The topology of the possible

Understanding Change: Models, Methodologies and Metaphors

Volumn , Issue , 2005, Pages 67-84

  Fontana, Walter ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85015863936     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1057/9780230524644_5     Document Type: Chapter

References (30)

1. Carroll, S. B., J. K. Grenier and S. D. Weatherfee (2001). From DNA to diversity. Maiden, Massachusetts, Blackwell Science.
2. Eigen, M. (1971). ‘Selforganization of matter and the evolution of biological macromolecules.’ Naturwissenschaften 58: 465-523.
3. Eldredge, N. and S. J. Gould (1972). ‘Punctuated equilibria: an alternative to phyletic gradualism.’ Models in Paleobiology. T. J. M. Schopf. San Francisco, CA, Freeman, Cooper & Co.: 82-115.
4. Fontana, W. and P. Schuster (1998a). ‘Continuity in evolution: on the nature of transitions.’ Science 280: 1451-5.
5. Fontana, W. and P. Schuster (1998b). ‘Shaping space: the possible and the attainable in RNA genotype-phenotype mapping.’ J. Theor. Biol 194: 491-515.
6. Gould, S. J. (2002). The Structure of Evolutionary Theory. Cambridge, MA, Belknap/Harvard University Press.
7. Griesemer, J. R. (2000). ‘Reproduction and the reduction of genetics.’ The Concept of the Gene in Development and Evolution: Historical and Epistemological Perspectives. P. Beurton, R. Falk and H.-J. Rheinberger (eds). Cambridge, MA, Cambridge University Press: 240-85.
8. He, L., R. Kierzek, Santa Lucia Jr, A. E. Walter and D. H. Turner (1991). ‘Nearest-neighbour parameters for G-U Mismatches.’ Biochemistry 30: 11124.
9. Huynen, M. A. (1996). ‘Exploring phenotype space through neutral evolution.’ J. Mol. Evol. 43: 165-9.
10. Huynen, M. A., P. F. Stadler and W. Fontana (1996). ‘Smoothness within ruggedness: the role of neutrality in adaptation.’ Proc. Natl. Acad. Sci. USA 93: 397-401.
11. Jaeger, J. A., D. H. Turner and M. Zuker (1989). ‘Improved predictions of secondary structures for RNA.’ Proc. Natl. Acad. Sci. USA 86: 7706-10.
12. Kimura, M. (1968). ‘Evolutionary rate at the molecular level.’ Nature 217: 624-6.
13. Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge, UK, Cambridge University Press.
14. Kirschner, M. and J. Gerhart (1998). ‘Evolvability.’ Proc Natl Acad Sci USA 95(15): 8420-7.
15. Mathews, D. H., J. Sabina et al. (1999). ‘Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.’ J. Mol. Biol. 288: 911-40.
16. Maynard-Smith, J., R. Burian, S. Kauffman, P. Alberch, J. Campbell, B. Goodwin, R. Lande, D. Raup and L. Wolpert (1985). ‘Developmental constraints and evolution.’ Quart. Rev. Biol. 60: 265-87.
17. Müller, G. B. and G. P. Wagner (1991). ‘Novelty in Evolution: Restructuring the Concept.’ Annu. Rev. Ecol. Syst. 22: 229-56.
18. Nimwegen, E. van, J. P. Crutchfield and M. Huynen (1999). ‘Neutral evolution of mutational robustness.’ Proc. Natl. Acad. Sci. USA 96: 9716-20.
19. Nussinov, R. and A. B. Jacobson (1980). ‘Fast algorithm for predicting the secondary structure of single-stranded RNA.’ Proc. Natl. Acad. Sci. USA 77(11): 6309-13.
20. Schultes, E. A. and D. P. Bartel (2000). ‘One sequence, two ribozymes: implications for the emergence of new ribozyme folds.’ Science 289: 448-52.
21. Schuster, P., W Fontana, P. F. Stadler and I. L. Hofacker (1994). ‘From sequences to shapes and back: a case study in RNA secondary structures.’ Proc. Roy. Soc. (London) B 255: 279-84.
22. Stadler, B. M. R., P. F. Stadler, G. Wagner and W Fontana (2001). ‘The topology of the possible: Formal spaces underlying patterns of evolutionary change.’ J. Theor. Biol. 213: 241-74.
23. Turner, D. H., N. Sugimoto and S. M. Freier (1988). ‘RNA structure prediction.’ Annual Review of Biophysics and Biophysical Chemistry 17: 167-92.
24. Waddington, C. H. (1942). ‘Canalization of development and the inheritance of acquired characters.’ Nature 3811: 563-5.
25. Wagner, A. (1996). ‘Does evolutionary plasticity evolve?’ Evolution 50(3): 1008-23.
26. Wagner, G. P. and L. Altenberg (1996). ‘Complex adaptations and the evolution of evolvability.’ Evolution 50: 967-76.
27. Walter, A. E., D. H. Turner, J. Kim, M. Lyttle, P. Muller, D. Mathews and M. Zuker (1994). ‘Coaxial stacking of helices enhances binding of oligoribonucleotides and improves prediction of RNA folding.’ Proc. Natl. Acad. Set 91: 9218-22.
28. Waterman, M. S. and T. R Smith (1978). ‘RNA secondary structure: A complete mathematical analysis.’ Mathematical Biosciences 42: 257-66.
29. Zuker, M. and D. Sankoff (1984). ‘RNA secondary structures and their prediction.‘Bull. Math. Biol. 46(4): 591-621.
30. Zuker, M. and P. Stiegler (1981). ‘Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information.’ Nucleic Acids Research 9: 133-48.