Notes to the Biologist's Tale

1 See "Epilogue to the Astronomer's Tale," lines 237-245.

2 Technically these are "postdictions" (Gould 1995, 409); see "The Cosmologist's Tale," lines 173-176.

3 The fossil record goes from simpler to more complex forms in that invertebrates appear before vertebrates, fish before amphibians, amphibians before reptiles, etc. On fossils and Noah's flood, see "The Geologist's Tale," lines 87-112.

4 See Eldredge 1981.

5 See "The Biochemist's Tale," lines 21-51 and 350-358.

6 On Vertebrata embryos, see Ecker 1990, 76. On speciation, see Coyne and Orr 2004. On evolutionary developmental biology ("evo-devo"), important in the debate on how macroevolution or speciation occurs, see Carroll 2005; Minelli 2003; Davidson 2001; Carroll, Grenier, and Weatherbee 2001; Wray 2001; Arthur 2000; and Pennisi 2002b ("Small variations in genes involved in development might be springboards to both macroevolutionary and microevolutionary changes"). On macroevolution, see "The Biochemist's Tale," 141-169 and notes 7-9.

7 On man and chimpanzee (Pan troglodytes) as "next of kin," see Fouts 1997; Matsuzawa 2001; and Elango et al. 2006. The draft genome sequence of the chimp was published in 2005 (Nature 437:69-87; Culotta 2005b); on its similarity to the human genome, see Khaitovich et al. 2005. Humans and chimps genetically differ only about 1 percent in their alignment of nucleotide bases; noncoding material brings the total DNA difference to about 4 percent (Culotta and Pennisi 2005). On humanlike behavior in chimps and bonobos (a kinder, gentler species of chimp), see de Waal 2005. The morphological, behavioral, and cognitive differences between man and chimp, despite nearly identical DNA, may be due to "altered gene expression," with "changes in protein and gene expression . . . particularly pronounced in the human brain" (Enard et al. 2002; Pennisi 2002a; ScienceDaily). On human accelerated regions (HARs) in comparing the two genomes, see Pollard et al. 2006.

For a study of male violence, as favored by natural selection, in closely related human and ape, see Wrangham and Peterson 1996. For the nicer side of animal nature, see de Waal 1996 and (on bonobos) de Waal 2001, 1995, and de Waal and Lanting 1997. See also Ridley 1997, Wright 1994, and Small 1997. On culture (variation in both tool technology and social customs) among chimp populations, see Whiten 2007; de Waal 1999; Miller 2005; A. Gibbons 2007a; on orangutan culture, see van Schaik et al. 2003.

8 Cytochrome-c has the identical order of 104 amino acids in man and chimp. The rhesus monkey differs from this order in one amino acid, the horse in eleven amino acids, the tuna in twelve, and so on (National Academy of Sciences 1984, 22). This is evidence of common descent to evolutionists, and of common design to creationists.

9 The construction of evolutionary family trees based on molecular data is called molecular phylogenetics. On its complementary relationship to family-tree building based on morphological or fossil data, see Pennisi 2003d and Benton and Ayala 2003. See also Hall 2001; Pennisi 2001e; Pagel 1999; Doolittle 1999; Huelsenbeck and Rannala 1997; Pace 1997; Jukes 1983 and 1988; Lewin 1988; and "The Biochemist's Tale," note 39.

A 1999 study of Hox genes, which are crucial in the development of different body parts, indicates that almost all modern animals (excluding jellyfish and sponges) inherited their Hox genes from a common ancestor (for which there is no known fossil) that lived 600 million years ago (Rosa et al. 1999.) On Hox genes, see "The Biochemist's Tale," 128-136.

10 On insects, see Glenner et al. 2006; Grimaldi and Engel 2005. On ants, see Moreau et al. 2006. On bees, see Pennisi 2006b.

On convergent evolution, for teeth evolving at least twice independently in jawed vertebrates, see Meredith Smith and Johanson 2003; for the mammalian middle ear evolving independently in living monotremes and therians (marsupials and placentals), see Rich et al. 2005.

