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M. Eigen P.

Schuster

The Hypercycle
A Principle of Natural Self-Organization

With 64 Figures

Springer-Verlag
Berlin Heidelberg New York 1979
Professor Dr. Manfred Eigen,
Direktor am MPI fur biophysikal. Chemie,
Am FaBberg, D-3400 Gottingen

Professor Dr. Peter Schuster,


Institut fUr theoret. Chemie und Strahlenchemie
der Universitat Wien,
WahringerstraBe 17, A-1090 Wien

This book is a reprint of papers which were published


in Die NatUlwissenschajten, issues 1111977,111978, and 7/1978

ISBN-13: 978-3-540-09293-3 e-ISBN -13: 978-3-642-67247-7


DOl: 10.1007/978-3-642-67247-7

This work is subject to copyright. All rights are reserved, whether the whole or part of the material
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© by Springer-Verlag Berlin' Heidelberg 1979
Softcover reprint of the hardcover 1st edition 1979
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and therefore free for general use.

2152/3140-543210
Preface

This book originated from a series of papers which were published in "Die
Naturwissenschaften" in 1977178. Its division into three parts is the reflection
of a logic structure, which may be abstracted in the form of three theses:
A. Hypercycles are a principle of natural selforganization allowing an inte-
gration and coherent evolution of a set of functionally coupled self-rep-
licative entities.
B. Hypercycles are a novel class of nonlinear reaction networks with unique
properties, amenable to a unified mathematical treatment.
C. Hypercycles are able to originate in the mutant distribution of a single
Darwinian quasi-species through stabilization of its diverging mutant
genes. Once nucleated hypercycles evolve to higher complexity by a
process analogous to gene duplication and specialization.

In order to outline the meaning of the first statement we may refer to another
principle of material selforganization, namely to Darwin's principle of natural
selection. This principle as we see it today represents the only understood
means for creating information, be it the blue print for a complex living
organism which evolved from less complex ancestral forms, or be it a
meaningful sequence of letters the selection of which can be simulated by
evolutionary model games.

Natural selection - and here the emphasis is on the word "natural" - is


based on selfreproduction. Or: given a system of self-reproducing entities
building up from a common source of material of limited supply, natural
selection will result as an inevitable consequence. In the same way evolll-
tionary behaviour governed by natural selection is based on noisy self-
reproduction. These physical properties are sufficient to allow for the re-
producible formation of highly complex systems, i.e. for the generation of
such information as the blue print of a living organism. However, there are
quantitative limitations in the extent of information to be gained, which
are inherent to the Darwinian mechanism of natural selection. This is where
the hypercycle comes onto the scene. The hypercycle, too, is a principle
of selforganization - based on different prerequisites and hence yielding
different consequences.

v
The theory of Darwinian systems as outlined in part A shows essentially
two results:
a) Self-replicative entities compete for selection. This competition may be
relaxed for unrelated species retreating to niches. It nevertheless has to
be effective within each mutant distribution in order to keep the wild-type
stable. Without such a competitive stabilization its information would
melt away.
b) The information content of a stable wild-type is limited. In other words,
the amount ofinformation has to remain below a threshold, the magnitude
of which is inversely proportional to the average error rate (per symbol).
The threshold value furthermore depends on the logarithm of the su-
periority of the wild-type, which is the average selective advantage relative
to the mutants of the total (stable) distribution. The distribution gets
unstable whenever a mutant appears which violates this condition in
being advantageous to the previously stable Wild-type.

These properties are inherent to Darwinian systems. They guarantee evo-


lutionary behaviour, characterized by selection and stable reproduction of
the best adapted self-replicative entity and its replacement by any mutant
that is still better adapted. On the other hand, the evolution of such a system
is limited to a certain level of complexity defined by the threshold for maxi-
mum information content.

