Appendix B Malaria Drug Resistance
1.Sibley, C. H., Hyde, I. E., Sims, P. F., Plowe, C. V., Kublin, J. G., Mberu, E. K., Cowman, A. F., Winstanley, P. A., Watkins, W. M., and Nzila, A. M. 2001. Pyrimethamine-sulfadoxine resistance in Plasmodium falciparum : what next? Trends Parasitol. 17:582–88; Le Bras, J., and Durand, R. 2003. The mechanisms of resistance to antimalarial drugs in Plasmodium falciparum. Fundam. Clin. Pharmacol. 17:147–53. The authors point out that S/P should not be considered a drug combination because the sulfadoxine and pyrimethamine must act synergistically. If resistance to either drug develops, the therapy fails. Thus only one mutation is required for resistance.
2.Plowe, C. V. 2003. Monitoring antimalarial drug resistance: making the most of the tools at hand. J. Exp. Biol. 206:3745–52; Kublin, J. G., Cortese, J. F., Njunju, E. M., Mukadam, R. A., Wirima, J. J., Kazembe, P. N., Djimde, A. A., Kouriba, B., Taylor, T. E., and Plowe, C. V. 2003. Reemergence of chloroquine-sensitive Plasmodium falciparum malaria after cessation of chloroquine use in Malawi. J. Infect. Dis. 187:1870–75.
3.Korsinczky, M., Chen, N., Kotecka, B., Saul, A., Rieckmann, K., and Cheng, Q. 2000. Mutations in Plasmodium falciparum, cytochrome b that are associated with atovaquone resistance are located at a putative drug-binding site. Antimicrob. Agents Chemother. 44:2100–2108.
4.Meshnick, S. R. 2002. Artemisinin: mechanisms of action, resistance and toxicity. Int. J. Parasitol . 32:1655–60; Uhlemann, A. C., Cameron, A., Eckstein-Ludwig, U., Fischbarg, J., Iserovich, P., Zuniga, F. A., East, M., Lee, A., Brady, L., Haynes, R. K., and Krishna, S. 2005. A single amino acid residue can determine the sensitivity of SERCAs to artemisinins. Nat. Struct. Mol. Biol. 12:628–29.
5.White, N. J. 2004. Antimalarial drug resistance. J. Clin. Invest. 113:1084–92.
6.Ferdig, M. T., Cooper, R. A., Mu, J., Deng, B., Joy, D. A., Su, X. Z., Wellems, T. E., 2004. Dissecting the loci of low-level quinine resistance in malaria parasites. Mol. Microbio. 52:985–97; Mu, J., Ferdig, M. T., Feng, X., Joy, D. A., Duan, J., Furuya, T., Subramanian, G., Aravind, L., Cooper, R. A., Wootton, J. C., Xiong, M., Su, X. Z. 2003. Multiple transporters associated with malaria parasite responses to chloroquine and quinine. Mol. Microbiol. 49:977–89.
Appendix C Assembling the Bacterial Flagellum
1.Voet, D., and Voet, J. G. 1995. Biochemistry, 2nd ed. New York: J. Wiley & Sons, p. 1260.
2.Much of the following description of the structure and assembly of the flagellum is based on Minamino, T., and Namba, K. 2004. Self-assembly and type III protein export of the bacterial flagellum. J. Mol. Microbiol. Biotechnol. 7:5–17.
3.Minamino and Namba, 2004.
4.www.npn.jst.go.jp.
5.See the video at www.npn.jst.go.jp.
6.Macnab, R. M. 1999. The bacterial flagellum: reversible rotary propellor and Type III export apparatus. J. Bacteriol. 181:7149–53; Nguyen, L., Paulsen,I. T., Tchieu, J., Hueck, C. J., and Saier, M. H., Jr. 2000. Phylogenetic analyses of the constituents of Type III protein secretion systems. J. Mol. Microbiol. Biotechnol. 2:125–44; Galan, J. E., and Collmer, A. 1999. Type III secretion machines: bacterial devices for protein delivery into host cells. Science 284:1322–28; Saier, M. H., Jr. 2004. Evolution of bacterial Type III protein secretion systems. Trends Microbiol. 12:113–15.
7.Deriving the TTSS from the flagellum by a Darwinian process may be possible (although it is far from certain), since it would involve the production of a less complex structure whose essential mechanism already resides in the more complex structure from which it is derived. Yet that would not help in showing how a Darwinian process could produce the more complex structure.
Appendix D The Cardsharp
1.Ball, P. 2004. Synthetic biology: starting from scratch. Nature 431:624–26.
2.Pawson, T. and Nash, P. 2003. Assembly of cell regulatory systems through protein interaction domains. Science 300:445–52.
3.Bhattacharyya, R. P., Remenyi, A., Yeh, B. J., and Lim, W. A. 2006. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu. Rev. Biochem. 75:655–80.