11 Bliss 1988, iv; Moore 1976, 30; H. Morris 1985, 22, 33.

12 See Bowler 1989, 59-65.

13 Newell 1985, 135. See Carolus Linnaeus. On classification and biodiversity, see Tudge 2000. Unlike the time-honored Linnaean system, a controversial new naming system called PhyloCode takes evolutionary relationships into account, by assembling organisms into clades (any set of organisms with a common ancestor), hence the term cladistics. (See Pennisi 2001c and Foer 2005.) On the Consortium for the Barcode of Life (CBOL), which wants to classify species by giving each one a short but specific DNA tag or bar code, see Marshall 2005.

14 See lines 216-240 and notes 27-28.

15 See "The Philosopher's Tale," lines 156-188.

16 Newell 1985, 125, 129. On the main divisions of life--prokaryotes (bacteria and archaea) and eukaryotes (animals and plants)--see Margulis et al. 1998 and Kurland et al. 2006. See also History of Life through Time, and "The Biochemist's Tale," note 39.

The five "kingdoms" of animals and plants (one animal kingdom and four plant kingdoms, with fungi actually closer to animals than to plants) are only one small branch of the tree of life, most of Earth's life being composed of single-celled, still poorly known organisms (ScienceDaily). A group of evolutionary biologists is now pushing for the construction of one all-inclusive tree of life, an ambitious 10- to 20-year project based on genetic as well as morphological and fossil data, mapping the evolution of all known species and how they split off from one another over time (Pennisi 2003d and 2001e; see also Ciccarelli et al. 2006).

On plant evolution see also Labandeira 1998; Niklas 1997; Kenrick and Crane 1997.

The ICR's John Morris (1991)--son of Henry (see "General Prologue," note 21)-- says that plants are "biologically alive" but not "biblically alive" (emphasis in original). He compares them to protozoans and viruses, which he considers "not truly living." This allows fundamentalists like Morris to say that there was no death in the original creation even though Adam and Eve ate plants (H. Morris 1978, 37-38; 1984a, 236, 370-371; 1985, 211; Ham 1991a).

17 Quoted in Cohen and Cohen 1960, 200. The insect order Coleoptera contains some 330,000 species of beetles, far outnumbering any other animal or plant group. This prompted the British biologist J.B.S. Haldane to say that God had an "inordinate fondness for beetles."

18 In Memoriam 56. See Gould 1995, 63-75.

19 Raup 1991, 3-4; Mayr 1988, 106; Newell 1985, 63.

20 Genesis 3:17,19; see H. Morris 1985, 211-212. Young-Earth creationists attribute such things as parasites, imperfections, death, and predation to God's "Curse on creation as a result of Adam's sin" (Wood 2001).

21 McGowan 1984, 5.

22 Newell 1985, 131.

23 See "The Geologist's Tale," lines 49-68.

24 Hummingbirds today are found only in the New World. However, little is known of their early evolution, and fossils have been surprisingly found in Germany of a modern-type hummingbird, Eurotrochilus inexpectatus ("unexpected European Trochilidae"), dating back 30 to 34 million years (G. Mayr 2004).

25 Whitcomb and Morris 1961, 79, 86.

26 See Ecker 1990, 41-43. On biogeography, see Lomolino and Heaney 2004.

27 "The theory of intelligent design (ID)," states the Intelligent Design Network website, "holds that certain features of the universe and of living things are best explained by an intelligent cause rather than an undirected process such as natural selection."

The movement espousing this theory was born after the 1987 U.S. Supreme Court decision (Edwards v. Aguillard) barring the required teaching in public school of "creation science" whenever evolution is taught. Two books, the 1989 "intelligent design" biology text Of Pandas and People by creationist biologists Percival Davis and Dean Kenyon, and the 1991 book Darwin on Trial by law professor Phillip E. Johnson, were instrumental in inspiring the ID movement, much as Henry Morris's and John Whitcomb's 1961 book The Genesis Flood was credited with inspiring the "creation science" movement. For a critique of Of Pandas and People, see Scott 1990. The word "creation" in early drafts of Of Pandas and People was simply replaced by the term "intelligent design" after the Edwards decision, as revealed in the Kitzmiller v. Dover testimony of Barbara Forrest (Lebo 2005; on Kitzmiller, see "General Prologue," note 15).] For reviews of Darwin on Trial, see Scott 1993 and Gardner 1997.)