The first self-replicative entities - owing to this limitation - must have been
relatively short chains of nucleic acids. They were the only class of macro-
molecules fulfilling the condition of being inherently self-replicative. How-
ever, the specificity of physical forces on which the fidelity of selfreplication
is based, is limited. Improvements of fidelity could result only from catalytic
support, where the catalyst, in order to be subject to evolutionary adaptation
had to be reproducible, too. Translation of information inherited by the
reproductive material became a requirement at this stage of evolution.

The hurdle was immensely high. Evolution must have come almost to a
standstill. Required was a machine, but in order to produce it this very
machine had to be available right away. Even a primitive translation ap-
paratus would have to involve a minimum of four adaptors assigning four
different amino acids plus a corresponding number of enzymes and their
messengers. The amount of information needed for such a system is com-
parable to that of a single stranded RNA-virus. However these particles can
utilize the perfect translation apparatus of their host cell. They furthermore
reproduce with the help of a highly adapted enzyme machinery, which
represents a final- that is an optimal- product of evolution.

The genome of an RNA-phage hardly exceeds a few thousand nucleotides


just enough to encode for a few (e.g. four) protein molecules. As is shown
in part A, this limit is set by the fidelity which only could be reached with
the help of a well adapted replication enzyme. Any further extension of
the information content would require such sophisticated mechanisms as
proofreading including exo-nuclease and ligase action, which is available
only to the DNA-polymerases at quite avanced stages of evolution. How could
even a primitive translation system originate, if reproduction fidelity was

VI
based solely on the physical properties inherited by the nucleic acids not per-
mitting the reproducible accumulation of more than fifty to hundred nu-
cleotides in any individual nucleotide chain? The amount of information
required for a translation system, without which no improvement of fidelity
could be achieved, amounts to a multiple of what was available in the single
self-reproducible chains.

The hypercycle is the tool for integrating length-restricted self-replicative


entities into a new stable order, which is able to evolve coherently. No other
kind of organization, such as mere compartmentation, or non-cyclic net-
works could fulfill simultaneously all three of the following conditions

~ to maintain competition among the wild-type distribution of every self-


replicative entity in order to preserve their information
~ to allow for a coexistence of several (otherwise competitive) entities and
their mutant distributions, and
~ to unify these entities into a coherently evolving unit, where advantages
of one individual can be utilized by all members and where this unit as a
whole remains in sharp competition with any unit of alternative compo-
sition.

Our statement which comprises the results of part A represents a logical


inference:
If we ask for a physical mechanism that guarantees the continuous evolu-
tion of a translation apparatus, hypercyclic organization is a minimum re-
quirement. It is not sufficient - though necessary - that the information
carriers involved are of a self-replicative nature. Ifwe analyze the conditions
of hypercyclic organization we immediately see their equivalence to the
prerequisites of Darwinian selection. The latter is based on self-reproduction
which is a kind of linear autocatalysis. The hypercycle is the next higher
level in a hierarchy of autocatalytic systems (as shown in part A). It is made
up of auto catalysts or reproduction cycles which are linked by cyclic catalysis,
i.e. by another superimposed autocatalysis. Hence a hypercycle is based on
non-linear (e.g. second or higher order) autocatalysis.

Hypercycles, because they show "regular" behaviour can be analyzed as a


particular class of reaction networks. Such a general analysis is carried out
in part B (cf. second statement). The fact that they show unique physical
properties, which other types of couplings are devoid of, calls for a unified
treatment of the "abstract hypercycle". Such a representation of the subject
matter in itself justifies textbook representation.

On the other hand, hypercycles are by no means just abstract products of


our mind. The principle is still retained in the process of RNA-phage infec-
tion, though there it applies to the closed world of the host cell. The phage
genome upon translation provides a factor which acts as a subunit of the
replicase complex, the other parts of which are recruited from host factors.
This phage-encoded factor turns the enzyme into absolute phage specificity.
In disregarding all RNAs from host origin the phage-specific replicase com-
plex now represents a superimposed feedback loop for the autocatalytic
amplification of the phage genome.

