Self-Production of Supramolecular Structures: From Synthetic Structures to Models of Minimal Living

308 Pages·1994·12.23 MB·English

by  S. Hoffmann (auth.), Gail R. Fleischaker, Stefano Colonna, Pier Luigi Luisi (eds.)

Self-Production of Supramolecular Structures
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Series C: Mathematical and Physical Sciences - Vol. 446
Self-Production of
Supramolecular Structures
From Synthetic Structures to
Models of Minimal Living Systems
edited by
Gail R. Fleischaker
Center for the Philosophy & History of Science,
Boston University,
Boston, Massachusetts, U.S.A.
Stefano Colonna
Departimento di Chimica,
Universitä degli Studi di Milano,
Milano, Italy
and
Pier Luigi Luisi
Institut für Polymere,
ETH-Zürich, Switzerland
Springer-Science+Business Media, B.V.
Proceedings of the NATO Advanced Research Workshop on
Self-Production of Supramolecular Structures
From Synthetic Structures to Models of Minimal Living Systems
Acquafredda di Maratea, Italy
September 12-16, 1993
A C.I.P. Catalogue record for this book is available from the Library of Congress.
ISBN 978-94-010-4324-3 ISBN 978-94-011-0754-9 (eBook)
DOI 10.1007/978-94-011-0754-9
Printed on acid-free paper
All Rights Reserved
© 1994 Springer Science+Business Media Dordrecht
Originally published by Kluwer Academic Publishers in 1994
Softcover reprint of the hardcover 1st edition 1994
No part of the material protected by this copyright notice may be reproduced or
utilized in any form or by any means, electronic or mechanical, including photo
copying, recording or by any information storage and retrieval system, without written
permission from the copyright owner.
This book contains the proceedings of a NATO Advanced Research Workshop held within the programme
of activities of the NATO Special Programme on Supramolecular Chemistry as part of the activities of the
NATO Science Committee.
Other books previously published as a result of the activities of the Special Programme are:
WlPFF, G. (Ed.), Computational Approaches in Supramolecular Chemistry. (ASIC.426) 1994.
ISBN 0-7923-2767-5
TABLE OF CONTENTS
Introduction (Pier Luigi Luisi) IX
Acknowledgments (The Organizing Committee) xiii
Workshop Speakers xv
HISTORICAL AND PHILOSOPHICAL PERSPECTIVES
S Hoffmann
Historical overview to the quest of self-reproduction and artificial life 3
FJ Varela
On defining life 23
GR Fleischaker
A few precautionary words concerning terminology 33
TEMPLATE CHEMISTRY
D Sievers, T Achilles, J Burmeister, S Jordan, A Terfort &
G von Kiedrowski
Molecular replication: From minimal to complex systems 45
ESzathmary
Self-replication and reproduction: From molecules to protocells 65
J Rebek,Jr.
Extrabiotic replication and self-assembly 75
JP Ferris
The prebiotic synthesis and replication of RNA oligomers: The
transition from prebiotic molecules to the RNA world 89
JT Goodwin, P Luo, JC Leitzel & DG Lynn
Template-directed synthesis of oligomers: Kinetic vs. thermodynamic
control 99
CHIRALITY AND REPLICATION
A W Schwartz & MJ Van Vliet
Chirality and the first self-replicating molecules 107
A Brack
Are peptides possible support for self-amplification of sequence
information? 115
viii
THE RNA WORLD
RR Breaker & GF Joyce
Minimonsters: Evolutionary by-products of in vitro RNA amplification 127
L Giver, S Lato & A Ellington
Models for the autocatalytic replication of RNA 137
CK Biebricher
RNA species that multiply indefinitely with RNA polymerase 147
PV Coveney
Chemical oscillations and non-linear chemical kinetics 157
THE CELL VIEW AND CELL MODELS
PL Luisi
The chemical implementation of autopoiesis 179
JS Nowick, JS Chen, T Cao & G Noronha
Molecular recognition in micelles 199
PWalde
Self-reproducing vesicles 209
DWDeamer
Sources and syntheses of prebiotic amphiphiles 217
V Garci'a-Meza, A Gonzalez-Rodriguez & A Lazcano
Ancient paralogous duplications and the search for Archean cells 231
POSTERS
C Bohler, W Bannwarth & PL Luisi
Self-replication of oligonucleotides in reverse micelles 249
S Bonaccio, C Cescato, P Walde & PL Luisi
Liposomes from lipidonucleotides and from lipidopeptides 255
S Campagna, G Denti, S Serroni, A Juris, M Venturi & V Balzani
Dendritic luminescent and redox-active supermolecules made of
transition metal complexes 261
G Decher, J-D Hong, K Lowack, Y Lvov & J Schmitt
Layer-by-Iayer adsorption: The solidlliquid-interface as a template
for the controlled growth of well-defined nanostructures of
polyelectrolytes, proteins, DNA and polynucleotides 267
P Burgstaller, D Faulhammer & M Famulok
Molecular recognition of amino acids by RNA 273
ix
DL Gerloff
Towards nature's structural guidelines: Conclusions on the unsolved
structures of RNA-dependent RNA polymerases 279
M Fresta, M Maestro & F Mavelli
A self-catalyzed (autopoietic) synthesis of an anionic surfactant:
Experimental evidence and theoretical modeling 285
V Rotello, Q Feng, J-I Hong & J Rebek, Jr
Competition, reciprocity, and mutation at the molecular level:
Irradiation of a synthetic replicator generates a superior species 291
R Wick, P Walde & PL Luisi
Giant vesicles 295
Index 303
INTRODUCTION
The term "self-replication" has a strong representational power: it calls to mind the
capability of a natural or synthetic system to make copies of itself as well as the fact
that the copying must be an autocatalytic process. The qualifying "selt"--so often
misused in current biologicalliterature--has here a very precise meaning: it is the
original system that is the primary cause of its own replication.
It was timely to call a conference on the subject, and this for two good reasons.
First, the field of self-replication has undergone a considerable development in the
past three to four years with on-going discussion of new concepts and new semantics.
