Explanatory Integration Challenges in Evolutionary Systems Biology
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Alon U (2007) An introduction to systems biology: design principles of biological circuits. Chapman and Hall, Boca Raton
Amundson R (1994) Two concepts of constraint: adaptationism and the challenge from developmental biology. Philos Sci 61:556–578
Amundson R (2001) Adaptation and development: on the lack of common ground. In: Orzack SH, Sober E (eds) Adaptationism and optimality. Cambridge University Press, Cambridge, pp 303–334
Ashyraliyev M, Fomekong-Nanfack Y, Kaandorp JA et al (2009) Systems biology: parameter estimation for biochemical models. FEBS J 276:886–902
Beatty J (1995) The evolutionary contingency thesis. In: Wolters G, Bechtel W, Richardson RC (1993) Discovering complexity: decomposition and localization as strategies in scientific research. Princeton University Press, Princeton
Bechtel W, Richardson R (1993) Discovering complexity: decomposition and localization as strategies in scientific research. Princeton University Press, Princeton, New Jersey
Berlin I (1953) The hedgehog and the fox: an essay on Tolstoy’s view on history. Weidenfeld & Nicolson, London
Burian RM, Richardson RC (1990) Form and order in evolutionary biology: Stuart Kauffman’s transformation of theoretical biology. PSA 2:267–287
Cain CJ, Conte DA, García-Ojeda ME et al (2008) What systems biology is (not, yet). Science 320:1013–1014
Collins JP, Gilbert S, Laubichler MD, Müller GB (2007) Modeling in EvoDevo: how to integrate development, evolution, and ecology. In: Laubichler MD, Müller GB (eds) Modeling biology: structures, behaviors, evolution. MIT Press, Cambridge, pp 355–378
Craver C (2007) Explaining the brain: mechanisms and the mosaic unity of neuroscience. Clarendon, Oxford
Darwin C (1859) On the origin of species by means of natural selection. John Murray, London
Dawkins R (1976) The selfish gene. Oxford University Press, Oxford
De Vries H (1940) Species and varieties: their origin by mutation. Open Court, Chicago
Delbrück M (1949) Discussion. In Unités biologiques douées de continuité génétique. Editions du Centre National de la Recherche Scientifique, Paris
Depew DJ, Weber BH (1995) Darwinism evolving: systems dynamics and the genealogy of natural selection. MIT Press, Cambridge, MA
Enver T, Pera M, Peterson C, Andrews PW (2009) Stem cell states, fates, and the rules of attraction. Cell Stem Cell 4:387–397
Espinosa-Soto C, Martin OC, Wagner A (2011) Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits. BMC Evol Biol 11:5
Fagan MB (2012) Waddington redux: models and explanation in stem cell and systems biology. Biol Philos 27:179–213
François P (2012) Evolution in silico: from network structure to bifurcation theory. In: Soyer S (ed) Evolutionary systems biology. Springer, New York, pp 157–182
Goodwin B (1994) How the leopard changed its spots: the evolution of complexity. Phoenix, London
Goodwin B (2009) Beyond the Darwinian paradigm: understanding biological forms. In: Ruse M, Travis J (eds) Evolution: the first four billion years. Harvard University Press, Cambridge, MA, pp 299–312
Goodwin B, Kauffman S, Murray JD (1993) Is morphogenesis an intrinsically robust process? J Theor Biol 163:135–144
Gould SJ (1989) Wonderful life. Norton, New York
Haag ES (2007) Compensatory vs. pseudocompensatory evolution in molecular and developmental interactions. Genetica 129:45–55
Hochedlinger K, Plath K (2009) Epigenetic reprogramming and induced pluripotency. Development 136:509–523
Hogeweg P (2012) Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability. In: Soyer O (ed) Evolutionary systems biology. Springer, London, pp 195–223
Huang S (2009a) Non-genetic heterogeneity of cells in development: more than just noise. Development 136:3853–3862
Huang S (2011a) Systems biology of stem cells: three useful perspectives to help overcome the paradigm of linear pathways. Phil Trans R Soc B 366:2247–2259
Huang S (2011b) The molecular and mathematical basis of Waddington’s epigenetic landscape: a framework for post-Darwinian biology? BioEssays 34:149–157
Huang S, Ernberg I, Kauffman S (2009) Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective. Semin Cell Dev Biol 20:869–876
Jaeger J, Crombach A (2012) Life’s attractors: understanding developmental systems through reverse engineering and in silico evolution. In: Soyer O (ed) Evolutionary systems biology. Springer, London, pp 93–119
Jaeger J, Monk N (2010) Reverse engineering of gene regulatory networks. In: Lawrence ND, Girolami M, Rattray M et al (eds) Learning and inference in computational systems biology. MIT Press, Cambridge, MA, pp 9–34
Jaeger J, Monk N (2013) Keeping the gene it its place. In: Lambert D, Chetland C, Millar C (eds) The intuitive way of knowing: a tribute to Brian Goodwin. Floris Books, Glasgow, pp 153–189
Jaeger J, Monk N (2014) Bioattractors: dynamical systems theory and the evolution of regulatory processes. J Physiol 592:2267
Jaeger J, Sharpe J (2014) On the concept of mechanism in development. In: Minelli A, Pradeu T (eds) Towards a theory of development. Oxford University Press, Oxford, pp 56–78
Jaeger J, Surkova S, Blagov M et al (2004a) Dynamic control of positional information in the early Drosophila embryo. Nature 430:368–371
Jaeger J, Blagov M, Kosman D et al (2004b) Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics 167:1721–1737