VII
Our statement regarding the necessity of a hypercyclic organization of a
primitive translation apparatus is of an "if-then" nature and does not yet refer
to historical reality. There, unexpected singular events, fluctuations that do
not represent any regularity of nature, might occur and then influence the
historical route. If we want to show that historical evolution indeed took
place under guidance of a particular physical principle, we have to look for
witnesses of history, namely remnants of early organizational forms in present
organisms. This is done in part C and our third statement refers to it.

Transfer RNAs as the key substances of translation provide some informa-


tion about their origin. They seem to offer a natural way by which the dif-
ficulties of a start of the nonlinear network - the nucleation problem - can
be solved. All members of the network are descendents of the same master
copy, a t-RNA precursor. Mutants of the quasi-species distribution of this
precursor could accumulate before the organization principle of a hyper-
cycle came into effect. Being closely related mutants all adaptors and mes-
sengers as well as their translation products provide very similar functions
(as targets and as executive factors), hence automatically "fall" into a highly
cross linked organization including a cycle. As shown in part C this cycle
can gradually stabilize itself through evolving specificities of the couplings,
which all may be of the replicase-target type still utilized by RNS-phages.
The realistic hypercycle is subject to experimental testing, which includes
detailed studies of the present translation mechanism.

We hope this book may contribute to raise the right kinds of questions for
a study of problems of evolution. There is no absolute value in any theory, if
its inferences cannot be checked by experiments. On the other hand, theory
has to offer more than just an explanation of experimental facts. As Einstein
said: Only theory can tell us which experiments are to be meaningful.

In this sense the book is written not only for the physicist who seeks for
the uniform application of physical laws to nature. It addresses the chemist,
biochemist and biologist as well, to provoke him to carry out new experi-
ments which may provide a deeper understanding of life as "regularity of
nature" and of its origin.

Our work was greatly stimulated by discussions with FRAN CIS CRICK, STANLEY
MILLER, and LESLIE ORGEL; which for us meant some "selection pressure"
to look for more continuity in molecular evolution. Especially helpful were
suggestions and comments by CHRISTOPH BIEBRICHER, IRVING EpSTEIN,
BERND GUTTE, DIETMAR PORSCHKE, KARL SIGMUND, PAUL WOOLEY, and
ROBERT WOLFF. RUTHILD WINKLER-OSWATITSCH designed most of the il-
lustrations and was always a patient and critical discussant.

Thanks to all for their help.

Gottingen, 6. November 1978 MANFRED EIGEN


PETER SCHUSTER

VIII
Contents

A. Emergency of the Hypercycle. . . . . . C. The Realistic Hypercycle. . . . . . 60


I. The Paradigm of Unity and Diversity XI. How to Start Translation 60
in Evolution. . . . 1 XII. The Logic of Primordial Coding 62
II. What Is a Hypercycle? . . . 2 XIII. Physics of Primordial Coding . . 65
III. Darwinian System . . . . . 6 XIV. The GC-Frame Code . . . . . 68
IV. Error Threshold and Evolution . 15 XV. Hypercyclic Organization of the Early
Translation Apparatus 72
B. The Abstract Hypercycle. . . . . 25 XVI. Ten Questions . . . . . . . 76
V. The Concrete Problem. . . . 25 XVII. Realistic Boundary Conditions 83
VI. General Classification of Dynamic XVIII. Continuity of Evolution 86
Systems . . . . . . . . . . 28
VII. Fixed-Point Analysis of Self-Organizing References . 89
Reaction Networks . . . . . . . . 32 Subject Index 91
VIII. Dynamics of the Elementary Hypercycle 44
IX. Hypercycles with Translation 50
X. Hypercyclic Networks . . . . . . . 54

A. Emergence of the Hypercycle


I. The Paradigm of Unity and Diversity in Evolution The geneticists of our day would not hesitate to give
Why do millions of species, plants and animals, exist, an immediate answere to the first part of this ques-
while there is only one basic molecular machinery tion. Diversity of species is the outcome of the tremen-
of the cell: one universal genetic code and umque dous branching process of evolution with its myriads
chiralities of the macromolecules? of single steps of reproduction and mutation. It in-

