Conceptual and methodological biases in network models

Annals of the New York Academy of Sciences

Volumn 1178, Issue , 2009, Pages 291-304

  Lamm, Ehud ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

Epigenetic inheritance; Evo devo; Evolutionary transitions; Variation; Weak linkage

Indexed keywords

CELLULAR, SUBCELLULAR AND MOLECULAR BIOLOGICAL PHENOMENA AND FUNCTIONS; CONFERENCE PAPER; EPIGENETICS; GENETIC VARIABILITY; MOLECULAR EVOLUTION;

EID: 70350444934     PISSN: 00778923     EISSN: 17496632     Source Type: Book Series    
DOI: 10.1111/j.1749-6632.2009.05009.x     Document Type: Conference Paper

References (42)

1. Shapiro, J.A. 2002. Genome organization and reorganization in evolution: Formatting for computation and function. Ann. N. Y. Acad. Sci. 981: 111-134.
2. Shapiro, J.A. 2006. Genome informatics: The role of DNA in cellular computations. Biol. Theor. 1: 288-301.
3. Bechtel,W. 2008. Mental Mechanisms: Philosophical Perspectives on Cognitive Neuroscience. Routledge. New York.
4. Wilkins, A.S. 2005. Recasting developmental evolution in terms of genetic pathway and network evolution. . . and the implications for comparative biology. Brain Res. Bull. 66: 495-509.
5. Kellis, M., B.W. Birren & E.S. Lander. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
6. Olson, E.N. 2006. Gene regulatory networks in the evolution and development of the heart. Science 313: 1922-1927.
7. Oliveri, P. & E.H. Davidson. 2007. DEVELOPMENT: Built to run, not fail. Science 315: 1510-1511.
8. de Silva, E. & M.P.H. Stumpf. 2005. Complex networks and simple models in biology. J. R. Soc. Int. 2: 419-430.
9. Keeling, P.J. & J.M. Archibald. 2008. Organelle evolution: What's in a name? Curr. Biol. 18: R345-R347.
10. Lane, C.E. & J.M. Archibald. 2008. The eukaryotic tree of life: Endosymbiosis takes its TOL. Trends Ecol. Evol. 23: 268-275.
11. Bhattacharya, D. et al. 2007. How do endosymbionts become organelles? Understanding early events in plastid evolution. BioEssays 29: 1239-1246.
12. Kiers,E.T. et al. 2003. Host sanctions and the legumerhizobium mutualism. Nature 425: 78-81.
13. Martinez-Zapater, J.M. et al. 1992. Mutations at the arabidopsisCHMlocus promote rearrangements of the mitochondrial genome. Plant Cell. 4: 889-899.
14. Lamm, E. & E. Jablonka. 2008. The nurture of nature: Hereditary plasticity in evolution. Phi. Psych. 21: 305-319.
15. Doolittle, W.F. & E. Bapteste. 2007. Inaugural article: Pattern pluralism and the tree of life hypothesis. Proc. Natl. Acad. Sci. USA 104: 2043.
16. Goldenfeld, N. & C.Woese. 2007. Connections biology's next revolution. Nature 445: 369.
17. Lopez-Maury, L., S. Marguerat & J. Bahler. 2008. Tuning gene expression to changing environments: Fromrapid responses to evolutionary adaptation. Nat. Rev. Genet. 9: 583-593.
18. Kitano, H. & K. Oda. 2006. Self-extending symbiosis: A mechanism for increasing robustness through evolution. Biol. Theor. 1: 61-66.
19. Rosenberg, E. et al. 2007.The role of microorganisms in coral health, disease and evolution. Nat. Rev. Micro. 5: 355-362.
20. Nicholson, J.K., E. Holmes & I.D. Wilson. 2005. Gut microorganisms, mammalian metabolism and personalized health care. Nat. Rev. Micro. 3: 431-438.
21. Xu, J. & J.I. Gordon. 2003. Inaugural article: Honor thy symbionts. Proc. Natl. Acad. Sci. USA 100: 10452-10459.
22. Hooper, L.V. et al. 2001. Molecular analysis of commensal host-microbial relationships in the intestine. Science 291: 881-884.
23. Nicholson, J.K. & I.D. Wilson. 2003. Understanding 'global' systems biology: Metabonomics and the continuum of metabolism. Nat. Rev. Drug Discov. 2: 668-676.
24. Nicholson, J.K. et al. 2004. The challenges of modeling mammalian biocomplexity. Nat. Biotech. 22: 1268-1274.
25. Jablonka, E. 2004. From replicators to heritably varying phenotypic traits: The extended phenotype revisited. Biol. Phil. 19: 353-375.
26. Davidson, E.H. et al. 2002. A genomic regulatory network for development. Science (New York, N.Y.) 295: 1669-1678.
27. Zuckerkandl, E. & G. Cavalli. 2007. Combinatorial epigenetics, "junk DNA", and the evolution of complex organisms. Gene 390: 232-242.
28. Ptashne, M. 2008. Transcription: A mechanism for short-term memory. Curr. Biol. 18: R25-R27.
29. Zacharioudakis, I., T. Gligoris &D. Tzamarias. 2007. A yeast catabolic enzyme controls transcriptional memory. Curr. Biol.: CB 17: 2041-2046.
30. Zordan, R.E., D.J. Galgoczy & A.D. Johnson. 2006. Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop. Proc. Natl. Acad. Sci. USA 103: 12807-12812.
31. Griesemer, J. 2000. Development, culture, and the units of inheritance. Phil Sci. 67: S348-S368.
32. West-Eberhard, M.J. 2003. Developmental Plasticity and Evolution. Oxford University Press. New York.
33. Gerhart, J. & M. Kirschner. 2007. The theory of facilitated variation. Proc. Natl. Acad. Sci. USA 104(Suppl 1): 8582-8589.
34. Arnold, M.L. 1997. Natural Hybridization and Evolution. Oxford University Press. New York.
35. Arnold, M.L. 2006. Evolution Through Genetic Exchange. Oxford University Press. Oxford, New York.
36. Pfennig, K.S. 2007. Facultative mate choice drives adaptive hybridization. Science 318: 965-967.
37. Maynard-Smith, J. & E. Szathḿary. 1995. The Major Transitions in Evolution. WH Freeman. Oxford.
38. Jablonka, E. & M.J. Lamb. 2006. The evolution of information in the major transitions. J. Theor. Biol. 239: 236-246.
39. Chung, W.-J. et al. 2008. Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr. Biol. 18: 795-802.
40. Gu, X., Z. Zhang & W. Huang. 2005. Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc. Natl. Acad. Sci. USA 102: 707-712.
41. Zilber-Rosenberg, I. & E. Rosenberg. 2008. Role of microorganisms in the evolution of animals and plants: The hologenome theory of evolution. FEMS Microbiol. Rev. 32: 723-735.
42. Grewal, S.I.S. & S. Jia. 2007. Heterochromatin revisited. Nat. Rev. Genet. 8: 35-46.