Index

actualism, 42, 52

adaptation, xxxi, 10, 13, 28, 34, 50, 92, 98; basis of, 37; biological, xix, xx, 41; definitions of, 56n7; ecological, 35, 45, 56n15, 57n15; evolutionary, 45, 51, 57n15; framework, 29, 41, 44, 48, 52; functional, 33, 37, 41, 44; heuristics and, 11; inference, 32, 49; proxy by, 37–38; structures, 14, 15

Adler, Mortimer J., 66–68

aetiology, 217, 218

affordances, 86, 88–89, 92, 102, 108, 110n1

aggression, 122, 137 (fig.), 138, 140

allopatric speciation, 243

alternative splicing, 160–61

Alzheimer’s disease, 231n14

amino acids, 13, 160, 169, 174n4, 175n15

Andersen, Holly, 86

Angraecum sesquipedale, 55n1

Antarctic fur seal (Arctocephalus gazella), 123

Antennapedia genes, 197

anti-realism, realism and, 55

ants (Cataglyphis), navigation by, 94

architecture: biological, 3, 4, 6, 8; causal, 213, 214 (fig.), 220, 221, 223, 224, 225, 228; common genetic, 221; structural, 44

Arias, A. M., 193

Arrhenius, Svante, 63

Aspen Institute, 66

Aufbau (Carnap), 65, 71, 80n8

autism spectrum disorder, 221

Autzen, Bengt, 203n15

Avigad, Jeremy, 14

bacteria, 126, 128, 134, 196, 197, 230, 242

Baum, D., 258

Bausman, William, viii, x, xxxi

Baxter, Janella, viii, xiv, xxxiv–xxxv, 203n15

Bechtel, W., 28, 87, 106

beetles, phenotypes of, 128

behavior, 106, 131, 140; animal, 21n2, 94; brain and, 228; computer simulations of, 22n6; human, 21n2, 22n6; methodological, 20–21; psychological, 250; withdrawal, 203n13

Bennett, Karen, 79n2

Bergson, Henri, xxxii; Carnap and, 68–76; Einstein and, 63, 68, 71, 72, 80n7, 80n9, 80n14; metaphysics and, 64, 66, 75; microbes and, 73; mind and, 68–70; philosophical intuition and, 71; on positive science, 68–69; psychological determinations and, 75; scientific theories and, 70; visceral conviction of, 70; vitalism of, 72

Bergstrom, C. T., 86, 93

biases, 9, 166; cognitive, 10; systematic, 18

big data, impact of, 20

biochemical processes, 157, 160, 174n6

biological functions, 3, 108, 201

biological information, xxxiii, 86, 88, 94, 95, 105, 108, 110; biological systems and, 106; substantive account of, 87

biological phenomena, xxvii, xxxiii, 85–86, 88, 94, 107–8, 182; attributing information to, 106; coordination and, 106

Biological Species Concept (BSC), 245, 246, 252, 254, 258

biological systems, xxxii, 84, 85, 161; complexity of, vii, xxxvii; functional, 109

biology, vii, xxiv, xxv, 20, 29, 30, 49, 51, 53, 54, 67, 123, 128, 161, 221, 243, 244; behavioral, 199; causal reasoning in, xxvi, xxvii; causal/physical aspects of, 84; cell, 121; classical, xxxiv, 198; complexity of, 12; contemporary, 153, 159; coordination functions in, 105–9; determinism/essentialism in, xv; digital ontologies in, xvii; epistemic practices of, 118; evolutionary, xviii, 117, 199; information in, 86; phenomena of, 83; relationships in, 90; special status in, 157; transformation of, 38, 183. See also developmental biology; molecular biology

biomedicine, xxvi, 167, 211, 212, 228

biomolecules, xxxv, 157, 165, 169

bipolar disorder, 221

Bird, A., 239, 244, 251, 252

Blasi, Damian, 53

blastomeres, 186, 202n6

bone morphogenic proteins (BMPs), 195

Boyd, R., 246, 257

brachydonts, 30, 55n5, 56n14

breast cancer, 231n13

bridge principles, 182, 201n3

Bridgman, P. W., 192

BSC. See Biological Species Concept

CAG (cytosine-adenosine-guanine) repeats, 170

calibration, 8, 33, 47, 96, 98, 99

Campbell, Donald, 3, 8, 17, 22n5

Canadian permanent resident, 248, 250

Canis familiaris, 256

Carnap, Rudolf, xxxii, 53, 57n20, 79n1, 80n8; Adler and, 66–68; Bergson and, 68–76; metaphysics and, 64–65, 66, 69, 76, 79; philosophy and, 71, 77, 78

Cartwright, Nancy, 2, 154, 156, 173

Casey, B. J., 228

“Categorical Bottleneck” (Franklin-Hall), 240

causal action, 125; level of, 218–19

causal chains, 202n10; intervention in, 89 (fig.)