1
volves selection among competitors feeding on com- code looks like the product of such a multiple step
mon sources, but also allows for isolation, or the evolutionary process [2], which probably started with
escape into niches, or even for mutual tolerance and the unique assignment of only a few of the most
symbiosis in the presence of sufficiently mild selection abundant primordial amino acids [3]. Although the
constraints. Darwin's principle of natural selection code does not show an entirely logical structure with
represents a principle of guidance, providing the dif- respect to all the final assignments, it is anything
ferential evaluation of a gene population with respect but random and one cannot escape the impression
to an optimal adaptation to its environment. In a that there was an optimization principle at work. One
strict sense it is effective only under appropriate may call it a principle of least change, because the
boundary conditions which mayor may not be structure of the code is such that consequences of
fulfilled in nature. In the work of the great schools single point mutations are reduced to minimum
of population genetics of Fisher, Haldane, and Wright changes at the amino acid level. Redundant codons,
the principle of natural selection was given an exact i.e., triplets coding for the same amino acids, appear
formulation demonstrating its capabilities and restric- in neighbored positions, while amino acids exhibiting
tions. As such, the principle is based on the prerequi- similar kinds of interaction differ usually in only one
sites of living organisms, especially on their reproduc- of the three, preferentially the initial or the terminal
tive mechanisms. These involve a number of factors, position of the codon. Such an optimization, in order
which account for both genetic homogeneity and het- to become effective during the evolutionary process,
erogeneity, and which have been established before requires by trial and error the testing of many alterna-
the detailed molecular mechanisms of inheritance be- tives including quite a number of degenerated assign-
came known (Table I). ments. Hence, precellular evolution should be charac-
terized by a similar degree of branching as we find
Table 1. Factors of natural selection (according to S. Wright [I])
at the species level, provided that it was guided by
Factors of genetic Factors of genetic a similar Darwinian mechanism of natural selec-
homogeneity heterogeljeity tion.
However, we do not encounter any alternative- of the
Gene duplication Gene mutation genetic code, not even in its fine structure. It is quite
Gene aggregation Random division of aggregate unsatisfactory to assume that it was always acci-
Mitosis Chromosome aberration
Conjugation Reduction (meiosis) dentally the optimal assignment which occurred just
Linkage Crossing over once and at the right moment, not admitting any
Restriction of population Hybridization of the alternatives which, undoubtedly, would have
size led to a branching of the code into different fine
Environmental pressure(s) Individual adaptability
Crossbreeding among Subdivision of group
structures. On the other hand, it is just as unsatisfac-
subgroups tory to invoke that the historical route of precellular
Individual adaptability Local environment of subgroups evolution was uniquely fixed by deterministic physical
events.
Realizing this heterogeneity of the animate world The results of our studies suggest, that the Darwinian
there is, in fact, a problem to understand its homogen- evolution of species was preceded by an analogous
eity at the subcellular level. Many biologists simply stepwise process of molecular evolution leading to
sum up all the precellular evolutionary events and a unique cell machinery which uses a universal code.
refer to it as 'the origin of life'. Indeed, if this had This code became finally established, not because it
been one gigantic act of creation and if it - as a unique was the only alternative, but rather due to a peculiar
and singular event, beyond all statistical expectations 'once-forever'-selection mechanism, which could
of physics - had happened only once, we could satisfy start from any random assignment. Once-forever se-
ourselves with such an explanation. Any further at- lection is a consequence of hypercyclic organization
tempt to understand the 'how' would be futile. [4]. A detailed analysis of macromolecular reproduc-
Chance cannot be reduced to anything but chance. tion mechanism suggests that catalytic hypercycles
Our knowledge about the molecular fine structure are a minimums requirement for a macromolecular
of even the simplest existing cells, however, does not organization that is capable to accumulate, preserve,
lend any support to such an explanation. The regula- and process genetic information.
rities in the build up of this very complex structure
leave no doubt, that the first living cell must itself
II. What Is a Hypercycle?
have been the product of a protracted process of
evolution which had to involve many single, but not Consider a sequence of reactions in which, at each
necessarily singular, steps. In particular, the genetic step, the products, with or without the help of addi-

