Protocells, bridging nonliving and living matter s rasmussen (MIT, 2008)

Protocells Bridging Nonliving and Living Matter Mark A Bedau, Liaohai Chen, David Deamer, David C Krakauer, Norman H Packard, and Peter F Stadler Protocells Protocells Bridging Nonliving and Living Matter edited by Steen Rasmussen, Mark A Bedau, Liaohai Chen, David Deamer, David C Krakauer, Norman H Packard, and Peter F Stadler The MIT Press Cambridge, Massachusetts London, England 2009 Massachusetts Institute of Technology All rights reserved No part of this book may be reproduced in any form by any electronic or mechanical means (including photocopying, recording, or information storage and retrieval) without permission in writing from the publisher For information about special quantity discounts, please email special sales@mitpress.mit.edu This book was set in Times New Roman and Syntax on 3B2 by Asco Typesetters, Hong Kong Printed and bound in the United States of America Library of Congress Cataloging in Publication Data Protocells : bridging nonliving and living matter / edited by Steen Rasmussen [et al.] p ; cm Includes bibliographical references and index ISBN 978 262 18268 (hardcover : alk paper) Artificial cells Life (Biology) I Rasmussen, Steen [DNLM: Cells Biogenesis Cell Physiology Models, Biological QU 300 P967 2008] QH501.P76 2008 2007049243 576.8 dc22 10 Contents Preface ix Acknowledgments Introduction xiii xi I Overview: Bridging Nonliving and Living Matter 1 The Early History of Protocells: The Search for the Recipe of Life Martin M Hanczyc Experimental Approaches to Fabricating Artificial Cellular Life David Deamer Semisynthetic Minimal Cells: New Advancements and Perspectives Pasquale Stano, Giovanni Murtas, and Pier Luigi Luisi A Roadmap to Protocells 71 Steen Rasmussen, Mark A Bedau, John S McCaskill, and Norman H Packard II Integration Steps Toward a Synthetic Protocell 107 Martin M Hanczyc, Irene A Chen, Peter Sazani, and Jack W Szostak Assembly of a Minimal Protocell 125 Steen Rasmussen, James Bailey, James Boncella, Liaohai Chen, Gavin Collis, Stirling Colgate, Michael DeClue, Harold Fellermann, Goran Goranovic´, Yi Jiang, Chad Knutson, Pierre-Alain Monnard, Fouzi Mouffouk, Peter E Nielsen, Anjana Sen, Andy Shreve, Arvydas Tamulis, Bryan Travis, Pawel Weronski, William H Woodruff, Jinsuo Zhang, Xin Zhou, and Hans Ziock 19 39 101 vi Contents Population Analysis of Liposomes with Protein Synthesis and a Cascading Genetic Network 157 Takeshi Sunami, Kanetomo Sato, Keitaro Ishikawa, and Tetsuya Yomo Constructive Approach to Protocells: Theory and Experiments Kunihiko Kaneko Origin of Life and Lattice Artificial Chemistry 197 Naoaki Ono, Duraid Madina, and Takashi Ikegami 10 Models of Protocell Replication 213 Ricard V Sole´, Javier Macı´a, Harold Fellermann, Andreea Munteanu, Josep Sardanye´s, and Sergi Valverde 11 Compositional Lipid Protocells: Reproduction without Polynucleotides Doron Lancet and Barak Shenhav 12 Evolutionary Microfluidic Complementation Toward Artificial Cells John S McCaskill III Components 13 Self-Replication and Autocatalysis 299 Volker Patzke and Guănter von Kiedrowski 14 Replicator Dynamics in Protocells 317 Peter F Stadler and Baărbel M R Stadler 15 Peptide Nucleic Acids as Prebiotic and Abiotic Genetic Material Peter E Nielsen 16 The Core of a Minimal Gene Set: Insights from Natural Reduced Genomes Toni Gabaldo´n, Rosario Gil, Juli Pereto´, Amparo Latorre, and Andre´s Moya 17 Parasitism and Protocells: Tragedy of the Molecular Commons 367 Jeffrey J Tabor, Matthew Levy, Zachary Booth Simpson, and Andrew D Ellington 18 Forming the Essential Template for Life: The Physics of Lipid Self-Assembly Ole G Mouritsen and Ask F Jakobsen 19 Numerical Methods for Protocell Simulations 407 Yi Jiang, Bryan Travis, Chad Knutson, Jinsuo Zhang, and Pawel Weronski 169 233 253 295 337 347 385 