References

[1]
J. Ackermann, U. Tangen, B. Böddeker, J. Breyer, E. Stoll, and J. S. McCaskill. Parallel random number generator for inexpensive configurable hardware cells. CompPhyCom, 140:293-302, 2001. URL http://linkinghub.elsevier.com/retrieve/pii/S0010465501002429.
[2]
C. Adami and C. T. Brown. Evolutionary learning in the 2d artificial life system "avida". In R. Brooks and P. Maes, editors, Artificial Life IV, pages 377-381. MIT Press, Cambridge, MA, 1994.
[3]
S. Altmeyer and J. S. McCaskill. Error threshold for spatially resolved evolution in the quasispecies model. Phys. Rev. Lett., 86:5819-5822, 2001.
[4]
N. A. Barricelli. Symbiogenetic evolution processes realized by artificial methods. Methodos, 9:143-182, 1957.
[5]
N. A. Barricelli. Numerical testing of evolution theories part i theoretical introduction and basic tests. JournalActa Biotheoretica, 16:69-98, 1962.
[6]
G. J. Bauer, J. S. McCaskill, and H. Otten. Traveling waves of in vitro evolving RNA. Proc. Natl. Acad. Sci. USA, 86:7937-7941, 1989.
[7]
E. R. Berlekamp, J. H. Conway, and R. K. Guy. Winning Ways for Your Mathematical Plays. Academic Press, New York, 1982.
[8]
M. C. Boerlijst and P. Hogeweg. Spiral wave structure in pre-biotic evolution: Hypercycles stable against parasites. Physica D, 48:17-28, 1991.
[9]
M. Cohn and A. Lempel. On fast m-sequence transforms. IEEE Trans. Information Theory, 23:135-137, 1977.
[10]
A. K. Dewdney. Computer-Kurzweil. Spektrum der Wissenschaft, 10:8-11, 1988.
[11]
P. Dittrich, J. Ziegler, and W. Banzhaf. Artificial chemistries - a review. Artif. Life, 7:225-275, 2001.
[12]
R. Ehricht, T. Ellinger, and J. S. McCaskill. Cooperative amplification of templates by cross-hybridisation (CATCH). Eur. J. Biochem., 243:356-364, 1997.
[13]
M. Eigen. Selforganization of matter and the evolution of biological macromolecules. Z. Naturwissenschaften, 58:465-523, 1971.
[14]
W. Fontana. Algorithmic chemistry: A model for functional self-organization. In C. G. Langton, editor, Artificial Life II, pages 159-202. Addison-Wesley, Reading, Massachusetts, 1991.
[15]
W. Fontana, D. A. M. Konings, P. F. Stadler, and P. Schuster. Statistics of rna secondary structures. Biopolymers, 33:1389-1404, 1993.
[16]
R. Füchslin, T. Maeke, U. Tangen, and J. S. McCaskill. Evolving inductive generalization via genetic self-assembly. Adv. in Compl. Systems, 9:1-29, 2005.
[17]
R. Füchslin and J. S. McCaskill. Evolutionary self organization of cell-free genetic coding. Proc. Natl. Acad. Sci. USA, 98:9185-9190, 2001.
[18]
R. M. Füchslin, T. Maeke, and J. S. McCaskill. Multipolar reactive dpd: A novel tool for spatially resolved systems biology. CMSB 07 (arXiv:0705.1445v1), 2007. URL http://arxiv.org/abs/0705.1445. Preprint.
[19]
D. G. Gibson, G. A. Benders, C. Andrews-Pfannkoch, E. A. Denisova, H. Baden-Tillson, J. Zaveri, T. B. Stockwell, A. Brownley, D. W. Thomas, M. A. Algire, C. Merryman, L. Young, V. N. Noskov, J. I. Glass, J. C. Venter, C. A. Hutchison III, and H. O. Smitch. Complete chemical synthesis, assembly, and cloning of a mycoplasma genitalium genome. Science, 319:1215-1220, 2008.
[20]
W. Gilbert. Origin of life: The rna-world. Nature, 319:618, 1986.
[21]
S. W. Golomb. Shift Register Sequences. Holden-Day, San Fransisco, 1967.
[22]
J. H. Holland. Adaptation in Natural and Artificial Systems. University of Michigan Press, Ann Arbor, 1975.
[23]
J. H. Holland. Studies of the spontaneous emergence of self-replicating systems using cellular automata and formal grammars. In A. Lindenmayer and G. Rozenberg, editors, Automata, Languages, Development, pages 385-404. North Holland Publishing Company, Amsterdam, 1976.
[24]
J. H. Holland. A mathematical framework for studying learning in classifier systems. Physica D, 22:307-317, 1986.
[25]
S. A. Kauffman. Autocatalytic sets of proteins. J. Theor. Biol., 119:1-24, 1986.
[26]
N. Lahav. The rna-world and coevolution hypotheses and the origin of life - implications, research strategies and perspectives. Origins of Life and Evolution of the Biosphere, 23:329-344, 1993.
[27]
L. F. Landweber. Testing ancient rna-protein interactions. Proc. Natl. Acad. Sci. USA, 96:11067-11068, 1999.
[28]
A. Lazcano and S. L. Miller. How long did it take for life to begin and evolve to cyanobacteria. J. Mol. Evol., 39:546-554, 1994.
[29]
R. E. Lenski, C. Ofria, R. T. Pennock, and C. Adami. The evolutionary origin of complex features. Nature, 423:139-144, 2003.