causal complexity, xxxvii, 209, 210–11, 213, 214, 218, 220, 221, 223, 228; types of, 214 (fig.), 230n11

causal dependence, 199, 249, 260n3

causal explanation, xxv, 211, 218

causal factors, 217, 222, 224, 225, 241; identifying, 219; manipulation of, 215

causal homogeneity, 213, 220, 223

causality, xxv, xxvi, xxxii, 102, 109, 157, 213, 215; developmental, 188; guides, 88; interventionist framework for, 93; meaning of, 91; notion of, xxv–xxvii; understanding, 90

causal kinds, 241, 242, 243, 244

causal power, 92, 193, 197, 198, 230n9

causal processes, 89, 96, 103, 125, 210, 212, 227; higher-level, 219; single, 219

causal reasoning, xxvi, 94, 95, 102, 109–10, 244, 245; control/intervention and, 88–92; functional account of, 254

causal relationships, 89, 90, 93, 95, 99–100, 101, 102 (fig.), 103–4, 103 (fig.), 108, 131; intentionality and, 96

causal role, 194, 199, 203n13

causal specificity, 86, 90, 108, 202n9

causation, xxvii, 107, 108, 215; disease, 211, 212, 225–28; information and, 102, 102 (fig.), 105, 109; interventionist account of, xxvi, 87, 88, 110n1

cDNA, 196, 197, 198

CEE. See classical experimental embryology

cell differentiation, 181, 185

Chang, Hasok, xxiii, xxiv, 44, 57n17, 203n14; scientific realism and, xxi

chemistry, classificatory practices in, 244

Chen, Reuy-Lin, 57n22

Cheng, P. W., 230n9

chicken pox, 214, 230n7

Chomsky, Noam, 14

chromosomes, 158, 163, 183, 191, 192, 197

cis-regulatory sequences, 163, 164, 166, 172

cladists, 258

classical experimental embryology (CEE), 184, 190, 194, 195; knowledge of, 185–89; molecular developmental biology and, 181

classification, xix, xxvii–xxx, xxxviii, 18, 213, 227, 239, 240; constructing, 237; disease, 211, 226–27; function of, 254, 260n1; grounding, 258–59; natural, 237, 258, 259; nonarbitrary, 259; nonnatural, 258; pathological, 259; practices, 237, 241, 244, 256, 259, 260; programs, 245, 247, 248, 255; schemes, xxxvii–xxxviii; scientific, xxvii, xxix, xxxvii, 252, 259, 260

climate change, 29, 30

coding, 83; molecular, 154, 155, 156, 159, 160, 161, 163, 164, 167, 171, 174n3, 174n7; qualitative, 119; sequences, 160, 165, 167. See also protein coding genes

codons, 159–60

Collaboratory Research Centre (CRC), xxxiv, 119, 121, 123, 124, 125, 127, 130, 131, 133, 141–42; explanatory practices of, 136; NC3 mechanisms and, 128; strategies of, 120

Collier, J., 86

common buzzards (Buteo buteo): environmental conditions and, 139; niche construction among, 138–39, 138 (fig.)

control, xxvi, 50, 98–99, 222; causal reasoning and, 88–92; conduit for, 105 (fig.); coordination and, 102–5; fine-grained, 108

convergence, 44, 46–47; ecological adaptation and, 56n15; evolutionary, 36–37; trait, 46

Cooper, D. N., 217

coordination, xxix; chances of, 100; control and, 103–5; informational reasoning and, 93–109; problems, 84

CRC. See Collaboratory Research Centre

Creath, Richard, xxxii

Creative Evolution (Bergson), 80n7

Crick, Francis, 12

crystallin genes, 194

crystallography, 170, 171, 173, 174

culture, 13, 21; epistemic, 167; increasing complexity of, 12

Currie, Adrian, 54, 55n3

cystic fibrosis, 231n14

cytology, 183, 197

DAG. See directed analytic graph

Dalton’s system, xxii

Darwin, Charles, 34, 55n1, 70

Daston, Lorraine, xxvii–xxviii

data, 5, 33; classification of, xxix; collecting/interpreting, xix; correlation, 36; evaluating, 20; genomic, 153, 154, 165, 166, 173, 174; global, 30; information in, 30; models, 55n5, 96; representation, xxix; sharing/reusing, xxix

decision making, computer simulations of, 22n6

deductive argument, 6, 15, 18

De Robertis, Edward M., 196, 203n11

Descartes, René, 6, 15, 53, 80n12

determinism, xii, xv, xvi

developmental biology, xxxvi, 181–82, 193, 199, 200; advances in, 196; molecular, 189, 197, 201

Dewey, John, xxvi

Dhein, Kelle, 94, 106

Diagnostic and Statistical Manual of Mental Disorders (DSM), 227, 231n19

difference: individual, 130–36; principle, 189, 190, 192; sameness and, 71

directed analytic graph (DAG), 89; example of, 89 (fig.)