4.Writing of researchers who are trying to manipulate the cell, Phillip Ball (Ball, 2004) observes, “Synthetic biology is the logical corollary of the realization that cells, like mechanical or electronic devices, are exquisitely ‘designed’—albeit by evolution rather than on the drawing board.”
5.Lim, W. A. 2002. The modular logic of signaling proteins: building allosteric switches from simple binding domains. Curr. Opin. Struct. Biol. 12:61–68.
6.Pawson, T., and Nash, P. 2003. Assembly of cell regulatory systems through protein interaction domains. Science 300:445–52.
7.Park, S. H., Zarrinpar, A., Lim, W. A. 2003. Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science 299:1061–64.
8.Dueber, J. E., Yeh, B. J., Chak, K., and Lim, W. A. 2003. Reprogramming control of an allosteric signaling switch through modular recombination. Science 301:1904–8.
9.Ibid.
10.Lenski, R. E., Ofria, C., Pennock, R. T., and Adami, C. 2003. The evolutionary origin of complex features. Nature 423:139–44.
11.http://dllab.caltech.edu/avida/v2.0/docs/genesis.html. This website describes the Avida program, including the setting SIZE_MERIT_METHOD: “This setting determines the base value of an organism’s merit. [“organisms get CPU time (that is, ‘food’) proportional to their merit.”] Merit is typically proportional to genome length otherwise there is a strong selective pressure for shorter genomes (shorter genome => less to copy => reduced copying time => replicative advantage). Unfortunately, organisms will cheat if merit is proportional to the full genome length—they will add on unexecuted and uncopied code to their genomes creating a code bloat. This isn’t the most elegant fix, but it works.”
Acknowledgments
My citation of results or use of figures from the scientific literature, of course, does not imply that the authors of those works agree with the controversial conclusions of this book. I’m grateful to many people for discussions that clarified the ideas presented in this book. For reading portions of the manuscript in draft form I heartily thank Lydia and Tim McGrew, Peter and Paul Nelson, George Hunter, David DeWitt, Doug Axe, Bill Dembski, Jonathan Wells, Tony Jelsma, Neil Manson, Jay Richards, and Guillermo Gonzalez. I am much obliged to my editor, Bruce Nichols, for his encouragement over the years, and for whipping the klunky draft manuscript into more readable prose. I appreciate the continuing support of the folks at the Discovery Institute, especially Bruce Chapman, Steve Meyer, John West, and Rob Crowther. Far above all, I’m grateful to my wife, Celeste, for her constant love for, and preternatural patience with, a hopelessly distracted husband, and also for bearing, and bearing with, our children—Grace, Benedict, Clare, Leo, Rose, Vincent, Dominic, Helen, and Gerard—who make our house a (very noisy) home.
Index
“Abdication of Pope Mary III…or
Galileo’s Revenge”
actin
Africa
HbC in
HPFH in
malaria in
sickle cell disease in
thalassemia in
African Americans, sickle trait in
Afzelius, Björn
AIDS: evolution and
HIV as cause of
human toll of
treatment of
air
bad, see malaria
Alberts, Bruce
algorithms
amino acids
alpha chains of
beta chains of
cellular biochemical pathways of
gamma chains of
glutamic
hydrophobic
mutation of
positions of
positive vs. negative electrical charging of
randomized
sequencing of
substitution of
valine
see also proteins anemia
in sickle cell diseas
e
animals
common ancestors of
complex cells of
design and body shapes of
genomes of
misshapen
observing large changes in
regulatory systems of
reproduction of
studies of
survival of
see also specific animals
Antarctica
Antarctic Ocean
Anthropic Bias (Bostrom)
antibiotics
carbapenems
evolved resistance of bacteria to
antibodies
artificial
arachnids
archeology
Arctic Ocean
Aristotle
arms race (U.S.-Soviet)
Army, U.S.