Second, this development derives from different schools of thought--from different
fields and different philosophies--and is therefore anything but homogeneous. It was
important at this time to compare notes, possibly confronting differences, not only
on the subject of self-replication but on more general themes such as the definition
of 'life' or 'minimal life.'
Of these different schools, I recognize three as most influential, both in the
general field and at the Maratea meeting. First, is the molecular biological
approach, which presents self-replication within the framework of the "RNA world,"
an approach represented here by the work of Gerald Joyce at the Scripps Research
Institute and Jack Szostak at Massachusetts General Hospital. For these authors,
self-replication is intrinsically linked to molecular darwinian evolution. Accordingly,
the main hero is the RNA molecule which provides at one and the same time the
capability both of replication and mutation. Extrapolated to the limits, this view
traces the emergence of life to the point at which a family of RNA molecules were
able to catalyze their own formation and mutate in the process. One can say that
this school of thought has its matrix in the classic work of Sol Spiegelman and
Eigen's group in G6ttingen, although in the literature at large this fact is not always
recognized. At the Maratea meeting, the G6ttingen group was represented by
Christof Biebricher and by John McCaskill (now in Jena, Germany).
The second school is that of small chemical replica tors, epitomized by the work
of Julius Rebek at the Massachusetts Institute of Technology and Gunter von
Kiedrowski, originally at G6ttingen and now in Freiburg i.B. Germany. Here the
main ingredient is an oligonucleotide template or other parent structure which binds
two smaller components via recognition (most usually, base-pairing). These two
components are generally the two halves of the template, and the tight binding to the
template facilitates their chemical coupling, transforming them into a copy (usually
palindromic) of the template. Both template-recognition and base-pairing are
expressed on synthetic structures obtained with the classic tools and handouts of
organic chemistry.
The philosophy underlying this work is much like that underlying the RNA
xi
xii
World in that the basis for self-replication and for life processes is the chemistry of
nucleic acids. Both for small chemical replicators and RNA-world scenarios, there
is a single molecule or family of parent chemical structures which "does it all."
By contrast, the third school emphasizes the fact that basic life processes are not
the attribute of any single kind of molecule but the result of an organized complex
system of molecular interactions that occur within and also produce the system's
physical boundary structure. The philosophical matrix of this school lies in the
concept of 'autopoiesis,' a term introduced in the early 1970's by the biologists
Humberto Maturana and Francisco Varela. Autopoiesis emphasizes the organiza
tional pattern of life processes, including the notion of dynamic compartmentation-
that is, that an inside space is made distinct from an outside space by virtue of a
closed, spherical cell-like boundary that is itself a product of those life processes.
This is exemplified most clearly in the simplest contemporary bacterial cell. It is in
these simple cell systems that one may discover the basic mechanisms of life, and
from which one may model a minimal living system. Based on this concept of
autopoiesis, the experimental work of Luisi's group at the ETH-Ziirich centers on
self-replication within spherically-bounded structures such as micelles and vesicles,
arriving at definitional patterns of minimal living systems without invoking the
particular structures and properties of nucleic acids. This school has an historical
scientific matrix in Oparin's work of the 1920's and 1930's with its emphasis on
metabolism and, more recently, in David Deamer's work on bio-membranes and
liposomes.
These three schools, albeit so different, are part of the general field of
supramolecular chemistry. In work concerning the RNA world or small replicators,
intermolecular interactions between template and subtrates play a major role; in
work concerning autopoiesis, supramolecular assemblies (micelles, vesicles), held
together by intermoleular interactions, have the major role. It is for this reason that
the Maratea workshop was held within the Supramolecular Chemistry Programme
of the NATO Research Institute.
Despite the importance of recognition chemistry and assembly within this field
at large, we decided in advance not to solicit contributions on these subjects so that
we could focus the workshop on self-replication. Likewise, we did not include talks
explicitly on the origins of life, although this subject is also closely related to self
replication. We felt, however, that because these two themes would be intense even
in the background, they could and would make their presence known.
Mixing people together with such differences in approach is an act of some
courage. And what could one expect from such a mix? If one were to take a very
optimistic stand, one may expect that it would be possible to find a common
philosophical ground, a unified nomenclature, and hope that joint research programs
between and across the three schools might spontaneously arise. A more down-to
Earth view would suggest instead that the first two expectations (to find a common
philosophy, to carve out a common nomenclature) are illusions: molecular biologists
may not even take notice of the autopoietic approach which does not pay respect to
the holy RNA molecules; synthetic chemists probably will show their traditionally