disease categories, 212, 226, 228

disease discovery, 225–28, 229, 229n2

diseases: causal framework for, 211–14; controlling, 216, 230n8; defining, 226; genetic, 171; heterogenous/homogeneous, 230n6; Mendelian, 214, 222; monocausal, 213, 214, 215, 216, 218, 220, 230n6; monogenetic, 174, 214; multicausal, 211, 213, 214–20, 230n6, 230n8; nonpsychiatric, 229; occurrence/nonoccurrence of, 215; “physical medicine,” 210; physical/somatic, 211; preventing, 216; single-gene, 214

disease traits, 222, 223, 224; defining, 225, 226

Disorder of Things, The (Dupré), xvi

dissociative personality disorder, 250

diversity, xxxvii, 12, 67, 162, 237, 259, 260; ecological, 35; genetic, 173; scientific, 52

DNA, 40, 41, 83, 159, 160, 161, 163, 164, 174n3, 183, 189, 196, 197, 198, 199; hybridization, 246; methylation, 203n13; replication of, 200

DNA Databank of Japan (DDBJ), 165

Dretske, F. I., 86, 104

Driesch, Hans, 185, 188, 202n6

Drosophila genes, 148n4, 196, 197, 201n5

DSM. See Diagnostic and Statistical Manual of Mental Disorders

Dupré, John, xv, xvi, 260n1

Duration and Simultaneity: With Reference to Einstein’s Theory (Bergson), 80n7

ecological selection, 36, 57n15

ecology, xxxii, 12, 45, 29, 116, 117, 130, 135, 142; behavioral, 117; evolutionary, 117; mechanisms in, 121, 141

ectoderm, 195, 202n8

effect size, concept of, 216

Einstein, Albert, xxxii, 57, 64, 70; Bergson and, 63, 68, 71, 72, 80n7, 80n9, 80n14; psychological/physical and, 74; stopping time and, 72; theory of relativity of, 63

ejaculate, 123, 128, 137 (fig.), 138, 140

Elliott, Steve, 80n14

Ellis, B., 239

embryology, 192, 193, 195, 198, 199. See also classical experimental embryology

embryonic axis, 194, 195–96

embryonic cells, 186, 196, 203n19

embryos, 184, 185, 186, 187, 195, 200; dorsalized, 197; ventralized, 196–97

empirical studies, 19, 72, 131, 250

“Empiricism, Semantics, Ontology” (Carnap), 65

Engineer’s Illustrated Thesaurus (Herkhimer), 11, 14

Entwicklungsmechanik, 185, 186

environment, 9, 28, 33, 52, 106, 117, 118, 159; abiotic/biotic, 121, 127, 139; changes in, 32, 122, 131, 148n3; external, xix; genetics and, 191; individual and, 130, 135, 143; nonsocial, 140; organisms and, 29–37, 123, 126; phenotype and, 124, 125–30, 133, 134, 137, 140, 142; physical, 53; social, 122, 131; systems and, 17; water and, 34

environmental factors, 47, 133, 134, 216, 221

epidermis, 186, 188, 189, 193, 194, 195

epistemic agents, 240, 241

epistemic aims, 238, 242, 245, 247, 254, 260

epistemic reasons, 244, 247, 248

epistemology, x, xviii, xxx, 1, 2, 3, 21, 38, 40, 85, 95, 173; evolutionary, 51, 57n23; metaphysics and, xix, xx; science and, xx, 27; social, xviii

Ereshefsky, Marc, 87, 237; classification systems and, xix, xxix; ICW and, 92; natural kinds and, xxxvii–xxxviii; sex categories and, xxiv

error, 1, 4, 9, 22, 63, 70; localization of, 14; metabolism of, 5, 17–21; notion of, 101; reduction of, 8

essentialism, xv, xvi, 238

etiology, 210, 218, 229, 229n3, 231n20; causal, 209, 211–12, 213, 219, 220, 221, 223, 224, 225, 226, 227; disease, 217, 221; shared, 220; symptoms and, 212; unambiguous, 212

“Euclidian” methodology, 6

Euclid’s geometry, 14

eukaryotes, 160, 164

European Molecular Biology Laboratory (EMBL), 165

Everett, Caleb, 53

evolution, 2, 29, 45, 116, 117, 141, 254; cumulative, 7; process, 4, 11, 12

Experimentelle Beiträge (Spemann), 202n8

experiments, 9, 40, 173; counterfactual, 90–91; transplantation, 194

explanatory practices, 49, 181, 183, 224, 236; diverse, 125–26

exportation model, 48, 49

fallibility, 2, 5, 8, 15, 21

Feest, U., 203n14

Feynman, Richard, 6, 7

fire salamanders (Salamandra salamandra), 117, 122, 136, 139, 140; niche choice mechanism in, 139 (fig.)

fitness, 51, 118; changes in, 125–30; ecological, 127; evolutionary models of, 44; gradient, 134; phenotype-environment, 133, 134, 142

fluorescence, 169, 170

focal activities, 118, 121–22, 127, 136, 137 (fig.), 138, 138 (fig.), 139, 139 (fig.), 140, 141, 143