artemisinin
Asia
Atlantic Ocean
atovaquone
Avery, Oswald
Avida
bacteria
fighting of
first sequencing of
as most numerous organism on earth
resistance to antibiotics evolved in
studies of
see also specific bacteria
baker’s yeast (Saccharomyces cerevisiae)
band 3 protein
bears
Berra, Yogi
Big Bang
bile
biochemistry
biological arms races
biology
advances in
classification system of
developmental
evolutionary developmental (evo-devo)
modern
molecular
teaching of
Black Death
black holes
Blair, Tony
Blind Watchmaker, The (Dawkins)
blood
circulation of
clotting of
freezing point of
independent changes in
invasion of disease organisms in
red color of
testing of
waste products of
see also hemoglobin; red blood cells bloodletting
blueprints
bones
Bostrom, Nick
Brownlee, Donald
Brown University
butterflies
C-A-G (three nucleotide segment)
California, University of: at Berkeley
at San Francisco
California Institute of Technology
Cambridge University
capillaries
carbon
albuminous combination of
Carrey, Jim
Carroll, Sean
Carter, Brandon
Cast Away
caterpillars
Catholic Encyclopedia
Catholic University
cats
CCC, see chloroquine-complexity clusters
CCR5 (protein)
cells: aging of
automatic mechanisms of, see nanobots
ciliated
complex molecular machinery of
construction of
design of
destruction of
genetic debris in
inner segments (IS) vs. outer segments (OS) of
membranes of
movement of
multiplication of
mutation of
nuclei of
protein-binding sites in
pumps and portals of
routine tasks of
stress on
supply and exchange of materials in
waste products of
C-Eve
C-Harlem hemoglobin
cheetahs
chemistry
Chicago, University of
children
disease immunity of
malarial deaths of
sickle cell disease deaths of
chimpanzees
humans compared with
Chlamydomonas (alga)
chloroquine
initial effectiveness of
resistance to
chloroquine-complexity clusters (CCC)
chromosomes
cilium
biological functions of
building and maintenance of
deletion of
elegant complexity of
interior of
length of
modified
origin of
pieces of
proteins in
railroad train metaphor and
shortening of
transition fibers in
cinchona tree
circulatory system
Clinton, Bill
cloning
Cole, Douglas
common descent
correctness of
definition of
differences not accounted for in
examples of
finding ancestors and
general acceptance of
natural selection vs.
random mutation vs.
similarities accounted for in
compartmentation
complexity theory
Compositional Evolution (Watson)
computers
consilience
Consilience (Wilson)
cosmology
cows
Coyne, Jerry
creationism
Crichton, Michael
Crick, Francis
crime
crustacean gills
Darwin, Charles
“branching tree of life” image of
defenses of
emphasis on common descent by
(Darwin, Charles, cont’d) intellectual descendants of
kinship marriage of
methods of
mistakes of
multifaceted theory of
see Darwinism publication of theories by
step-by-step evolution affirmed by
Darwinism: aggressive promotion of
apparent simplicity and logic of
appraisal of processes in
arms race metaphor of
assumption vs. demonstration of conclusions in
best available evidence for
blind search metaphor and
complete acceptance vs. complete rejection of
degrees of correctness in
dogma vs. data and
elements of
failure of process without favorable pathway in
incoherence of
intent mimicked by unintelligent forces in
limits of
mixture of concepts in
as most influential idea of our time
predictions in
principles of illness in
questioning truth of
rival theories of
separate evaluation of ideas in
serious consequences of acceptance of
teaching of
testing of
as theory-of-everything
three most important concepts of
time and
as tinkering vs. engineering
uniquely biological processes of
see also evolution Darwin’s Black Box (Behe)
Darwin’s Dangerous Idea (Dennett)
Davidson, Eric
Davies, Paul
Dawkins, Richard
DDT
death: from fever
infant
prenatal
see also specific diseases
Dennett, Daniel
Denton, Michael
Descartes, René
design
agent of
animal
arrangement of parts and
fitting of parts and
intelligent
of universe
DHFR
DHPS
DNA
building blocks of, see nucleotides cloning of
&
nbsp; control elements in
copying of
cutting pieces out of
double copies of
excess
family relationships determined by
genetic information carried in
HPFH and
“junk”
mistakes in
mobile transpositions of
molecular structure of
mutation of
proteins and
repairing of
sequencing of
shape of, see double helix
single units of, see nucleotides structure of
studies of
synthesizing of
testing of
trading sections of
see also genes; genomes; human genome dogs
double helix
duplication of chunks of
“flipping” of DNA segment in
Drexler, Eric
Drosophila melanogaster (fruit fly)
drugs
antimalarial
combinations of
discovery and invention of
miracle
production costs of
research and development of
resistance to
side effects of
synthetic
see also specific drugs Duffy antigen
Earth
E. coli
continuous generation of
studies of
eggs
Einstein, Albert
embryos
Endless Forms Most Beautiful (Carroll)
endomesoderm
energy, storing of
Engines of Creation (Drexler)
environmental policy
enzymes
chemical processes of
digestive
production of
Erwin, Douglas
Escherichia coli, see E. coli “Ether” (Maxwell)
eukaryote
Everest, Mount
evolution: biological pathway in
coherence in
destructive vs. constructive changes in
explanations of
finding the “edge” of
foggy rhetoric of
general understanding of
hemoglobin changes through
irreducible complexity of
long-term studies in
rich evidence of
steps in
time and
trench warfare of
see also Darwinism “Evolution in Action”
eyes
features
creation of
inheritance of
similar vs. different
transformation of
fetal hemoglobin
fever: death from
The Edge of Evolution Page 34