12.Stone, J. R., and Wray, G. A. 2001. The following quotation omits references cited in the paper.
It is likely that in many cases, the appearance of a new binding site will have no effect on the expression of a nearby gene. For example, some transcription factors must interact with other DNA-binding proteins to affect gene expression, and therefore the appearance of a single new binding site might be functionally neutral. Alternatively, nearby silencer sites might override any new binding site that appears. Nevertheless, it is plausible that in some cases the appearance of a new binding site will alter gene expression. Because most promoters are inactive by default, activation of transcription by the appearance of a single new binding site seems less likely than does modulation or restriction of an existing phase of gene expression. Of course, even if a new binding site does affect gene expression, there is no way to predict what, if any, phenotypic consequences might ensue. As with amino acid substitutions within coding regions of genes, we predict that in many cases the consequences of a new binding site appearing within a promoter will be either detrimental or neutral; only in rare cases will it be beneficial. The salient prediction yielded by our computer simulation is that local point mutations will constantly produce new binding sites that in principle [emphasis added] are capable of altering gene expression and that such sites may be subject to selection.
It is useful to reiterate here the Coyne-Orr principle, that “the goal of theory, however, is to determine not just whether a phenomenon is theoretically possible, but whether it is biologically reasonable —that is, whether it occurs with significant frequency under conditions that are likely to occur in nature.” In other words, showing something could occur “in principle” should not be the end of the story.
13.Stone, J. R., and Wray, G. A. 2001.
14.Coyne, J. A. 2005. Switching on evolution. Nature 435:1029–30.
15.“The origin of insect wings has long been a contentious mystery…. But here again is where Evo Devo has stepped in with some powerful new evidence…. In order to test the theory that wings might be derived from the gill branches of crustaceans, Michalis Averof and Stephen Cohen traced how the Apterous and Nubbin [master regulatory] proteins are expressed in the appendage of other arthropods, especially crustaceans. They found [the proteins] were selectively expressed in the respiratory lobe of the outer branch of crustacean limbs. The best explanation for this observation is that the respiratory lobe and insect wing are homologous—that is, the same body part in different forms in the two animals” (Carroll, S. B. 2005. Endless forms most beautiful: the new science of evo devo and the making of the animal kingdom. New York: W.W. Norton & Co., pp. 175–76).
16.Carroll dismisses another eventuality. “The only other possibility would be the extraordinary coincidence that, of the hundreds of tool kit proteins that could be used to make gills and wings, these two proteins were independently selected by crustaceans and insects for building these structures.” I find this dismissal odd from someone who touts the extraordinary power of switches and regulatory proteins. If those two proteins could trigger some useful developmental pathway, and if, like eyes on antennae, the pathway could be triggered at some arbitrary point in the animal’s body, why should an evo-devo devotee not think wings are a new invention?
17.Erwin, D. H. 2005. A variable look at evolution. Cell 123:177–79; Charlesworth, B. 2005. On the origins of novelty and variation. Science 310:1619–20; Hartl, D. L. 2005. Better living through evolution. Harvard Magazine (November–December), pp. 22–27.
18.quoted in Hartl, 2005. Hartl tries to give this a positive spin. “Darwin could not have dreamed of such a spectacular confirmation of his theory of descent with modification [that is, similar molecules in different animals].” But Jacob was using Darwin’s theory to reason that cows should have cow molecules. If that had transpired, no Darwinist would have been surprised. The surprise to Darwinists was that their expectations based on Darwin’s theory were wrong, that cows in fact didn’t have special cow molecules. Hartl goes on: “For creationists, this must be a nightmare, for any sensible model of creationism would predict cows to have cow molecules, goats to have goat molecules, and snakes to have snake molecules.” But it was Jacob and other leading Darwinists themselves who confidently expected different molecules for different species.
19.Carroll. 2005, pp. 71–72.
20.Ibid., pp. 123, 318.
21.Ibid., p. 285.
22.Ibid., p. 173.
23.Kirschner, M., and Gerhart, J. 2005, p. 195.
24.Ibid., p. 196.
25.Gehring. 1996.
26.Alberts, B. 1998. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92:291–94.