The leading ID organization is the Discovery Institute, a conservative think-tank in Seattle, Washington. The institute's Center for Science and Culture (CSC) has not advocated the teaching of ID in public school science classes ("probably," notes critic Chris Mooney [2005], "because of its obvious unconstitutionality"), but rather advocates "critical analysis of evolution" or "teaching the controversy" (when in fact no controversy over evolution exists in mainstream science). Directed by philosopher Stephen C. Meyer, the CSC, to quote from its website, seeks "nothing less than the overthrow of materialism." The CSC explores ways to "raise serious doubts about scientific materialism" and to reopen "the case for the supernatural." On the impact that this movement has had on state and local school boards in the U.S., see "General Prologue," note 15.

Young-Earth creationist (YEC) leader Henry Morris attacked the ID movement as being "not enough," as ID theory is not accompanied by or followed up with biblical teaching (H. Morris 1999a; 2001). Likewise the YEC ministry Answers in Genesis (AiG) says ID's "failure to align itself with Biblical history" leaves ID "open to gibes about a clumsy Designer," or the question "What sort of God would design a world with death and suffering?" (Answers Update, May 2002). (On AiG's position, see also Wieland 2002b.) But Biblical creationism is exactly what the ID movement, in seeking scientific and public school respectability, has wished not to be identified with. ID proponents have preferred not to be called creationists, though the label "neocreationists" (Scott 1996b, Pigliucci 2001, H. Morris 1998) or "neo-creos" (Holt 2002) has been appropriately applied to them. (Jerry Coyne [2005b] has labeled ID "The Faith that Dare Not Speak Its Name.") "I'm not a creationist," says ID luminary Michael J. Behe, "I'm a biochemist." Another leading light of the ID movement, mathematician/philosopher William A. Dembski, sounded almost agnostic when he wrote that while intelligence is involved in the production of complex biological systems, "just when and how" intelligence is involved "is a matter for further study" (Dembski and Orr 2002).

Still, the ID movement's goal, as set forth in a CSC document called The Wedge Strategy (originally "stolen from our offices," Meyer has stated, "and placed on the Web without permission" [Mooney 2002]), is clearly religious: first to "defeat scientific materialism and its destructive moral, cultural and political legacies," and then to "replace materialistic explanations with the theistic understanding that nature and human beings are created by God." (For more on the Wedge strategy, modeled after splitting a tree trunk [in this case, science] with a wedge applied at the trunk's weakest point, see Forrest and Gross 2003 and Johnson 2000.) Most of the CSC's funding comes from evangelical Christian sources (Mooney 2005 and 2002), and the CSC's parent Discovery Institute produces evangelical Christian videos through Discovery Media (see Thomas 2003b). Dembski himself has stated, "Any view of the sciences that leaves Christ out of the picture must be seen as fundamentally deficient" (1999, 206). When he joined the Southern Baptist Theological Seminary as director of its Center for Science and Theology, Dembski called it a chance "to mobilize a new generation of scholars and pastors not just to equip the saints but also to engage the culture and reclaim it for Christ. That's really what is driving me" (J. Robinson 2004).

For more on intelligent design, see "General Prologue," note 15; Petto and Godfrey 2007; Coyne 2005b; Mooney 2005 and 2002; Wilgoren 2005; Pennock 1999 and 2001; Forrest and Gross 2003; Miller 1999; Scott 2004; Wallis 2005; Scott and Branch 2002; Leshner 2002;; Shanks 2004; Ruse 2003a; Dembski et al. 2000; Dembski and Kushiner 2001; Shulevitz 2000; Gilchrist 1997; Adler 2005; and an ID FAQ . On Dembski's work, see Wesley Elsberry's Dembski links page.

On the argument from design (including Paley's watchmaker analogy) as debunked by 18th-century philosopher David Hume, see "The Philosopher's Tale," 147-182.

