Ingenious Genes: How Gene Regulation Networks Evolve to Control Development

Index

Index Adaptive reactivity, 23, 67–69, 75 Average node perturbation effect, 60–62 Bateson, William, 11–16 Behe, Michael, 20 Canalizing functions, 49–53, 60, 63 Cell type, 42, 43, 48, 52, 65–68 Complexity accidental vs. expected, 37, 38, 43–46 adaptive developmental, 1–19, 110 evolutionary trend toward, 92–94 in gene regulation networks, 51–53, 91 genetic, 13–16, 53 gradual evolution, 7–9, 18, 29, 87, 95 irreducible, 20, 21 and robustness, 90–92 Condorcet’s jury theorem, 84 Control causal, 98–104 design, 98, 102–106 importance of understanding, 25, 97 Controller of development, 98, 100, 104–111 of a process, 104, 105, 106 of a system, 105, 106 Conway Morris, Simon, 43 Darwin, Charles, 6–10, 14, 15, 18, 21, 29, 38, 87 Darwin, Erasmus, 2, 3, 8, 14 Dawkins, Richard, 16–20, 108 Development, 2, 17, 18, 25, 26, 34–38, 43–46, 51–69, 110, 111 Evolvability, 18–22, 26, 29, 33, 34 Fisher, Ronald, 15 Gene centricism, 18, 21, 22, 108, 109 Gene expression profile, 25, 80, 84, 90, 111 Generative entrenchment, 93, 94 Gene regulation adaptive, 25, 80–88 connectionist framework, 59, 68–95, 98, 110, 111 deterministic modeling, 39–41 evolvability, 26, 46, 69, 79, 86–94, 108, 110 and organism development, 21, 22, 25, 26, 33–35, 86, 87, 107, 108 Gould, Stephen Jay, 17, 18, 43–46 Hurley, Susan, 98 Indicators, 77, 81, 87, 89, 95 Inheritance of acquired characteristics, 5, 10, 15 adding factors, 12 blending view, 9–12, 15 128 Index gain in knowledge, 16 Mendelian view, 10–16 unknown mechanism, 9, 13 Intelligent design, 20 Jenkin, Fleeming, 10, 15 Kauffman network, 38–42, 47–53, 58–62, 88, 89 Kauffman, Stuart, 26–68, 76, 79, 80, 85, 88–90, 94, 95 Krüppel regulation network, 70, 74, 75, 81, 86–89 Lamarck, Jean-Baptiste, 3–10, 14 Leclerc, Robert, 90–92 Lewontin, Richard, 18, 21, 29 Linear separability, 54, 78. See also Quantitative consistency Malthus, Thomas Robert, 7, 8 Maynard Smith, John, 108 McShea, Daniel, 46 Mendel, Gregor, 10–13 Methylation, 79 Modern synthesis, 16 Moss, Lenny, 107 Mutation continuity, 11, 12, 18, 21, 22, 25, 29–31, 34 random, 9, 19, 28, 73, 87 somatic, 79 NETtalk, 72, 73 Network accuracy, 67–69, 75–78, 82–88, 91, 92, 95 balance, 62–64, 67, 82–87 Boolean, 39–41, 47–51, 54, 81 complexity, 26–28, 32–35, 46, 47, 59, 80, 85, 88–95 generic, 31, 32, 38, 42, 89 learning, 71, 73, 74, 85 order, 38, 41–68, 76, 85 overfitting, 85 representation, 72–74, 85, 86 Origin of life, 2, 6, 14, 15, 44, 46, 68 Paley, William, 1, 2 Parity thesis, 109 Positional information, 70, 81, 86 Qualitative consistency, 54–63, 68, 78–84, 88, 89, 95, 110 Quantitative consistency, 54–61, 78–84, 88, 89 Quasi-independence, 18, 21, 22, 25, 29 Raeymaekers, Luc, 47, 62–64 RNA, 79 Robustness, 90–94 Selection gene as unit of, 16–18, 108, 109 pressures, 90–92 stabilizing, 90, 92 Sensitivity network, 60, 61, 62, 85, 88–90 microenvironment, 88, 89 Kauffman network, 61, 89 Sterelny, Kim, 19, 21 Training set, 73, 85 Transcription factor, 24, 40, 51–54, 57–59, 62, 63, 67, 68, 70, 76, 77, 93, 94, 105, 108, 110 Waddington, Conrad, 23–25, 110 Weismann, August, 15 Wray, Gregory, 33, 52, 62, 63 Inheritance (cont.) ...