27.Erwin, D. H. 2005. The books Erwin cites are: Kirschner, M., and Gerhart, J. 2005. The plausibility of life: great leaps of evolution. New Haven, Conn.: Yale University Press; Carroll, S. B. 2005: Endless forms most beautiful: the new science of evo devo and the making of the animal kingdom . New York: W.W. Norton & Co; Jablonka, E., and Lamb, M. J. 2005. Evolution in four dimensions: genetic, epigenetic, behavioral, and symbolic variation in the history of life. Cambridge, Mass.: MIT Press; West-Eberhard, M. J. 2003. Developmental plasticity and evolution. Oxford: Oxford University Press; Schlichting, C., and Pigliucci, M. 1998. Phenotypic evolution: a reaction norm perspective. Sunderland, Mass.: Sinauer.
28.Kirschner, M., and Gerhart,
29.Watson, R. A. 2006. Compositional evolution: the impact of sex, symbiosis, and modularity on the gradualist framework of evolution. Cambridge, Mass.: MIT Press, p. 272.
30.Carrol
31.The number of the tiniest animals such as nematode worms at best may be comparable to malaria, but larger animals such as insects are much fewer in number.
32.Orr, H. A. 2003. A minimum on the mean number of steps taken in adaptive walks. J. Theor. Biol. 220:241–47.
33.Stone, J. R., and W
34.Levine, M., and Davidson, E. H. 2005. Gene regulatory networks for development. Proc. Natl. Acad. Sci. USA 102:4936–42.
35.Davidson, E. H., and Erwin, D. H. 2006. Gene regulatory networks and the evolution of animal body plans. Science 311:796–800.
36.Singh, H., Medina, K. L., and Pongubala, J. M. 2005. Contingent gene regulatory networks and B cell fate specification. Proc. Natl. Acad. Sci. USA 102:4949–53. See Figure 9. 3.
37.Valentine, J. W., Collins, A. G., and Meyer, C. P. 1994. Morphological complexity increase in metazoans. Paleobiology 20:131–42.
38.Davidson, E. H., pp. 11–12.
39.Fondon, J. W., III, and Garner, H. R. 2004. Molecular origins of rapid and continuous morphological evolution. Proc. Natl. Acad. Sci. USA 101:18058–63.
40.Culotta, E., and Pennisi, E. 2005. Breakthrough of the year: evolution in action. Science 310:1878–79.
41.Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villarreal, G., Jr., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Schluter, D., and Kingsley, D. M. 2005. Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science 307:1928–33.
42.Gompel, N., Prud’homme, B., Wittkopp, P. J., Kassner, V. A., and Carroll, S. B. 2005. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433:481–87.
43.Gould, S. J., and Lewontin, R. C. 1979. The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. R. Soc. Lond. B. Biol. Sci. 205:581–98.
44.Gould, S. J. 1997. The exaptive excellence of spandrels as a term and prototype. Proc. Natl. Acad. Sci. USA 94:10750–55.
10 All the World’s a Stage
1.White, M., and Gribbin, J. R. 2002. Stephen Hawking: a life in science, 2nd ed. Washington, D.C.: Joseph Henry Press, p. 261.
2.Carter, B. 1974. Large number coincidences and the anthropic principle in cosmology. In Confrontation of cosmological theories with data, M. S. Longair, ed. Dordrecht: Reidel, pp. 291–98. A recent
, balanced discussion of fine-tuning is Collins, R. 2003. Evidence for fine-tuning. In God and design: the teleological argument and modern science. Neil Manson, ed. Routledge, pp. 178–99.
3.Davies, P. C. W. 1982. The accidental universe. Cambridge: Cambridge University Press, p. vii.
4.Hawking, S. W. 1998. A brief history of time, tenth anniversary ed. New York: Bantam Books, pp. 129–30.
5.Dyson, F. J. 1979. Disturbing the universe. New York: Harper & Row, p. 250.
6.Denton, M. J. 1998. Nature’s destiny: how the laws of biology reveal purpose in the universe. New York: Free Press.
7.A possible objection is that chemical properties are derived from physical ones, so why count them as a separate category? As a matter of bookkeeping, I’m categorizing fine-tuning by the level at which the effects become noticeable to us. The fine-tuning of laws and constants becomes apparent at the level of physics and astronomy, such as whether atoms or stars would be stable. The properties of water and carbon that are necessary for life, however, become apparent only at the level of chemistry.
8.National Academy of Sciences. 1999. Science and creationism: a view from the National Academy of Sciences, 2nd ed. Washington, D. C.: National Academy Press, p. 7.