Contents vii 20 Core Metabolism as a Self-Organized System 433 Eric Smith, Harold J Morowitz, and Shelley D Copley 21 Energetics, Energy Flow, and Scaling in Life William H Woodruff IV Broader Context 22 Ga´nti’s Chemoton Model and Life Criteria James Griesemer and Eoărs Szathmary 23 Viral Individuality and Limitations of the Life Concept David C Krakauer and Paolo Zanotto 24 Nonlinear Chemical Dynamics and the Origin of Life: The Inorganic-Physical Chemist Point of View 537 Jerzy Maselko and Maciej Maselko 25 Early Ancestors of Existing Cells Andrew Pohorille 26 Prebiotic Chemistry, the Primordial Replicator, and Modern Protocells Henderson James Cleaves II 27 Cell-like Entities: Scientific Challenges and Future Applications 615 John M Frazier, Nancy Kelley-Loughnane, Sandra Trott, Oleg Paliy, Mauricio Rodriguez Rodriguez, Leamon Viveros, and Melanie Tomczak 28 Social and Ethical Issues Concerning Protocells Mark A Bedau and Emily C Parke Glossary 655 About the Authors Index 679 461 475 667 481 513 563 641 583 Preface The idea for this book grew out of two international protocell workshops in September 2003 One meeting, at Los Alamos National Laboratory and the Santa Fe Institute, was organized by Steen Rasmussen, Liaohai Chen, David Deamer, David Krakauer, Norman Packard, and Peter Stadler The other meeting, at the European Conference on Artificial Life (ECAL) in Dortmund, Germany, was organized by Steen Rasmussen and Mark Bedau We published a short summary of the state of the art of protocell research as reflected in those workshops in early 2004 (Rasmussen et al., 2004), and we planned to collect more details about this research in a longer volume That plan was the seed for this book But a series of events intervened, changing and delaying the book Those events grew out of the Seventh Artificial Life Conference in Portland, Oregon, organized by Mark Bedau, John McCaskill, Norman Packard, and Steen Rasmussen in August 2000 Coinciding with the millennium, the conference aimed to take stock of the young field of artificial life Out of the Oregon meeting came a community consensus of specific grand challenges in artificial life One of these challenges is to create wet artificial life from scratch Over the next three years, our activities were a portfolio of projects, most involving, in one way or another, the creation of life from scratch In 2001 we coined the term living technology as an umbrella for our activities The next year we realized how computer-controlled microfluidics could act as life support for the evolution of minimal chemical systems, and two months later we started creating a new roadmap to protocells Our meetings led to a proposal for a new Center for Living Technology at which scientific developments in this area could be nurtured and developed along the way to producing practical applications The European Commission’s program on complex systems funded the first phase of these plans Just before the first protocell workshops in 2003, we learned that our EC proposal on Programmable Artificial Cell Evolution (PACE) was funded John McCaskill led the PACE project, which consisted of fourteen European and U.S partners and included plans for a European Center for Living Technology in Venice ... in bridging the gap between nonliving and living matter To truly understand what it would take to create a minimal living cell, the obvious challenge is xx Introduction to verify this understanding... appropriate mix of nonliving molecules and then let them react and self-assemble into a living protocell This process begins with molecular constituents and so may be considered a bottom-up approach... functional organization is spanned by top-down approaches beginning with living matter (contemporary cells) and bottom-up approaches beginning with nonliving matter, as illustrated in figure I.2 Once