Table Of ContentProtocells
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
6 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
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Contents
Preface ix
Acknowledgments xi
Introduction xiii
I Overview: Bridging Nonliving and Living Matter 1
1 The Early History of Protocells: The Search for the Recipe of Life 3
Martin M. Hanczyc
2 Experimental Approaches to Fabricating Artificial Cellular Life 19
David Deamer
3 Semisynthetic Minimal Cells: New Advancements and Perspectives 39
Pasquale Stano, Giovanni Murtas, and Pier Luigi Luisi
4 A Roadmap to Protocells 71
Steen Rasmussen, Mark A. Bedau, John S. McCaskill, and Norman H. Packard
II Integration 101
5 Steps Toward a Synthetic Protocell 107
Martin M. Hanczyc, Irene A. Chen, Peter Sazani, and Jack W. Szostak
6 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
vi Contents
7 Population Analysis of Liposomes with Protein Synthesis and a Cascading Genetic
Network 157
Takeshi Sunami, Kanetomo Sato, Keitaro Ishikawa, and Tetsuya Yomo
8 Constructive Approach to Protocells: Theory and Experiments 169
Kunihiko Kaneko
9 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 Mac´ıa, Harold Fellermann, Andreea Munteanu, Josep Sardanye´ s,
and Sergi Valverde
11 Compositional Lipid Protocells: Reproduction without Polynucleotides 233
Doron Lancet and Barak Shenhav
12 Evolutionary Microfluidic Complementation Toward Artificial Cells 253
John S. McCaskill
III Components 295
13 Self-Replication and Autocatalysis 299
Volker Patzke and Gu¨ nter von Kiedrowski
14 Replicator Dynamics in Protocells 317
Peter F. Stadler and Ba¨ rbel M. R. Stadler
15 Peptide Nucleic Acids as Prebiotic and Abiotic Genetic Material 337
Peter E. Nielsen
16 The Core of a Minimal Gene Set: Insights from Natural Reduced Genomes 347
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 385
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
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 461
William H. Woodruff
IV Broader Context 475
22 Ga´nti’s Chemoton Model and Life Criteria 481
James Griesemer and Eo¨ rs Szathma´ ry
23 Viral Individuality and Limitations of the Life Concept 513
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 563
Andrew Pohorille
26 Prebiotic Chemistry, the Primordial Replicator, and Modern Protocells 583
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 641
Mark A. Bedau and Emily C. Parke
Glossary 655
About the Authors 667
Index 679
Preface
The idea for this book grew out of two international protocell workshops in Sep-
tember 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, Ore-
gon, organized by Mark Bedau, John McCaskill, Norman Packard, and Steen Ras-
mussen 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 com-
munity 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 involv-
ing, 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.
