Johnson, Norman A. Darwinian detectives
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References
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Adam. See Y chromosome
adaptation, , , , , , , , , ,
, , , . See also
maladaptation, positive selection
bipedalism,
click languages,
to cold water, –
in computer programs,
ghosts of adaptations past,
to pesticides,
plant adaptations against fungi, –
of viruses, –
Adh (alcohol dehydrogenase),
and use of McDonald-Kreitman test, –
Africa, , , , , , , , , ,
, ,
and ancestors of Alex Haley, ,
chimpanzee populations,
languages, , –, –
malaria and sickle cell anemia, –
origin of dogs,
origin of mitochondrial Eve, , –,
, –,
origin of Y chromosome Adam, , ,
, –
aging, evolution of, –
agriculture, , , , . See also dog
domestication of maize, –
AIDS. See HIV
alcohol dehydrogenase. See Adh
Alu, , , , . See also transposable
element
Alzheimer’s disease,
ancestor, –, , , , , ,
–, , ,
of Alex Haley, ,
“ancestor of all or ancestor of none,”
common ancestry (languages), –,
–
common ancestry (organisms) , , –,
, , , , , , , –, ,
,
most recent common, , –, , ,
, (see also mitochondrial Eve, Y
chromosome Adam)
ancestral polymorphism. See polymorphism
Anopheles (mosquito),
Antarctic Ocean,
fish, ,
antifreeze, natural,
aphasia,
Apolipoprotein-E,
Aquinas, Thomas,
Arabidopsis thaliana (mustard plant),
,
argument from design,
Index
artificial selection, , , , –, .
See also natural selection
Asimov, Isaac, ,
ASPM, –
Australopithecus, , , ,
Baby Fae, ,
baboon, ,
bacteria, , , , , ,
antibiotic resistant,
related to mitochondria,
streamlined genomes, , –
Bailey, Leonard, ,
balancing selection, , –, , , ,
. See also heterozygote advantage,
natural selection, negative selection,
positive selection
CCR, –
cystic fibrosis, –
HLA/MHC, –,
and linkage disequilibrium, ,
sickle cell anemia, –
Bamshad, Michael, –
Basque,
Behe, Michael, –, –,
exchange with Miller,
Belyaev, Dimitry, –
Bible, –, –
Bierne, Nicholas,
bipedalism,
Biston betularia (peppered moth), –
Black Plague,
blood clotting, , –, –
bonobo, , , –, , , .
See also chimpanzee
effective population size, –
morphological differences with common
chimpanzee,
population genetics, –
sexual habits, –
bootstrap, . See also phylogeny
Brace, Loring,
brain evolution. See evolution
Brainerd, Elizabeth,
Broca, Pierre Paul,
Broca’s area, –
Bryan, William Jennings, ,
burden of proof, –
Burling, Robbins,
Bush, George W.
appointment of Judge Jones,
avian flu plan, ,
Callender, James,
Cann, Rebecca, , –,
Caramelli, David, –
Catholic Church,
Cavalli-Sforza, Luca, , –
CCR (chemokine receptor), –,
Center for Science and Culture (CSC). See
Discovery Institute
Chang, Joseph,
Chapman, Bruce,
Chardin, Pierre Teilhard de,
Charybdis,
chemokines, . See also CCR
chimpanzee, , , , , , , , –,
, , –, –, , ,
. See also bonobo
comparison of common chimpanzee and
bonobo, –
effective population size, –
gene flow, –
genome project results, –, –
HLA/MHC variants shared with humans,
,
language, ,
sialic acids,
chitinase,
Chomsky, Noam,
Churchill, Winston,
cilliates, –
circumstantial evidence, ,
Clark, Andrew,
click languages, –, –. See also
language
cline, , –
CMAH,
codon,
Competitive Exclusion Principle, ,
conservation biology, ,
constraint, functional, , , , , ,
. See also negative selection
Coppinger, Ray, –,
corn. See maize
coronary heart disease,
correlation, , , ,
brain size and intelligence, ,
of genetic variants, , –, –
(see also linkage disequilibrium)
versus causation, –
creationism, –, , , , , , ,
. See also Intelligent Design
and American politics, –
Day-Age,
Young Earth,
Crick, Francis H. C., ,
Crow, James,
cubitus interruptus (ci),
Currant, Mathias,
C value, . See also genome, size
Cystic fibrosis, –, ,
