Evolution As Computation

by Landweber, Laura F.; Winfree, Erik

• ISBN13: 9783540667094
• ISBN10: 3540667091
• Format: Hardcover
• Copyright: 2003-01-01
• Publisher: Springer-Verlag New York Inc

Summary

The study of the genetic basis for evolution has flourished in this century, as well as our understanding of the evolvability and programmability of biological systems. Genetic algorithms meanwhile grew out of the realization that a computer program could use the biologically-inspired processes of mutation, recombination, and selection to solve hard optimization problems. Genetic and evolutionary programming provide further approaches to a wide variety of computational problems. A synthesis of these experiences reveals fundamental insights into both the computational nature of biological evolution and processes of importance to computer science. Topics include biological models of nucleic acid information processing and genome evolution; molecules, cells, and metabolic circuits that compute logical relationships; the origin and evolution of the genetic code; and the interface with genetic algorithms and genetic and evolutionary programming.

Table of Contents

Introduction: Evolution and Computation: Where Do They Meet?	v
Erik Winfree
Laura F. Landweber
Genome System Architecture and Natural Genetic Engineering	1	(14)
James A. Shapiro
Evolutionary Computation as a Paradigm for DNA-Based Computing	15	(26)
Thomas Back
Joost N. Kok
Grzegorz Rozenberg
Evolution at the Edge of Chaos: A Paradigm for the Maturation of the Humoral Immune Response	41	(26)
Patricia K. Theodosopoulos
Theodore V. Theodosopoulos
The Evolutionary Unfolding of Complexity	67	(28)
James P. Crutchfield
Erik van Nimwegen
Genetic Programming: Biologically Inspired Computation That Creatively Solves Non-trivial Problems	95	(30)
John R. Koza
Forrest H. Bennett III
David Andre
Martin A. Keane
Is Ours the Best of All Possible Codes?	125	(15)
Stephen J. Freeland
The Impact of Message Mutation on the Fitness of a Genetic Code	140	(20)
Guy Sella
David H. Ardell
Genetic Code Evolution in the RNA World and Beyond	160	(19)
Robin D. Knight
Imposing Specificity by Localization: Mechanism and Evolvability	179	(22)
Mark Ptashne
Alexander Gann
Towards a Predictive Biology: The Example of Bacteriophage T7	201	(9)
Drew Endy
Using Artificial Reagents to Dissect Cellular Genetic Networks	210	(6)
Roger Brent
Computational Aspects of Gene (Un)Scrambling in Ciliates	216	(41)
Andrzej Ehrenfeucht
David M. Prescott
Grzegorz Rozenberg
Universal Molecular Computation in Ciliates	257	(18)
Laura F. Landweber
Lila Kari
Toward in vivo Digital Circuits	275	(21)
Ron Weiss
George E. Homsy
Thomas F. Knight, Jr.
Evolution of Genetic Organization in Digital Organisms	296	(18)
Charles Ofria
Christoph Adami
Toward Code Evolution by Artificial Economies	314
Eric B. Baum
Igor Durdanovic