2
tional reactants, undergo further transformation. If,
in such a sequence, any product formed is identical
with a reactant of a preceding step, the system resem-
bles a reaction cycle and the cycle as a whole a cata-
lyst. In the simplest case, the catalyst is represented
by a single molecule, e.g., an enzyme, which turns
a substrate into a product:
sLp
Fig. 3. The tricarboxylic or citric acid cycle is the common catalytic
The mechanism behind this formal scheme requires tool for biological oxidation of fuel molecules. The complete
at least a three-membered cycle (Fig. I). More scheme was formulated by Krebs; fundamental contributions were
involved reaction cycles, both fulfilling fundamental also made by Szent-Gyorgyi, Martius, and Knoop. The major
constituents of the cycle are: citrate (C), cis-aconitate (A), isocitrate
catalytic functions are presented in Figures 2 and 3.
(I), IX-ketoglutarate (K), succinyl-CoA (S*), succinate (S), fumarate
The Bethe-Weizsacker cycle [5] (Fig. 2) contributes (F), I-malate (M) and oxaloacetate (0): The acetate enters in acti-
essentially to the high rate of energy production in vated form as acetyl-CoA (step l) and reacts with oxaloacetate
massive stars. It, so to speak, keeps the sun shining and H 2 0 to form citrate (C) and CoA (+H+). All transformations
and, hence, is one of the most important external involve enzymes as well as co-factors such as CoA (steps I, 5,
6), Fe2+ (steps 2, 3), NAD + (steps 4, 5, 9), TPP, lipoic acid (step 5)
prerequisites of life on earth. Of no less importance, and FAD (step 7). The additional reactants: H 20 (steps I, 3, 8),
although concerned with the internal mechanism of P, and GDP (step 6) and the reaction products: H 20 (step 2),
life, appears to be the Krebs- or citric acid cycle H+ (steps I, 9), and GTP (step 6) are not explicitly mentioned.
[6], shown in Figure 3. This cyclic reaction mediates Tl).e net reaction consists of the complete oxidation of the two
acetyl carbons to CO 2 (and H 20). It generates twelve high-energy
and regulates the carbohydrate and fatty acid metabo-
phosphate bonds, one formed in the cycle (GTP, step 6) and II
from the oxidation of NADH and FADH2 [3 pairs of electrons
are transferred to NAD+ (steps 4, 5, 9) and one pair to FAD
(step 7)].
~ N.B.: The cycle as a whole acts as a catalyst due to the cyclic
ES EP restoration of the substrate intermediates, yet it does not resemble

~Er
5 a catalytic cycle as depicted in Figure 4. Though every step in
this cycle is catalyzed by an enzyme, none of the enzymes is formed
via the cycle