Darrow, Clarence, ,
Index
Darwin, Charles, , –, , , ,
–, , –, , , , ,
, , . See also evolution,
natural selection
as a breeder, , ,
The Descent of Man and Selection in
Relation to Sex,
dogs, –
eye evolution, –
language,
The Origin of Species, , –, , ,
,
studies of finches,
Darwin’s Black Box (Behe), –
Darwin’s finches (Geospiza sp.), –
Dawkins, Richard
The Ancestor’s Tale,
Climbing Mount Improbable,
De Castro, Bermudez,
DeCode,
Dembski, William,
The Descent of Man and Selection in
Relation to Sex (Darwin),
de Waal, Franz, –
Diamond, Jared
agriculture,
Great Leap Forward, –, ,
The Third Chimpanzee, ,
deoxyribonucleic acid. See DNA
Discovery Institute, , –. See also
Intelligent Design
“Wedge Document,”
DNA, , , , , , , , , ,
, , , , , , , , , ,
, , , , , , , ,
, , , . See also dogs,
genetic code, genome, maize,
mitochondrial DNA, Neanderthal
DNA, Y chromosome
ancient,
coding versus noncoding, ,
–
comparison of human and chimpanzee,
–,
conservation of sequence,
databases,
elimination, –
HIV,
intron, , –
information in nucleotides,
junk DNA, –,
microsatellites,
rates of evolution, , , – (see also
molecular clock)
“selfish DNA,” –
structure,
transcription,
translation,
uniform use in all life,
DNA Polymerase,
Dobzhansky, Theodosius, ,
Doebley, John, –
dogs, , , –
Dover, Pennsylvania, , , –. See also
Kitzmiller et al. vs Dover et al.
Drosophila, , , , , , –,
Drosophila mauritiana,
Drosophila melanogaster, , –, ,
–
Drosophila sechellia,
Drosophila simulans, –, ,
Drosophila subobscura, ,
Drosophila willistoni,
Drosophila yakuba, –
Druyan, Ann,
effective population size, , , .
See also genetic drift, population size
and ancestral polymorphisms,
of bonobos and chimpanzees, –
defined,
of dogs,
and genome size, –
of humans, , , ,
males versus females, –
and mitochondrial Eve,
of Neanderthals,
relationship with genetic drift, –,
and Y chromosome Adam,
Ehrlich, Paul
Human Natures,
electrophoresis, protein, , –, ,
Enlightenment, , ,
Enterococcus (bacterium),
Episcopal Church, –
Establishment Clause (of U.S. Constitution),
, –
Evans, Patrick,
Eve, Biblical, –
Eve, mitochondrial. See mitochondrial Eve
evolution, –, , , , , , –,
–, , , , , , , –, ,
, , , , , –, ,
–, , , , , ,
–, . See also Darwin, genetic
drift, intelligent design, language,
mutation, natural selection, neutral
theory, phylogeny
and American politics, –
and animal and plant breeding,
atheistic,
blood clotting, –
brain, –, , , , –,
–, , , –
Index
evolution continued
computer,
as a conservative process, –, –
(see also negative selection)
Darwin’s finches, –,
dogs, –
evidence for, –,
eyes, –
as fact and theory, –
HIV,
and human origins, –, – (see
also Neanderthal)
influenza virus, –
legal applications,
linguistic ability, , (see also
FOXP, language)
maize, –
maladaptation, –
male-driven,
micro- versus macro-evolution,
“non-Darwinian evolution,”
nontheistic,
and religion, –,
of resistance, –
teaching of, , –, , –
theistic, –
evolutionary relationships. See genealogy,
phylogeny
Excoffier, Laurent,
eyes, –
blind spot,
Nilsson-Pelger model of evolution,
Eyre-Walker, Adam,
false negative,
false positive,
Fauci, Anthony,
fibrin\fibrinogen, , –. See also blood
clotting
fibrinopeptides, , –,
Fisher, Simon,
Fisher, Sir Ronald A.,
flu. See influenza
fish, , . See also pufferfish
cold adapted, –, ,
genome size, –, , ,
Forrest, Barbara, –
Fossey, Dian,
foxes, –
FOXP, –,
fungus,
Galapagos Islands, –
genealogy, –, , . See also
mitochondrial Eve, phylogeny,
Y chromosome Adam
author’s personal, –
of genes versus of people, ,
mitochondrial, –
Y chromosome, –
gene duplication, –,
gene inactivation,
generation time, , , ,
of elephants,
of insect pests,
of viruses,
genetic algorithm,
genetic bottleneck, –, , , , .