28 Behe argues that some biological systems, such as the cell and the bacterial flagellum, are "irreducibly complex" and must therefore have been designed (1996b). He uses the analogy of the mousetrap, all parts of which are needed in order to work. The noted zoologist Richard Dawkins opined, "Behe should stop being lazy and should get up and think for himself about how the flagellum evolved instead of this cowardly, lazy copping out by simply saying, oh, I can't think of how it came about, therefore it must have been designed" (radio interview 1996). For critiques of Behe's book Darwin's Black Box, see Robison 1996-1997 and Orr 1996. See also John Catalano's website Behe's Empty Box.

29 Pallen and Matzke 2006; Miller 2002a and 2002b; Musgrave 2000. For a study of how hormone-receptor complexity, an integrated biological system that Behe would call irreducible, "evolved by a stepwise Darwinian process," see Bridgham et al. 2006 and Adami 2006.

30 Bonhoeffer 1967, 190; Huchingson 1982; Polkinghorne 1986, 60; Barbour 1966, 414. "When we come to the scientifically unknown," wrote the Christian chemist Charles Coulson (1955, 2), "our correct policy is not to rejoice because we have found God; it is to become better scientists."

31 Paleontologist Leonard Krishtalka at the University of Kansas, quoted in Slevin 2005. Wired magazine has called ID "the 2.0 version of creationism" (Mooney 2005).

32 On Kitzmiller v. Dover, see "General Prologue," note 15.

33 See note 27 above and "General Prologue," note 15.

34 See Gould 1980, 19-26.

35 On the evolution of eyes, see Fernald 2006.

36 Dawkins 1986, 93; Diamond 1985; Thwaites 1983, 19. For a creationist argument that this is not poor design, see Bergman and Calkins 2005.

37 Edwords 1983, 169. On amphibians, see the UC Museum of Paleontology's page Introduction to the Amphibia.

38 Newell 1985, 156. A trait acquired in an organism's lifetime--as when, for example, an animal gets its tail cut off--does not affect the genes and thus cannot be inherited. The inheritance of acquired characteristics (a notion for which Lamarckism, a pre-Darwinian theory of evolution, is chiefly remembered) was a commonly held belief till refuted by the German zoologist August Weismann in the 1880s. Some creationists would have us think that evolutionists still espouse it. In 1981 a creationist schoolteacher on ABC-TV's "Nightline" pointed out that Jews have been circumcising their babies for thousands of years, yet no Jew has ever been born already circumcised (Ecker 1990, 120).

39 See Selim 2004 and Ecker 1990, 204-206.

40 Twenty-three cases of humans born with tails were documented in the literature as of 1985 (Gonzalez-Crussi 1985, 132; see also Gould 1982 on human tails). Two 95-million-year-old species of fossil snakes with hindlimbs, found near Jerusalem, are believed to be not primitive snake ancestors but advanced snakes whose limbs were evolutionary reversions (Tchernov et al. 2000; ScienceDaily). Whales and other cetaceans (dolphins and porpoises) are believed to have evolved from artiodactyls (a group of land mammals including cows, sheep, goats, pigs, deer, and hippopotamuses) who began adaptation to the sea about 55 million years ago, with their hind legs gradually disappearing and their forelegs adapting into fins. (See Thewissen et al. 2007; Gingerich et al. 2001; Rose 2001; Thewissen et al. 2001; Harder 2001a.)

41 For an excellent explanation of nipples on males, see Gould 1991, 124-138. For the theory that the female orgasm is similarly a byproduct of the parallel development of male and female embryos in the first weeks of life and has no evolutionary function, see Lloyd 2005 and Smith 2005.

42 Jacob 1977. See also "The Philosopher's Tale," note 26. For an article on "Darwinian medicine," which asks why the human body has evolved in such a way as to make us vulnerable to problems like cancer, atherosclerosis, and choking, as opposed to the more traditional approach in medical research of studying the body as it currently exists, see Nesse and Williams 1998.

43 See Greene 1959, 303.

44 See note 20.

45 See "The Philosopher's Tale," lines 274-324.

46 See note 20.

47 Gonzalez-Crussi 1985, 132.

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