Forman thesis, 57n24

Fortelius, Mikael, 30, 32–33, 34, 35

foundationalism, 12–15, 17, 21; absolute, 15; deductive, 5, 14; dynamic, 15; naturalistic, 15

fractals, 38, 43

Franklin-Hall, L., 240–41

fruit fly (Dropsophilia melanogaster), 132

functionality condition, 245, 254, 255, 260

fungi, 128, 134

Fushi tarazu genes, 197

Galileo, 6

gastrulation, 186, 196

GenBank, xxii, 153, 175n12; classificatory schemes, 167; database, 155, 167; gene concept, xxxv, 155, 163–68, 173; individuation/annotation practices of, 166

gene concept, 29, 45, 46, 154, 156, 158, 163–68, 175n9; classical, 155, 192; coding, 163, 165; molecular, 163; postgenomic, 165

generalizations: laws versus, 4–5; sloppy, gappy, 4, 11

general structure thesis, xxxi, 38, 40, 48, 198

generative entrenchment, 11–12, 12–15, 21

genes, xxviii, 154, 157, 160, 161, 219; classical, 158, 191, 193, 194; detecting, 192; protein-coding, 199; purple/red, 158

genetic code, 12, 13, 160

genetic factors, 214, 216, 218, 222, 229n4

genetics, 10, 28, 38, 116, 156, 216, 219, 253; characterizing, 154; classical, 16, 40, 153, 158–61, 181–85, 189–92, 194, 197, 198, 199, 201; dappled world of, 171–74; differences in, 158, 189; environment and, 191; molecular, xv, xxxv, 40, 154–55, 157, 161, 168, 175n8, 190, 212; population, 16; practice of, 45; psychiatric, 210

gene variants, 213, 217, 219, 221, 222, 229n4

genome-wide association studies (GWAS), 210, 212, 213, 217, 218; expectations of, 221

genotypes, 16, 102, 148n5, 216–17

geometry, 78, 107

GFA. See Grounded Functionality Account

Giardia parasite, 230n7

giardiasis, 214

Gigerenzer, G., 22n6

Gillet, Carl, 48, 57n20

Glymour, C., 7

“God and the Professors” (Adler), 67, 68, 79n5

Gödel, Kurt, 71

Goldstein, D. B., 218, 219

goosecoid, 196

Gould, Stephen J., 11, 56n7

greenery, 116; gathering/adding, 138 (fig.), 139, 140

green fluorescent protein, gene for, 173

Griffiths, Paul, 86, 90, 108, 165

Grounded Functionality Account (GFA), xxxvii, 87, 237, 238, 246, 247, 248–49, 251, 255, 260n2, 260–61n3; language of, xxxviii; local metaphysics and, 252; of natural kinds, 245; virtues of, 259–60

grounding: conditions, 251, 252, 253–55, 256, 257, 258–59, 260, 261n4, 261n7; metaphysical, 85, 253, 261n3

Gunter, P. A. Y., 70, 80n9

GWAS. See genome-wide association studies

Hacking, Ian, 27, 256, 258, 259, 261n7; looping kinds and, 249; natural kinds and, 237, 257; pessimism of, 260; slogan of, 27

Harland, Richard M., 196, 197

harmonic-equipotential system (harmonisch-aquipotenzielles System), 185–86

Harper, Douglas, 11–12

harvester ant (Pogonomyrmex californicus), 122

Haslanger, Sally, xxiv

Havstad, Joyce, 154

Hawley, K., 239

HD. See Huntington’s disease

hedgehog signaling molecule (SHH) gene, 166

Hegel, G. W. F., 66

herbivores, 31, 32, 34–36; hypsodonty in, 30, 36; populations of, 36; teeth of, 35

heredity, 10, 28, 29, 40, 45, 51, 217

Herkhimer, H., 11, 14

heterogeneity: allelic, 231n15; causal, 211, 213, 220–25, 228, 229, 230n6; etiologic, 221, 230n13; locus, 231n15

heterogeneous causes, 225; causal relevance and, 222–23, 224

heuristics, xxx–xxxi, 6, 14, 17, 18, 19, 20, 198; adaptations and, 11; application of, 10; cost-effective, 9; descent of, 10; in nature/us, 8–11; progressive, 15

Hitler, Adolf, 68

homologs, 46, 194, 196

homology, 164

horse molars, fossilized, 31 (fig.)

how possible, described, 44–45

Hoy, Ronald, 80n14

Hoyningen-Huene, P., 203n12

Human Genome Project, 164

Hume, David, xiii, 92

humidity, 29, 30, 32, 33, 53; teeth of ungulates and, 42

huntingtin gene, 170, 171, 216, 230n7; presence/absence of, 170

Huntington’s disease (HD), 156, 170, 171, 214, 216, 230n6

Hutchins, Robert M., 68

Hyman, S. E., 226

hypotheses, 30, 56n6, 189, 200, 250; adaptation, 32, 41, 46, 49, 51; alternative, 28; explanatory power of, 49; metaphysical, 44, 48; valid, 57n24

hypsodonty, 30, 31 (fig.), 33, 55n5; as adaptation, 32, 34; community and, 36; increase in, 31, 34–36; as paleoprecipitation proxy, 37