See also genetic drift, genetic variation
genetic code, ,
genetic drift, random, , , –, –,
, , , , , , –, , ,
, , , , . See also effective
population size, population size
genetic recombination,
absence in mitochondria, –,
and genetic hitchhiking, –
and linkage disequilibrium,
genetic variation, , –, , , ,
–, , , , , , , , ,
. See also polymorphism, SNP
among and within human populations,
, ,
in bonobos and chimpanzees,
in dogs, –
and effective population size,
maintained by balancing selection, , ,
, –
reduction due to selective sweep, –
requirement for natural selection, ,
gene tree, , . See also genealogy,
phylogeny
genome, , , , , –, , , ,
, ,
chimpanzee, –, , –
dog, –
“hitchhiker’s guide to the genome,”
human, –, –, , , –
mitochondrial,
noncoding DNA,
size, , , –
genomic conflict, . See also selfish DNA
Geospiza fortis. See Darwin’s finches
Gilchrist, George,
Gilkey, Langdon,
God of the Gaps, –
The Gods Must Be Crazy (film),
Goodall, Jane,
Gross, Paul, –
Gould, John,
Gould, Stephen Jay,
The Mismeasure of Man,
Grant, Bruce,
Grant, Peter, –
Index
Grant, Rosemary, –
Great Leap Forward, –, , ,
Gregory, Ryan, ,
Greenberg, Joseph, –
Grisham, John,
Haeckel, Ernst, ,
Haldane, J. B. S.,
Haley, Alex, ,
half-life,
haplotypes, ,
of ASPM, –
CCR,
dogs, –
of HLA/MHC, –
maize,
of Microcephalin, –
and mitochondrial Eve, ,
and Y chromosome Adam,
Harris, Sidney,
“helper T” cells. See T-cells
hemagglutinin. See influenza
Hemmings, Eston, ,
Hemmings, Sally,
hemoglobin, ,
cold adaptation, ,
loss,
nucleotide differences among
variants,
sickle cell anemia, –
heterozygote, , –
advantage, –, –, (see also
balancing selection)
Hey, Jody,
histone H, , , ,
hitchhiking, genetic, –
HIV (human immunodeficiency virus)
cause of AIDS, ,
and chemokine receptor CCR,
–,
court case,
rapid evolution, ,
use of RNA and reverse transcriptase,
HLA (human leukocyte antigen system),
–
Homer,
Homo erectus, –
Homo floresiensis, –,
homology,
Homo neanderthalis. See Neanderthal
Homo sapiens, , –, , ,
,
Hoss, Matthias,
Huey, Raymond,
human immunodeficiency virus. See HIV
human leukocyte antigen system. See HLA
Huxley, Thomas, ,
hypothesis, , , , , , , ,
, , ,
cooking hypothesis, – (see also
Neanderthal)
Coppinger’s hypothesis about dog
evolution, –
definition,
multiregional versus out-of-Africa,
null, –
phylogenetic trees as hypotheses, –,
,
testing, –
versus theory,
icefish, –
Iceland,
immune system, , , , , .
See also HLA
HIV/AIDS, ,
insect,
influenza
avian (HN), –
Bush plan, ,
hemagglutinin,
pandemic,
Ingram, Vernon,
Inherit the Wind (film, play),
Intelligent design (ID), –, , ,
–, . See also creationism
court cases, –, –
Discovery Institute and Wedge agenda,
–
irreducible complexity, ,
introns, , –
introns early versus introns late,
irreducible complexity, ,
Jackendoff, Ray,
Jefferson, Thomas, ,
Johnson, Philip,
Jones, Judge John E., , –
Jones, William,
Judson, Olivia,
Ju/’hoansi. See !Kung
Jukes, Thomas,
Khan, Genghis,
Kansas board of education, –, .
See also Intelligent Design
Katz, Laura,
KE family, –
Kennedy, Ted,
Kimura, Motoo, –, , , .
See also neutral theory
biographical information,
legacy, ,
King, Jack,
Index
Kinte, Kunta, ,
Kitzmiller et al. v. Dover Area School District
et al., , –. See also Intelligent
Design
Kitzmiller, Tammy,
Krauthammer, Charles, ,
Kreitman, Martin, –
Krings, Matthias, –
Kuiken, Thijs,
!Kung, , –
Lahn, Bruce, –,
language, , , , , –.
See also FOXP, Great Leap
Forward
click languages, –, –
defects, –
language evolution versus biological
evolution, ,
Neanderthal,
origins, , ,
Larson, Edward
Summer for the Gods,
Law and Order (television program),
legal system
comparisons to scientific reasoning, ,
Lehrer, Rabbi Michael,
Lewontin, Richard, ,
Lilith,
lineage, , , , , –, , , ,
, , , , , . See also
mitochondrial DNA, Y chromosome
of dogs, –
positive selection in human lineage, ,
–, –
linkage disequilibrium, , –
dogs, –
HLA/MHC,
Lysenkoism, ,
maize (corn, Zea mays), –
major histocompatibility complex.
