Although the whole history of computer science is marked by events related to and inspired from “computations” taking place in living cells and organisms (human being included), in the last decades, this became a mainstream research direction, with important and well-established areas, such as evolutionary computing and neural computing, and with exciting new areas, such as DNA and membrane (cellular) computing. All these have both consequences on the efficiency of using standard computers, hopefully leading also to new types of hardware, and—maybe more importantly—on the very understanding of the notion of computing and, at the edge of science towards science fiction. Topics of this kind will be touched in the paper, mainly in relation with DNA and membrane computing.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
L.M. Adleman: Molecular computation of solutions to combinatorial problems. Science, 226(Nov. 1994), 1021-1024.
B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, P. Walter: Molecular Biology of the Cell, 4th ed. Garland Science, New York, 2002.
A. Alhazov, M. Margenstern, V. Rogozhin, Y. Rogozhin, S. Verlan: Communicative P systems with minimal cooperation. In Membrane Computing. International Workshop WMC5, Milan, Italy, 2004. Revised Papers (G. Mauri, Gh. P ăun, M.J. Pérez-Jiménez, G. Rozenberg, C. Zandron, eds.), Lecture Notes in Computer Science, 3365, Springer, Berlin, 2005, 162-178.
J.A. Anderson: An Introduction to Neural Networks. The MIT Press, Cambridge, MA, 1996.
Y. Benenson, T. Paz-Elizur, R. Adar, E. Keinan, Z. Livneh, E. Shapiro: Programmable and autonomous computing machine made of biomolecules. Nature, 414 (Nov. 2001), 430-434.
Y. Benenson, E. Shapiro, B. Gill, U. Ben-Dor, R. Adar: Molecular computer. A ‘smart drug’ in a test tube. Proc. of Tenth DNA Computing Conference, Milano, 2004 (C. Ferretti, G. Mauri, C. Zandron, eds.), Univ. of Milano-Bicocca, 2004, 49 (abstract of invited talk).
D. Bray: Protein molecules as computational elements in living cells. Nature, 376 (July 1995),307-312.
R. Brooks: The relationship between matter and life. Nature, 409 (Jan. 2001), 409-411.
C. Calude, Gh. P ăun: Bio-steps beyond Turing. BioSystems, 77 (2004), 175-194.
J. Mc Carthy: Problems and projection in CS for the next 49 years. Journal of the ACM, 50,1 (2003),73-79.
J.L. Casti. Computing the uncomputable, The New Scientist, 154/2082, 17 (May 1997), 34.
S. Cook: The importance of the P versus NP question. Journal of the ACM, 50, 1 (2003),27-29.
G. Ciobanu, Gh. P ăun, M.J. Pérez-Jiménez, eds.: Applications of Membrane Computing.Springer, Berlin, 2006.
M. Conrad: The price of programmability. In The Universal Turing Machine: A Half-Century Survey (R. Herken, ed.), Kammerer and Unverzagt, Hamburg, 1988, 285-307.
B.J. Copeland: Hypercomputation. Minds and Machines, 12, 4 (2002), 461-502.
B.J. Copeland, D. Proudfoot: Alan Turing’s forgotten ideas in computer science. Scientific American, 280 (April 1999), 77-81.
E.W. Dijkstra: The end of computer science? Communications of the ACM, 44, 3 (2000), 92.
A. Ehrenfeucht, T. Harju, I. Petre, D.M. Prescott, G. Rozenberg: Computation in Living Cells. Gene Assembly in Ciliates. Springer, Berlin, 2004.
A.E. Eiben, J.E. Smith: Introduction to Evolutionary Computing. Springer, Berlin, 2003.
G. Franco, C. Giabulli, C. Laudana, V. Manca: DNA extraction by cross pairing PCR. Proc. of Tenth DNA Computing Conference, Milano, 2004 (C. Ferretti, G. Mauri, C. Zan-dron, eds.), Univ. of Milano-Bicocca, 2004, 193-201.