Jaeger J, Irons D, Monk N (2012) The inheritance of process: a dynamical systems approach. J Exp Zool B 318:591–612
Kaneko K (2011) Characterization of stem cells and cancer cells on the basis of gene expression profile stability, plasticity, and robustness. BioEssays 33:403–413
Kaplan DM, Craver CF (2011) The explanatory force of dynamical and mathematical models in neuroscience: a mechanistic perspective. Philos Sci 78:601–627
Kauffman S (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22:437–467
Kauffman S (1970) Articulation of parts explanation in biology and the rational search for them. Proceedings of the Biennial Meeting of the Philosophy of Science Association, PSA, pp 257–272
Kauffman S (1993) Origins of order in evolution: self-organisation and selection. Oxford University Press, New York
Kauffman S (1995) At home in the universe: the search for laws of self-organization and complexity. Oxford University Press, New York
Kimura M (1985) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
Knight CG, Pinney JW (2009) Making the right connections: biological networks in the light of evolution. BioEssays 10:1080–1090
Koonin EV, Wolf YI (2010) Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet 11:487–498
Krakauer D, Collins JP, Erwin D et al (2011) The challenges and scope of theoretical biology. J Theor Biol 276:269–276
Lu R, Markowetz F, Unwin RD et al (2009) Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature 462:358–362
Lynch M (2007a) The evolution of genetic networks by non-adaptive processes. Nat Rev Genet 8:803–813
Lynch M (2007b) The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA 104:8597–8604
MacArthur BD, Ma’ayan A, Lemischka IR (2009) Systems biology of stem cell fate and cellular reprogramming. Nat Rev Mol Cell Biol 10:672–681
MacLeod M, Nersessian N (2013) Coupling simulation and experiment: the bimodal strategy in integrative systems biology. Stud Hist Phil Biol Biomed Sci 44:572–584
Manu SS, Spirov AV, Gursky VV et al (2009a) Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biol 7:e1000049
Manu SS, Spirov AV, Gursky VV et al (2009b) Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors. PLoS Comput Biol 5:e1000303
Mayr E (2005) What makes biology unique? Considerations on the autonomy of a scientific discipline. Cambridge University Press, Cambridge
Melton D, Cowan C (2009) Stemness: definitions, criteria, and standards. In: Lanza R, Gearhart J, Hogan B et al (eds) Essentials of stem cell biology. Academic Press, San Diego, pp xxii–xxix
Mjolsness E, Sharp DH, Reinitz J (1991) A connectionist model of development. J Theor Biol 152:429–453
Newman SA (1994) Generic physical mechanisms of tissue morphogenesis: a common basis for development and evolution. J Evol Biol 7:467–488
O’Malley M (2012) Evolutionary systems biology: historical and philosophical perspectives on an emerging synthesis. In: Soyer O (ed) Evolutionary systems biology. Springer, London, pp 1–28
Papp B, Notebaart RA, Pál C (2011) Systems-biology approaches for predicting genomic evolution. Nat Rev Genet 12:591–602
Pigliucci M (2010) Genotype-phenotype mapping and the end of the “genes as blueprint” metaphor. Phil Trans R Soc Lond B 365:557–566
Ramalho-Santos M, Willenbring H (2007) On the origin of the term “stem cell”. Cell Stem Cell 1:35–38
Riedl R (1978) Order in living organisms: a systems analysis of evolution. Wiley, Chichester
Salazar-Ciudad I (2006) On the origins of morphological disparity and its diverse developmental bases. BioEssays 28:1112–1122
Salmon W (1989) Four decades of scientific explanation. University of Minnesota Press, Minneapolis
Smith KC (1992) Neo-rationalism versus neo-Darwinism: integrating development and evolution. Biol Philos 7:431–451
Steinacher A, Soyer O (2012) Evolutionary principles underlying structure and response dynamics of cellular networks. In: Soyer O (ed) Evolutionary systems biology. Springer, London, pp 225–247
Strogatz SH (2000) Nonlinear dynamics and chaos. With applications to physics, biology, chemistry and engineering. Perseus Books, New York
Tachibana M, Amato P, Sparman M et al (2013) Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153:1–11
Thom R (1976) Structural stability and morphogenesis. Benjamin, Reading
True J, Haag ES (2001) Developmental system drift and flexibility in evolutionary trajectories. Evol Dev 3:109–119
van den Berg, Debbie LC, Snoek T et al (2010) An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 6:369–381
Waddington CH (1940) Organisers and genes. Cambridge University Press, Cambridge
Waddington CH (1957) The strategy of the genes. Taylor and Francis, London
Wagner A (2011a) Genotype networks shed light on evolutionary constraints. Trends Ecol Evol 26:577–584
Wagner A (2011b) The origins of evolutionary innovations: a theory of transformative change in living systems. Oxford University Press, New York
Webster G, Goodwin B (1996) Form and transformation: generative and relational principles in biology. Cambridge University Press, Cambridge
Yamanaka S (2009) Elite and stochastic models for induced pluripotent stem cell generation. Nature 460:49–52
Zenobi R (2013) Single-cell metabolomics: analytical and biological perspectives. Science 342:124325
Zhou JX, Huang S (2011) Understanding gene circuits at cell-fates branch points for rational cell reprogramming. Trends Genet 27:55–62