9.Ward, P. D., and Brownlee, D. 2000. Rare earth: why complex life is uncommon in the universe. New York: Copernicus, p. 29.
10.Ibid., p. 231, fig
11.Davies, P. C. W. 1999. The fifth miracle: The search for the origin and meaning of life. New York: Simon & Schuster, p. 17.
12.Crick, F. 1981. Life itself: its origin and nature. New York: Simon and Schuster, p. 88.
13.Farley, J. 1977. The spontaneous generation controversy from Descartes to Oparin. Baltimore: Johns Hopkins University Press, p. 73.
14.Bostrom, N. 2002. Anthropic bias: observation selection effects in science and philosophy. New York: Routledge, p.12.
15.Brumfiel, G. 2006. Our universe: outrageous fortune. Nature 439:10–12; Carroll, S. M. 2006. Is our universe natural? Nature 440:1132–36.
16.Collins, R. 2002. The argument from design and the many-worlds hypothesis. In Philosophy of religion: a reader and guide, W. L. Craig, ed. New Brunswick, N. J.: Rutgers University Press.
17.It’s entirely possible a designer might set up a multiverse in order to generate one or more life-containing universes. But of course that would not be random; it would be intentional. In this section I’m considering what to expect just from a random collection of unintended universes.
18.Assuming each person bought just one ticket, roughly o
19.On the other hand, even if they aren’t absolutely necessary to produce intelligent life, a designer might make complex systems such as the flagellum, either for their own sake or for other, nonessential interactions with intelligent life.
20.Bostrom, N. 2002. Anthropic bias: observation selection effects in science and philosophy. New York: Routledge, pp. 52–53,55.
21.In one episode of the original Star Trek TV series (“Mirror, Mirror,” number 39), Captain Kirk enters a parallel universe where he meets a rather sinister, bearded Mr. Spock, plus other unsavory doubles of the nice-in-our-universe crew.
22.If there are infinite universes, how can there be no combinations of laws and constants that would allow an orderly progression to life? Here’s one possibility. One can have an infinite number of something, but still not have all values. For example, suppose in the multiverse some particular constant could take any real-numbered value between one and two. There are an infinite number of possible values within that range. But if life could arise only if the constant had a value of eight-and-a-half—a number outside the permitted range—then none of the infinite number of constants would work. Here’s another possibility. Suppose that in reality there are no laws and constants of nature, only chaos. The chaos might by chance give rise to delusional freak observers, but not to observers who have arisen by laws of nature, since none exist.
23.Bostrom, N. 2002. Anthropic bias: observation selection effects in science and philosophy. New York: Routledge, pp. 11–12. Bostrom takes designer in a very broad sense—in fact, too broad. I believe his inclusion of the words “principle or mechanism” in the second sentence is a category mistake on Bostrom’s part. A design hypothesis implies intentionality, choice, and other characteristics that cannot be attributed to a “principle or mechanism.”
24.Sawyer, R. J. 2000. The abdication of Pope Mary III…or Galileo’s revenge. Nature 406:23. The journal Nature is generally dismissive of scientific results suggestive of a reality beyond nature, whether the results be fine-tuning of the cosmos or a beginning to the universe. In 1989 the longtime editor of Nature, John Maddox wrote an editorial with the odd title “Down with the Big Bang.” Maddox decried the Big Bang theory as “philosophically unacceptable,” saying it gave aid and comfort to “Creationists.”
25.Quoted in Kirschner, M., and Gerhart, J. 2005. The plausibility of life: great leaps of evolution. New Haven, Conn.: Yale University Press. p. 265.
26.Hall, B. G. 2004. In vitro evolution predicts that the IMP-1 metallo-beta-lactamase does not have the potential to evolve increased activity against imipenem. Antimicrob. Agents Chemother. 48:1032–33.
Appendix A I, Nanobot
1.A self-replicating robot was recently reported in Nature (Zykov, V., Mytilinaios, E., Adams, B., and Lipson, H. 2005. Robotics: self-reproducing machines. Nature 435:163–64).
2.Giles, J. 2004. Nanotech takes small step towards burying “grey goo.” Nature 429:591.