[30]
R. E. Lenski, C. Ofria, R. T. Pennock, and C. Adami. The evolutionary origin of complex features. Nature, 423:139-144, 2003.
[31]
M. Levy and A. D. Ellington. Exponential growth by cross-catalytic cleavage of deoxyribozymogens. Proc. Natl. Acad. Sci. USA, 100:6416-6421, 2003.
[32]
J. S. McCaskill. Polymer Chemistry on Tape: A Computational Model for Emergent Genetics. Max-Planck-Society, Göttingen, Germany, 1988. Report.
[33]
J. S. McCaskill, S. Altmeyer, and R. M. Füchslin. The stochastic evolution of catalysts in spatially resolved molecular systems. J. Biol. Chem., 382:1343-1363, 2001.
[34]
B. McMullin. The Holland α-universes revisited. In F. J. Varela and P. Bourgine, editors, Toward a Practice of Autonomous Systems: Proceedings of the First European Conference on Artificial Life, pages 317-326. MIT Press, 1992.
[35]
L. E. Orgel. Molecular replication. Nature, 358:203-209, 1992. Review Article.
[36]
A. N. Pargellis. The spontaneous generation of digital "life". Physica D, 91:86-96, 1996.
[37]
A. N. Pargellis. Digital behavior in the amoeba world. Artif. Life, 7:63-75, 2001.
[38]
R. Pfeifer. "teaching powerful ideas with autonomous mobile robots". J. of Comp. Sci. Education, 7:161-186, 1997.
[39]
S. Rasmussen, J. A. Bailey, J. M. Boncella, L. Chen, G. Collis, S. Colgate, M. S. DeClue, H. Fellermann, G. Goranovic, Y. Jiang, C. Knutson, P.-A. Monnard, F. Mouffouk, P. Nielsen, A. Sen, A. Shreve, A. Tamulis, B. Travis, P. Weronski, J. Zhang, X. Zhou, H. Ziock, and W. H. Woodruff. ässembly of a minimal protocell". In "Bridging Nonliving and Living Matter", volume 2038, pages -. "MIT Cambridge", 2007. In press.
[40]
S. Rasmussen, C. Knudsen, R. Feldberg, and M. Hinsholm. The coreworld: Emergence and evolution of cooperative structures in a computational chemistry. Physica D, 42:111-134, 1990.
[41]
S. Rassmussen, L. Chen, M. Nilsson, and S. Abe. Bridging nonliving and living matter. Artif. Life, 9:269-316, 2004.
[42]
T. S. Ray. An approach to the synthesis of life. In C. G. Langton, C. Taylor, J. D. Farmer, and S. Rasmussen, editors, Artificial Life II, pages 371-408. Addison-Wesley, New York, 1991.
[43]
D. Sievers and G. von Kiedrowski. Self replication of complementary nucleotide-based oligomers. Nature, 369:221-224, 1994.
[44]
T. Smithers. äutonomy in robots and other agents". Brain Cogn., 34:88-106, 1997.
[45]
S. Spiegelman, I. Haruna, I. B. Holland, G. Beaudreau, and D. R. Mills. The synthesis of a self-propagating and infectious nucleic acid with a purified enzyme. Proc. Natl. Acad. Sci. USA, 54:919-927, 1965.
[46]
U. Tangen. The extension of the quasi-species to functional evolution. PhD Thesis, Jena, 1994. URL http://www.biomip.de/Uwe/publications/p1_main_tangen_thesis.pdf.
[47]
U. Tangen. A computational model for functional evolution. In H. Ritter, H. Cruse, and J. Dean, editors, Prerational Intelligence: Adaptive Behavior and Intelligent Systems Without Symbols and Logic - Volume 2 (1993), pages 299-320. Kluwer Academic Publishers, Dordrecht, NL, 2000.
[48]
U. Tangen. From evolving software towards models of dynamically self-assembling processing systems. In J. Jost, F. Reed-Tsochas, and P. Schuster, editors, "Proceedings of ECCS 2006", pages 50, p85.pdf. ËCSS, Paris", 2006. URL http://complexsystems.lri.fr/FinalReview/FILES/PDF/p85.pdf.
[49]
U. Tangen. The evolving micro-controller software evocpu. 2007. URL http://www.biomip.de/Uwe/projects/EvoCpu.
[50]
U. Tangen, R. M. Füchslin, T. Maeke, and J. S. McCaskill. Progress in digital evolution: 4-bit multiplier evolved using reconfigurable hardware. 2003. URL http://www.biomip.de/Uwe/publications/Multi_a.pdf. Preprint.
[51]
H. Trinks, W. Schröder, and C. K. Biebricher. Ice and the origin of life. Origins of Life and Evolution of Biospheres, 35:429-445, 2005.
[52]
A. V. Vlassov. Mini-ribozymes and freezing environment: a new scenario for the early rna world. Biogeosciences Discussions, 2:1719-1737, 2005.
[53]
J. von Neumann. Theory of Self-Reproducing Automata. Burks, A. W. University of Illinois Press, Urbana, 1966.
[54]
B. Wlotzka and J. S. McCaskill. A molecular predator and its prey: Coupled isothermal amplification of nucleic acids. Chem. & Biology, 4:25-33, 1997.
[55]
J. Yin and J. S. McCaskill. Replication of viruses in a growing plaque: A reaction-diffusion model. Bio. Phys. J, 61:1540-1549, 1992.
[56]
D. Y. Zhang, A. J. Turberfield, B. Yurke, and E. Winfree. Engineering entropy-driven reactions and networks catalyzed by dna. Science, 318:1121-1125, 2007.