Fox 1997, 1988; Fox and Dose 1977.
35 See "The Scholar's Tale," lines 84-175.
36 Bernstein et al. 1999; Ehrenfreund 1999; Chang et al. 1983, 91. In 2002 two research teams independently reported the laboratory production of amino acids in deep-space conditions, supporting the view that prebiotic molecules could have been delivered to the early Earth by meteorites, comets, or interplanetary dust particles (Bernstein et al. 2002; Munoz Caro et al. 2002; Gorman 2002). See also note 32 above. On comets, see Science 12/15/06 issue.
37 Miller and Orgel 1974, 193-196; de Duve 1995a, 428-429; Science News 124:150; ScienceDaily.
38 Cloud 1988, 248; Dobzhansky 1985, 746; Maynard Smith 1986, 19-20.