3.The terms “robot” and “machine” applied to the cell are not meant as analogies—they are meant quite literally. That cells and the systems they contain are robotic machinery is widely recognized in the scientific community. For example, Tanford and Reynolds dub proteins “Nature’s Robots” (Tanford, C., and Reynolds, J. A. 2001. Nature’s robots: a history of proteins. Oxford: Oxford University Press) and the term “molecular machines” is routinely used to describe protein complexes. For example, see the December 2003 BioEssays Special Issue on Molecular Machines, containing such articles as “The spliceosome: the most complex macromolecular machine in the cell?” and “Perpetuating the double helix: molecular machines at eukaryotic DNA replication origins.”
4.Much of the following discussion of the history of biology derives from Singer, C. J. 1959. A history of biology to about the year 1900: a general introduction to the study of living things , 3rd ed. London: Abelard-Schuman.
5.Singer. 1959.
6.Galen was born in Greece but traveled to Rome at the age of about thirty-two where he became the physician to the emperor.
7.The Englishman William Harvey first reasoned that blood had to circulate. He calculated that if each heartbeat pumped two ounces of blood, and if a heart beat seventy-two times per minute, then in an hour the heart pumps 540 pounds of blood—triple the weight of a large man! Clearly that much blood could not be continuously made by the body. Harvey’s elegant mathematical reasoning is cited as one of the earliest examples of modern scientific thinking (Singer. 1959).
8.Joseph Hook called them “cells” because they reminded him of medieval monks’ rooms.
9.So said Ernst Haeckel (Farley, J. 1977. The spontaneous generation controversy from Descartes to Oparin. Baltimore: Johns Hopkins University Press, p.73).
10.Improvements in computers and lab techniques have made crystallography much faster and more tractable, although it still involves considerable effort (Abbott, A. 2005. Protein structures hint at the shape of things to come. Nature 435:547).
11.Perutz, M. 1964. The hemoglobin molecule. Scientific American 211:64–76.
12.Other classes of biological molecules include DNA and RNA (which carry genetic information), and polysaccharides and lipids (which have structural and energy-storage roles).
13.Discussions of protein structure, myoglobin, and hemoglobin can be found in virtually any biochemistry textbook.
14.Most proteins are less than a thousand amino acids long. A sin
gle DNA, however, can be composed of a hundred million nucleotides. That vast length of DNA can contain many discrete genes that code for many different proteins.
15.Chains of amino acids (proteins) that can fold into discrete and functional forms are exceedingly rare, although the exact degree of rarity is a matter of debate. Estimates range roughly from one sequence in every 1030 (Hecht, M. H., Das, A., Go, A., Bradley, L. H., and Wei, Y. 2004. De novo proteins from designed combinatorial libraries. Protein Sci. 13:1711–23)to about one in 1070 (Axe, D. D. 2004. Estimating the prevalence of protein sequences adopting functional enzyme folds. J. Mol. Biol. 341:1295–1315).
16.For conceptual clarity, in the “water-loving” category here I have included only uncharged hydrophilic amino acids, and put charged residues in their own group. However, charged amino acids are “water-loving,” too. Some amino acids don’t clearly fit any of the categories.
17.Myoglobin was long thought to be required to store oxygen in tissues of all mammals, but its role is no longer so clear. A few years ago researchers destroyed the gene for myoglobin in a line of mice, so that the mice were entirely missing myoglobin, and yet adult mice did just fine without it (Garry, D. J., Ordway, G. A., Lorenz, J. N., Radford, N. B., Chin, E. R., Grange, R. W., Bassel-Duby, R., and Williams, R. S. 1998. Mice without myoglobin. Nature 395:905–8). Later work showed that unborn mice do have some need for the protein. The point, however, is that the role myoglobin plays in animals, which was thought to be very well understood, was not (Kanatous, S. B., and Garry, D. J. 2006. Gene deletional strategies reveal novel physiological roles for myoglobin in striated muscle. Respir. Physiol Neurobiol. 151:151–58; Garry, D. J., Kanatous, S. B., and Mammen, P. P. 2003. Emerging roles for myoglobin in the heart. Trends Cardiovasc. Med. 13:111–16; Meeson, A. P., Radford, N., Shelton, J. M., Mammen, P. P., DiMaio, J. M., Hutcheson, K., Kong, Y., Elterman, J., Williams, R. S., and Garry, D. J. 2001. Adaptive mechanisms that preserve cardiac function in mice without myoglobin. Circ. Res. 88:713–20).
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