Fig. I. The common cataiytic mechanism of an enzyme according CoA=coenzyme A, NAD=nicotine amide adenine dinucleotide,
to Michaelis and Menten involves (at least) three intermediates: GTP=guanosine triphosphate, FAD=flavine adenine dinucleo-
the free enzyme (E), the enzyme-substrate (ES) and the enzyme- tide, TPP=thiamine pyrophosphate, GDP=guanosine diphos-
product complex (EP). The scheme demonstrates the equivalence phate, P = phosphate
of catalytic action of the enzyme and cyclic restoration of the
intermediates in the turnover of the substrate (S) to the product
(P). Yet, it provides only a formal representation of the true mecha- Iism in the living cell, and has also fundamental func-
nism which may involve a stepwise activation of the substrate
tions in anabolic (or biosynthetic) processes. In both
as well as induced conformation changes of the enzyme.
schemes, energy-rich matter is converted into energy-
deficient products under conservation, i.e., cyclic
restoration of the essential material intermediates.
Historically, both cycles, though they are little related
in their causes, were proposed at about the same
time (1937/38).
Unidirectional cyclic restoration of the intermediates,
of course, presumes a system far from equilibrium
and is always associated with an expenditure of en-
ergy, part of which is dissipated in the environment.
On the other hand, equilibration occurring in a closed
Fig. 2. The carbon cycle, proposed by Bethe and v. Weizsiicker, system will cause each individual step to be in detailed
is responsible -at least in part -for the energy production of mas- balance. Catalytic action in such a closed system will
sive stars. The constituents: 12C, 13N, DC, 14N, 150, and 15N be microscopically reversible, i.e., it will be equally
are steadily reconstituted by the cyclic reaction. The cyclic scheme
as a whole represents a catalyst which converts four 1H atoms
effective in both directions of flow.
to one 4He atom, with the release of energy in the form of y-quanta, Let us now, by a straight forward iteration procedure,
positrons (0+) and neutrinos (v). build up hierarchies of reaction cycles and specify

3
Fig. 4. The catalytic cycle represents a higher level of organization Fig. 5. A catalytic cycle of biological importance is provided by
in the hierarchy of catalytic schemes. The constituents of the cycle the replication mechanism of single-stranded RNA. It involves
E, --+ En are themselves catalysts which are formed from some en- the plus and minus strand as template intermediates for their mu-
ergy-rich substrates (S), whereby each intermediate E, is a catalyst tual reproduction. Template function is equivalent to discriminative
for the formation of E, + ,. The catalytic cycle seen as an entity catalysis. Nucleoside triphosphates (NTP) provide the energy-rich
is equivalent to an autocatalyst, which instructs its own reproduc- building material and pyrophosphate (PP) appears as a waste in
tion. To be a catalytic cycle it is sufficient, that only one of the the turnover. Complementary instruction, the mechanism of which
intermediates formed is a catalyst for one of the subsequent reac- will be discussed in connection with Figure II, represents inherent
tion steps. autocatalytic, i.e., self-reproductive function

their particular properties. In the next step this means Double-stranded DNA, in contrast to single-stranded
we consider a reaction cycle in which at least one, RNA, is such a truely self-reproductive form, i.e.,
but possibly all of the intermediates themselves are both strands are copied concomitantly by the poly-
catalysts. Notice that those intermediates, being cata- merase [10] (cf. Fig. 6). The formal scheme applies
lysts, now remain individually unchanged during reac- to the prokaryotic cell, where inheritance is essentially
tion. Each of them is formed from a flux of energy- limited to the individual cell line.
rich building material using the catalytic halp of its Both plain catalytic and autocatalytic systems share,
preceding intermediate (Fig. 4). Such a system, com- at buffered substrate concentration, a rate term which
prising a larger number of intermediates, would have is first order in the catalyst concentration. The growth
to be of a quite complex composition and, therefore, curve, however, will clearly differentiate the two sys-
is hard to encounter in nature. The best known exam-
ple is the four-member cycle associated with the tem-
plate-directed replication of an RNA molecule
(Fig. 5). In vitro studies of this kind of mechanism
have been performed using a suitable reaction me-
dium, buffered with the four nucleoside-triphos-
phates, as the energy-rich building material and a
phage replicase present as a constant environmental
factor [7, 8], (A more detailed description will be given
by B.-O. Kiippers [9]). Each of the two strands acts
as a template instructing the synthesis of its comple-
mentary copy in analogy to a photographic reproduc-
tion process.
The simplest representative of this category of reac- D 0
tion systems is a single autocatalyst, or-in case of
PD DlP

I I
a whole class of information carrying entities Ii - the
self-replicative unit. The process can be formally writ-
ten as:
X---LI
Reactions of this type will be considered frequently Fig. 6. A true self-reproductive process exemplified by a one-member
in this paper, we characterize them by the symbol catalytic cycle can be found with DNA replication. The mechanism
which is quite involved (cf. Fig. 12), guarantees that each daughter
CD strand (D) is associated with one of the parental strands (P)