See MHC
maladaptation, –,
malaria, –, . See also sickle cell
anemia
male-driven evolution,
Marks, Jonathan, –,
What It Means to Be Chimpanzee,
,
Maynard Smith, John,
Mayr, Ernst, , ,
McDonald, John, –
McDonald-Kreitman test, –, .
See also positive selection
McLachlan, Sarah,
McVeigh, Timothy,
Mellars, Paul,
Mendel, Gregor,
MHC (major histocompatibility complex),
–, . See also HLA
Miller, Geoffrey
The Mating Mind,
mitochondria, –, , , ,
DNA, –, , , –
mitochondrial Eve, –, . See also Y
chromosome Adam
confirmation of results, ,
criticisms of study, –
defined,
initial study, ,
and Neanderthals, –
seven daughters of Eve, –
term coined,
molecular clock, –, , , , , .
See also neutral theory
Monaco, Anthony,
Mountain, Joanna,
mutation, , , , , , , , , ,
, , , , . See also genetic
drift, negative selection, positive
selection
beneficial (adaptive), , –, , –
caused by transposable elements,
in computer evolution,
deleterious, , –, , , , ,
–
in dogs,
effect on genetic variation, , , –
in FOXP, ,
in HIV,
in influenza virus,
and intron evolution, –
and male-driven evolution,
in mitochondrial DNA, –,
and the neutral theory, , –, ,
,
replacement versus silent, –
natural history, ,
of genomes, , –
varying among different genes,
naturalism,
methodological versus philosophical,
natural selection, , , , , , –, ,
, , , , , , , , ,
–, . See also balancing
selection, evolution, genetic drift,
negative selection, positive selection,
sexual selection
acting as a reaper, (see also negative
selection)
action on replacement versus silent
substitutions,
Index
and aging, –
Behe’s acceptance of,
comparison with artificial selection, , ,
,
comparison with selection seen in Tierran
system,
distinction between natural selection and
evolution, –
and dog evolution, –
and eye evolution, –
lack of forethought,
requirements for natural selection, , –
Neafsey, Dan,
Neanderthal, –, , –, , ,
, ,
discovery, –
DNA, , –,
effective population size,
interbreeding with modern humans, ,
–
morphology, –, –
population genetics,
sialic acid composition,
negative selection, , –, , , –,
, , , , , , , .
See also balancing selection, natural
selection, positive selection
and genome size,
in humans and chimpanzees,
and Kimura’s neutral theory, –,
–, ,
strength of negative versus positive
selection, , , , , ,
neutral model for genome size evolution,
–
neutral theory (of molecular evolution),
–, , , , , , , . See
also genetic drift, Kimura
deviations from neutrality at CCR
regulatory region, –
and the McDonald-Kreitman test,
predictions, , ,
Nilsen, Richard,
Nilsson, Dan,
Occam’s razor (principles of parsimony),
occipital bone,
The Odyssey (Homer),
An Open Letter Concerning Religion and
Science, –
optic nerve. See eye
Orgel, Leslie,
Ostrander, Elaine, –
“Out of Africa,” . See also mitochondrial
Eve
Ovchinnikov, Igor,
Overton, William,
Pääbo, Svante
chimpanzee population genetics,
FOXP evolution,
Neanderthal DNA, –,
Paley, William,
Palumbi, Stephen,
The Evolution Explosion,
Parish, Amy,
Parker, Heidi,
Pauling, Linus
hemoglobin structure, –
molecular clock, –
PCR (polymerase chain reaction), , ,
–
P element, –. See also transposable
element
Pelger, Suzanne,
Pennock, Robert
Tower of Babel, , –
peppered moth (Biston betularia), –
PET (positron emission tomography), –
Petrov, Dmitri, –
Peters, Ted,
phenotype, –, , ,
phenylketonuria (PKU),
phylogeny, , , –, , , .
See also genealogy
dog,
gene tree versus species tree,
language,
maize,
reconstruction, –
Phytophthora infestans. See fungus
PKU. See phenylketonuria
plasmodium. See malaria
pleiotropy,
polymerase chain reaction. See PCR
polymorphism, –, , , , , ,
, , . See also genetic variation,
SNP
ancestral, –
and linkage disequilibrium, –
maintained under balancing selection, ,
–,
and the McDonald-Kreitman test, –
Pomiankowski, Andrew,
Pope Benedict XVI,
Pope John Paul II,
population size, , , , –.
See also effective population size,
genetic drift
of bonobos,
census versus effective, –,
of cheetahs,
and endangered species, ,
expansion in humans, ,
Index