IBE. See inference to the best explanation

ICW, 88, 89, 101–2; causality and, 90, 92, 93, 108; control and, 98; ideal interventions and, 97; interventions and, 99–100, 109

ideal interventions, xxxiii, 89, 99, 99 (fig.), 102

individual, 117; environment and, 130, 135, 143

inference, 33, 39, 48–50; abductive, 49, 56n6, 57n21; biological architectures and, 8; exportation, 48; gene structure, 41; teeth-water, 31–32

inference to the best explanation (IBE), xiii, 49, 54, 55n6, 56n8, 57n21

information, xxxii, 85, 88, 101, 107; analysis of, 109; causation and, 86, 92, 102, 102 (fig.), 104, 105; complementary account of, 93; concept of, xxvii, 85, 87; conduit for, 96, 105 (fig.); encoding, 155; gathering, 1, 5, 97; genomic, 165, 166, 167; MTC and, 102; notion of, 103, 105, 108, 109; positional, 106; probabilistic, 89; readout and, 97; as representation, 96; semantic, 94; sources of, 100; treatment of, 87; using, 95, 102, 103, 104. See also biological information

informational reasoning, 88, 109–10; coordination/observation and, 93–103

inheritance, 159, 162, 183; patterns of, 157; principles of, 158

Insel, T. R., 229n3

interactions, 5, 219, 257; literal reading of, 148n2; social, 21

interbreeding, 158, 239, 254

interpretive problem, described, 64–65

intervention, 50, 93; causal reasoning and, 88–92; counterfactual, 90; hypothetical, 91, 92; ideal, 89, 91, 97, 109

interventionism, xxvi, xxvii, 89; motivation for, 88

Introduction to Metaphysics, An (Bergson), 68–69

intuition, xii–xiii, xxviii, 69, 98, 223, 238, 239; conflicting, 97; philosophical, xxxii, 70, 71, 73, 75, 77, 78; platonic, 71

Ismael, Jenann, 88, 102, 110n1

Israel-Jost, V., ix

Jacob, François, 10, 163

John Templeton Foundation, viii

Journal of Language Evolution, 53

Kahneman, D., 22n6

Kaiser, Marie, xxii, xxxiii–xxxiv

Kant, Immanuel, 53, 71, 80n8

Kendler, K. S., 216, 230n10

Khalidi, M. A., 241

Kight, C. R., 86

Kim, Jaegwon, xxxv–xxxvi, 181, 191, 194, 195, 199; explanatory reduction and, 184; molecular biology and, xxxvi; multiple realization and, 203n13; reduction and, 190, 198

Kitcher, P., 183

knowledge, x, xx, xxiv, 85, 97; biological, 190; causal, 184; metaphysical, 52; production of, 96; theoretical, 192, 201

Kosso, Peter, 95, 96

Kripke, S. A., 198

Kuhn, Thomas, xi, xxi, 19, 48; normal science and, 204n21; views of, 15

Kukla, A., 249

lac operon mdel, 163

Ladyman, J., xiv, xvii, xxiii

Lakatos, I., 19

Laudan, L., 244, 245, 254

Lavoisier, Antoine, 74

laws: exceptionless, 4; generalizations versus, 4–5

Lean, Oliver, viii, xxvii, xxxii, xxxiii, 86

Leibniz, Gottfried Wilhelm, 21n1

Lenat, Douglas, 10

Leonelli, Sabina, 167

Levins, Richard, 7

Lewis, Warren H., 186

limb development protein 1 (LMBR1), 166

linear sequences, 40, 154, 155, 159, 160, 161, 163, 164, 165, 167, 170, 171, 172

linguistics, 47, 53, 54, 71, 75, 77, 84

lithium chloride (LiCl), 196, 197

load: A and, 99; readout and, 95, 95 (fig.), 97, 97 (fig.), 98 (fig.); value of, 98, 100

Locke, John, 51, 261n4

looping kinds, 249, 257

Love, Alan, viii, 3, 204n22

Lowe, E. J., xii, 239

Luce, Henry, 68

Ludwig, David, 237, 259, 260

Lynch, M., ix

Maddy, Penelope, xxxi, 53

Maidak, Bonnie L., 166

Maienschein, Jane, 80n14, 185

mammalian teeth, morphological research on, 55n2

Mangold, Hilde, xxxvi, 186, 187, 188, 193, 198; experiment by, 189, 202n7

manipulation, xxvi, xxxiii, 41, 44, 46, 91, 104, 172, 173, 181, 197, 198, 217, 230; experimental, 199