R. Freund, L. Kari, M. Oswald, P. Sosik: Computationally universal P systems without priorities: two catalysts are sufficient. Theoretical Computer Sci., 330, 2 (2005), 251-266.
R. Gandy: Church’s thesis and principles for mechanisms. In The Kleene Symposium (J. Barwise , eds.), North-Holland, Amsterdam, 1980, 123-148.
M.R. Garey, D.S. Johnson: Computers and Intractability. A Guide to the Theory of NP-Completeness. Freeman, San Francisco, CA, 1979.
M. Gross: Molecular computation. Chapter 2 of Non-Standard Computation (T. Gramss, S. Bornholdt, M. Gross, M. Mitchel, Th. Pellizzari, eds.), Wiley-VCH, Weinheim, 1998.
S.R. Hameroff, J.D. Dayhoff, R. Lahoz-Beltra, A.V. Samsonovich, S. Rasmussen: Models for molecular computation: Conformational automata in the cytoskeleton. Computer, 25 (Nov. 1992), 30-39.
T. Head: Formal language theory and DNA: An analysis of the generative capacity of specific recombinant behaviors. Bulletin of Mathematical Biology, 49 (1987), 737-759.
J. Hartmanis: About the nature of computer science. Bulletin of the EATCS, 53 (June 1994),170-190.
J. Hartmanis: On the weight of computation. Bulletin of the EATCS, 55 (Febr. 1995), 136-138.
J. Hoffmeyer: Surfaces inside surfaces. On the origin of agency and life. Cybernetics and Human Knowing, 5, 1 (1998), 33-42.
J. Hoffmeyer: Semiosis and living membranes. First Seminário Avançado de Comunicação e Semiótica. Biossemiótica e Semiótica Cognitiva, São Paolo, Brasil, 1998, 9-19.
J. Horáková, J. Kelemen: Cˇ apek, Turing, von Neumann, and the 20th century evolution of the concept of machine. In Proceedings of the International Conference in Memoriam John von Neumann, Budapest Polytechnic, 2003, 121-135.
J. Hromkovic: Communication Complexity and Parallel Computing. Springer, Berlin, 1997.
S. Ji: The cell as the smallest DNA-based molecular computer. BioSystems, 52 (1999), 123-133.
S. Kauffman: At Home in the Universe. Oxford Univ. Press, New York, 1995.
J. Kelemen: Bodouci Altamira (The New Altamira). Votobia, Olomouc, 1996.
J. Kelemen: Kybergolem (Cybergolem). Votobia, Olomouc, 2001.
H. Kitano: Systems biology: A brief overview. Science, 295 (March 2002), 1662-1664.
H. Kitano: Computational systems biology. Nature, 420 (Nov. 2002), 206-210.
V. Kreinovich, L. Longprè: Fast quantum algorithms for handling probabilistic and interval uncertainty. Math. Logic Quart., 50 (2004), 405-416.
W.R. Loewenstein: The Touchstone of Life. Molecular Information, Cell Communication, and the Foundations of Life. Oxford University Press, New York, Oxford, 1999.
S. Marcus: Bridging P systems and genomics: A preliminary approach. In Membrane Computing. International Workshop, WMC-CdeA 2002, Curtea de Arges, Romania, Re-vised Papers (Gh. P ăun, G. Rozenberg, A. Salomaa, C. Zandron, eds.), Lecture Notes in Computer Science, 2597, Springer, Berlin, 2003, 371-376.
W. Mass: Networks of spiking neurons: The third generation of neural network models. Neural Networks, 10, 9 (1997), 1659-1671.
M.D. Mesarovi ć : System theory and biology - view of a theoretician. In System Theory and Biology (M.D. Mesarovi ć , ed.), Springer, New York, 1968, 59-87.
T.Y. Nishida: An application of P system: A new algorithm for NP-complete optimization problems. In Proceedings of the 8th World Multi-Conference on Systems, Cybernetics and Informatics (N. Callaos et al, eds.), vol. V, 2004, 109-112.