match: changes in, 125–30; phenotype-environment, 133, 134, 142

mathematical theory of communication (MTC), 96, 98, 102, 107

Mayr, E., 245, 246, 258

Meaning and Necessity (Carnap), 65

measurement, 7, 57, 74, 88; case of, 95–102; direct, 33; as representation, 96

mechanisms, xxv, xxvii, 14, 129, 181; biological, 112, 118, 121; construction, 41, 122, 123, 125, 126, 128, 131, 132 (fig.), 138, 138 (fig.), 142; ecological, 116, 117, 118, 120–23, 137, 141, 142; epigenetic, 121, 123; evolutionary, 1, 117, 118, 141; genetic, 120, 121; homeostatic, 256; hormonal, 121; individual-level, xxxiv, 116; molecular, xxxiii, 116, 120, 121, 124, 163, 182, 183; physiological, 121; term, 121, 125; transscriptonic, 121; understandings of, 125. See also niche choice/niche conformance/niche construction mechanisms

meiosis, 183

Mendel, Gregor, 16

Meno’s Paradox of Inquiry, 43

mental disorders, 210, 227

mermaids, term, 250

mesoderm, 197

mesodont, 30, 55n5

metaphysical claims, xvi, xxii, xxxiv, 27, 48

metaphysical discourse, vii, xiv, xvi

metaphysical features, 42, 47, 54

metaphysical problems, xvi, xxvii, 51, 261n3

metaphysical questions, xviii, xxiii, xxxi, 53, 236

metaphysics, vii, xxxi, 28, 40, 42, 43, 49, 118, 239; analytic, 238, 253, 260n3; approaches to, xii, xiii, xvii; biological practice and, xiv–xvi, 1; Carnapian, xxxii; definition of, xxvii, 69; doing, 76–79; interpreting, 65; nature of, xvii–xxv; ontology and, 76; realist, xxx, 48; rejection of, 64–65, 65–66; science and, xx, xxi, xxxii, 2–3, 29, 37, 42, 51, 52, 54; unifying theories and, xvii

methodologies, 1, 2, 3, 28, 48, 52, 228, 229, 244, 245; “Babylonian,” 6, 8; causation/information and, 109; heuristic, 15; inventing, 51; metaphysical, 47, 51; philosophical, 8, 17–21, 117; scientific, 8, 20, 54

mice (Mus musculus), 122

microbes, 73, 134, 241–42, 246

microbiology, 241, 242, 243, 246

microbiota, 122, 128

Mill, John Stuart, 242, 255

Millikan, R. G., 86

Miocene, 30, 31, 32

miscalibration, 96, 97, 98, 101

Mitchell, S. D., 230n11

molecular biology, xxxiv, xxxv, xxxvi, 13, 116, 124, 156, 161, 168, 182, 183, 194, 195, 219; causal webs and, 199–200; CEE and, 181; developmental biology and, 201

molecular gene concept, 40, 41, 44–45, 161, 168; alternative, 172; classificatory theories and, 173

molecular genes, xxxv, 153, 160, 161, 163, 164, 165, 167, 168, 192, 194, 198

monocausality, 213, 214, 215, 216, 219, 220; multicausality versus, 218

Monod, Jacques, 10, 163

Morgan, Thomas Hunt, 155, 158, 159

morphogenesis, 181, 194, 239, 240

Moss, Lenny: Gene-P/Gene-D distinction and, 175n9

mRNA, 159, 160, 163, 193, 195, 196, 197, 198, 200

MTC. See mathematical theory of communication

multicausality, 211, 213, 214–20, 228, 230n8; exhibits of, 229; monocausality versus, 218; understanding/explanation and, 219

mutations, 13, 35, 216, 224, 231n15

Nagel, Ernest, 189, 198

National Center for Biotechnology Information (NCBI), xxii, xxxv, 155, 173

National Institute of Health, 166

naturalism, 85, 86, 88; normative, 244–48, 254

natural kind classification, 237, 239, 240, 244, 245, 246, 247, 248, 251, 252, 253, 256, 257, 258, 260; functionality of, 254; necessary conditions of, 255

natural kinds, xxvii–xxx, xxxvii–xxxviii, 242, 247, 259; accounts of, 237, 238–44, 253, 254; grounding of, 251, 257; hierarchies of, 244; inductive, 243; interbreeding approach and, 240; mind-independence requirement of, 251; natural and, 238, 248–55; nonnatural kind and, 249, 250; philosophical research on, 255, 256, 260; skepticism about, 255–59; theories of, 236, 237, 238, 241, 244

natural selection, xxxiii, 5, 29, 30, 32, 33

nature, 237, 249, 251, 252; behavior of, 2; workmanship of, 261n4

NC3 mechanisms. See niche choice/niche conformance/niche construction mechanisms

NCBI. See National Center for Biotechnology Information

Neander, K., 86

nematode worm (C. elegans), 183

Neogene, 30

neural induction, 189, 194

Neurath, Otto: boat of, xx, 8, 15, 22n5

neurophysiology, 94

neuroscience, 116, 121

New Mechanists, 117, 123, 124, 125, 141

Newton, Sir Isaac, 54, 70, 72

niche choice, 116, 117, 121, 123, 127, 131, 133; characterizing, 124; construction and, 134; mechanisms for, 122, 125

niche choice/niche conformance/niche construction mechanisms (NC3 mechanisms), xxii, xxxiv, 116; abstract representation of, 129 (fig.); additional individuals and, 137, 138; change and, 134; commonalities between, 118; components of, 136–41; as constitutive mechanisms, 130; CRC and, 128; focal activities and, 139; general characterizations of, 141; individual differences and, 130–36; as individual-level mechanisms, 121, 123; introducing, 117, 119, 120–25; match/fitness and, 128; organism/environment and, 126; outcome of, 127; phenomena of, 129, 135 (fig.), 143; phenotypes and, 131–33, 141; project studying, 144–45 (table), 146–47 (table); understanding, 133, 136, 143

niche conformance, xxxiv, 116, 117, 121, 123, 127, 128, 133, 137; characterizing, 124; components of, 132 (fig.); mechanisms for, 122, 125, 132

niche construction, xvi, xxxiv, 116, 117, 121, 123, 127, 131, 133; buzzard, 138–39; characterizing, 124; mechanisms for, 122, 125

niches, 117, 136; ecological, 4, 130; individualized, 124, 125, 126, 130–31, 134, 135, 142, 148n6; social, 134, 137

Nickles, Thomas, 7, 22n6

NMR readings. See nuclear magnetic resonance readings

“No General Structure” (Waters), 38

noggin, 195, 196, 197, 200

non-causes, causes and, xxvi, 90

noncoding sequences, 160, 164, 167

nonepistemic aims, 238, 242, 247, 248, 260

nonnatural kind, 248; natural kind and, 249, 250

Novick, Rose, 49

nuclear magnetic resonance (NMR) readings, 169, 170, 171

nucleic acid, 154, 159, 169; bases, 156, 174n5; sequences, 155, 160, 161, 164, 165, 166, 174n7

observation, 71; empirical, 91; ideal, 95–102, 108, 109; informational reasoning and, 93–103

ontology, xxix, xxx, xxxiv, 1, 65, 79, 175n13; descriptive, 48; desert, 3; dualist, 51; internal, xxi, 48; metaphysics and, 76; realist versus antirealist, 50; theory/practice and, xxviii; ultimate, 48

operational concepts, 7, 87, 198; functional approach to reduction and, 189–94

operator genes, 163

organisms, 52, 53, 107, 108, 199, 243; environment and, 29–37, 123, 126; sexual, 246; transgenic, 196

organization, 8, 12, 21; analysis of, 16; biological, 7; functional, 3; social, 19

organizer, 187; term, 193, 202n9

Origin of the Species (Darwin), 34

ornithology, 54

Our Sunday Visitor, A Weekly Catholic National Newspaper, 79n5

“Overcoming Metaphysics Through the Logical Analysis of Language” (Carnap), 65–66, 79n4

paleobiology, 34, 41, 42

paleoecology, 29

paleontology, 30, 67

Panchen, A. L., 258

Paradox of Inquiry, 43

parental care, 137 (fig.), 138, 140

Parkinson’s disease, 221, 222, 225

pathogenesis, 218, 220

pathophysiology, 220, 221, 229n3

pathways, 219, 220; developmental, 256; final common, 224–25; genetic, 222; neural, 193, 195, 197

Paul, L. A., xii, xiii

Peirce, C. S., xiii, 87; abductive inference and, 49, 56n6, 57n21

perception, 74, 109–10

pheneticists, 246–47

Phenetic Species Concept, 246, 247

phenomena, 125, 134, 155, 194; coordination, 107, 110n4; epistemic, 85, 86; explaining, 184; physical, xxxiii, 84, 200; target, 141; types of, 172. See also biological phenomena

phenotype, 110, 118, 164, 167–68, 216–17, 221, 229n4; adaptive, 98; adjusting, 35, 122, 132, 139, 141; disease, 211; ecological interactions and, 130; environment and, 124, 125–30, 133, 134, 137, 140, 142; individual, 127, 130, 131–33, 140, 142

phenotypic differences, 155, 158, 190, 191

phenotypic traits, 7, 121, 127, 154, 159, 167, 172

phenylketonuria (PKU), 217, 218, 220, 229, 230n6

philosophical intuition, 70, 71

Philosophical Investigations (Wittgenstein), 17

philosophical literature, 127, 211, 237, 238

philosophical work, x, xvi, 121, 136, 237, 238, 256

philosophy, 53, 76, 241, 243, 244; analytic, xxvi, 17–18; conception of, 77, 78; history of, 21; metaphysics and, 65; methodologies of science and, 20; natural, 20; negative, 18; practice-oriented, xiv; science and, xi, 20, 67, 77, 78; systematic, 18, 68; traditional approach to, x

philosophy of biology, 120, 154

philosophy of science, ix–x, xi, xxiv, 153, 154; central task for, vii; empirical, 119; in practice, vii, ix, 119