T. Ord: Hypercomputation: Computing More Than the Turing Machine. Honours Thesis, Department of Computer Science, University of Melbourne, 2003.
C.H. Papadimitriou: Computational Complexity. Addison-Wesley, Reading, MA., 1994.
A. P ăun, Gh. P ăun: The power of communication: P systems with symport/antiport. New Generation Computing, 20, 3 (2002), 295-306.
Gh. P ăun: On the splicing operation. Discrete Appl. Math., 70 (1996), 57-79
Gh. P ăun: Computing with membranes. Journal of Computer and System Sciences, 61, 1 (2000),108-143 (and Turku Center for Computer Science-TUCS Report 208, November 1998, www.tucs.fi).
Gh. P ăun: Membrane Computing: An Introduction. Springer, Berlin, 2002.
Gh. P ăun, R. P ăun: Membrane computing and economics: Numerical P systems. Submitted, 2005 (available at [65]).
Gh. P ăun, G. Rozenberg, A. Salomaa: DNA Computing. New Computing Paradigms. Springer, Berlin, 1998.
R. Penrose: The Emperor’s New Mind. Concerning Computers, Minds, and the Laws of Physics. Oxford University Press, Oxford, 1989.
J.H. Reif, T.H. LaBean, S. Sahu, H. Yan, P. Yin: Design, simulation, and experimental demonstration of self-assembled DNA nanostructures and motors. Proceedings of the Workshop on Unconventional Programming Paradigms, UPP04, Le Mont Saint-Michel, September 2004, Springer, Berlin, 2005.
G. Rozenberg, A. Salomaa: Watson-Crick complementarity, universal computations, and genetic engineering. Techn. Report 96-28, Department of Computer Science, Leiden Univ., Oct. 1996.
P. Sosik: The computational power of cell division in P systems: Beating down parallel computers? Natural Computing, 2, 3 (2003), 287-298.
C. Teuscher, ed.: Alan Turing. Life and Legacy of a Great Thinker. Springer, Berlin, 2003.
C. Teuscher, E. Sanchez: A revival of Turing’s forgotten connectionist ideas: exploring unorganized machines. Proc. Connectionist Models of Learning, Development and Evo-lution, Liege, Belgium, 2000 (R.M. French, J.J. Sougne, eds.), Springer-Verlag, London, 2001,153-162.
F. Tipler: The Physics of Immortality. Doubleday, New York, 1994.
T. Toffoli: Nothing makes sense in computing except in the light of evolution. Int. J. of Unconventional Computing, 1 (2005), 3-29.
M. Tomita: Whole-cell simulation: A grand challenge of the 21st century. Trends in Biotechnology, 19 (2001), 205-210.
A.M. Turing: On computable numbers, with an application to the Entscheidungsproblem. Proceedings of the London Mathematical Society, Ser. 2, 42 (1936), 230-265; a correc tion, 43 (1936), 544-546.
V. Vinge: Technological singularity. VISION-21 Symposium, March 1993 (available at http://www.frc.ri.cmu.edu/ hpm/book98/com.chl/vinge.singularity.html.
O. Wolkenhauer: Systems biology: The reincarnation of systems theory applied in biol ogy? Briefings in Bioinformatics, 2, 3 (2001), 258-270.
The Web Page of Membrane Computing: http://psystems.disco.unimib.it
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Păun, G. (2008). From Cells to (Silicon) Computers, and Back. In: Cooper, S.B., Löwe, B., Sorbi, A. (eds) New Computational Paradigms. Springer, New York, NY. https://doi.org/10.1007/978-0-387-68546-5_15
Download citation
DOI: https://doi.org/10.1007/978-0-387-68546-5_15
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-36033-1
Online ISBN: 978-0-387-68546-5
eBook Packages: Computer ScienceComputer Science (R0)