Philosophy of Space and Time, The (Reichenbach), 65

phylogeny, 167, 258

Phylo-Phenetic Species Concept (PPSC), 242, 246, 252–53, 258; genetic markers and, 261n5; natural kind classification and, 254

physicalism, 14, 181

physics, ix, 6, 63, 173, 182; applied, xxvii–xxviii; fundamental, xv, xxiii, xxix

phytoliths, 33

Piatigorsky, J., 175n10

Piéron, Henri, 73, 74

PKU. See phenylketonuria

plasmids, 196, 197

pluralism, xxvii–xxx, 153, 168, 172; gene, 156–62; scientific, xxviii, xxxiv–xxxv, 154, 155, 156

Pluteus larva, 185

polycystic kidney disease, 231n14

PPSC. See Phylo-Phenetic Species Concept

practice turn, viii, ix–xii, 109

Pradeu, Thomas, 204n22

Price, H., 88

Project A02, 132

Project B05, 132

Project C01, 134

Project C04, 131

prokaryotes, 163, 164

Proofs and Refutations (Lakatos), 19

prospective fate (prospektive Bedeutung), 185

prospective potency (prospektive Potenz), 185

protein, 155, 172, 175n15, 199; classification, 154; fluorescent, 169; synthesis, 120, 159

protein coding genes, 154, 155, 159, 160, 161, 172, 173; biomolecules and, 170; explanatory scope of, 168–71; phenotypic traits and, 170

Protein Data Bank, 165

proxy, 48, 50, 53, 57n16; environmental, xxxi, 47; independent, 56n9; metaphysical, 47; variables, 29, 37

psychiatric disease, 210, 213, 224, 226, 229; etiologies of, 209, 227, 228; genetic causes of, xxxvi–xxxvii; intractable/enigmatic, 228; multicausality of, 218

psychiatry, 209, 210, 228, 229, 231n20

psychological, 20, 73, 74, 75, 250

Punnett square, 16

Putnam, H., 198, 238

quantum mechanics, 57n24

Quine, W. V., xxviii, 3, 20, 21, 76

Quine-Duhem hypothesis, 7

rDNA, 197

readout, 100, 101; A and, 99; information and, 97; load and, 95, 95 (fig.), 97, 97 (fig.), 98 (fig.), 99 (fig.)

realism, 50, 175n13; anti-realism and, 55; scientific, xvii–xxv, 2, 54, 76

reasoning, xxv, 55n1, 95; function of, 102; informational, 98, 108; kinds of, xxvii, 110; scientific, xxx, xxxii, 109

red flour beetles (Trilobium castaneum), 122, 134

reduction, xxxv, 5, 21, 181, 198, 199; diachronic, 182–90, 192; functional approach to, 189–94; inter-level, 182

Reichenbach, Hans, x, 65, 76

relationships: cause-effect, xxvi; dualistic perspective on, 104; feedback, 57n16; informational, 97 (fig.), 102 (fig.), 107, 108; logical/linguistic, 84; means-ends, xxx; probabilistic, 110n4; spatial, 107; statistical, 107, 110n2. See also causal relationships

research domain criteria (RDoC), 227–28

research programs, 28, 52, 136, 199

retinitis pigmentosa, 221, 225, 229, 231n14

Reydon, Thomas, 87, 237, 260n2; categorization systems and, xix, xxix; ICW and, 92; natural kinds and, xxxvii–xxxviii; sex categories and, xxiv

RNA, 155, 159, 161, 163, 169, 171, 172, 193, 196, 200, 246

Roberts, Seán, 53

Robinson, A., 86

robustness, xxiii, xxx, xxxi, 3, 4, 5–8, 11, 17–21, 32, 37, 41, 47, 50

Rosenberg, G., 86, 188

Rosenblatt, Frank, 21n3

Ross, Lauren, xiv, xvii; epistemic strategies and, xx; genetic causes and, xxxvi–xxxvii; on philosophy, xxiii

Rosvall, M., 86, 93

Rouse, Joseph, xvi

Roux, Wilhelm, 185, 202n6

Russell, Bertrand, xxv, 1, 5, 71

sameness, difference and, 71

schizophrenia, 221

science: allied, 28; analysis of, ix, 39–40; authority of, xxiii; biological, vii, xv, xxvi, xxviii, 83, 252; chemical, 252; cognitive, 86, 87; embryonic/immature, 209; empirical philosophy of, xi, 76, 77; epistemology and, xx, 27; experimental, 198; human, 4, 250; intellect and, 70; medical, 210, 244, 252; metaphysics and, vii, xvii, xx, xxi, xxiii, xxxii, 29, 51, 54, 84; natural, 4, 243; normal, 54; philosophy and, xi, 5, 20, 67, 78; physical, 3; positive, 68–69; practice-centered view of, 39; social, 244, 250, 252; structure of, 22n5, 54; tale of, 198–201; universality in, 223