4
terns. Under the stated conditions, the product of 0=
E,
the plain cytalytic process will grow linearly with time,
while the autocatalytic system will show exponential
growth.
In strict terminology, an autocatalytic system may
already be called hypercyclic, in that it represents
a cyclic arrangement of catalysts which themselves E,
are cycles of reactions. We shall, however, restrict
the use of this term to those ensembles which are
hypercyclic with respect to the catalytic function. They
are actually hypercycles of second or higher degree,
since they refer to reactions which are at least of
second order with respect to catalyst concentra-
E}
tions.
Fig. 8. A realistic model of a hypercyc/e of second degree, in which
the information carriers Ii exhibit two kinds of instruction, one
for their own reproduction and the other for the translation into
a second type of intermediates Ei with optimal functional prop-
erties. Each enzyme E, provides catalytic help for the reproduction
of the subsequent information carrier Ii+ l ' It may as well comprise
further catalytic abilities, relevant for the translation process, meta-
bolism, etc. In such a case hypercyclic coupling is of a higher
than second degree

The simplest representative in this category is, again,


the (quasi)one-step system, i.e., the reinforced autoca-
talyst. We encounter such a system with RNA-phage
infection (Fig. 9). If the phage RNA (+ strand) is
Fig. 7. A catalytic hypercyc/e consists of self-instructive units Ii injected into a bacterial cell, its genotypic information
with two-fold catalytic functions. As autocatalysts or - more gener- is translated using the machinery of the host cell.
ally -as catalytic cycles the intermediates Ii are able to instruct
their own reproduction and, in addition, provide catalytic support
for the reproduction of the subsequent intermediate (using the
energy-rich building material X). The simplified graph (b) indicates
the cyclic hierarchy

E '\I\I\J -
A catalytic hypercycle is a system which connects
autocatalytic or self-replicative units through a cyclic
linkage. Such a system is depicted in Figure 7. The
intermediates II to In' as self-replicative units, are
themselves catalytic cycles, for instance, combinations E
of plus- and minu~-strands of RNA molecules as
shown in Figure 5. However, the replication process,
Fig. 9. RNA-phage infection of a bacterial cell involves a sImple
as such, has to be directly or indirectly furthered, hypercyclic process. Using the translation machinery of the host
via additional specific couplings between the different cell, the infectious plus strand first instructs the synthesis of a
replicative units. More realistically, such couplings protein subunit (E) which associates itself with other host proteins
may be effected by proteins being the translation pro- to form a phage-specific RNA-replicase. This replicase complex
ducts of the preceding RNA cycles (Fig. 8). These exclusively recognizes the phenotypic features of the phage-RNA,
which are exhibited by both the plus and the minus strand due
proteins may act as specific replicases or derepressors, to a symmetry in special regions of the RNA chain. The result
or as specific protection factors against degradation. is a burst of phage- RNA production which - owing to the hypercy-
The couplings among the self-replicative cycles have elic nature - follows a hyperbolic growth law (cf. part B, Fig. 17)
to form a superimposed cycle, only then the total until one of the intermediates becomes saturated or the metabolic
supply of the host cell is exhausted. Graph (b) exemplifies that
system resembles a hypercycle. Compared with the
it is sufficient if one of the intermediates possesses autocatalytic
systems shown in Figures 4 and 5, the hypercyc1e is or self-instructive function presuming that the other partners feed
self-reproductive to a higher degree. back on it via a closed cyclic link

5
One of the translation products then associates itself properties. Non-coupled self-replicative units guar-
with certain host factors to form an active enzyme antee the conservation of a limited amount of infor-
complex which specifically replicates the plus and mation which can be passed on from generation to
minus strand of the phage RNA, both acting as tem- generation. This proves to be one of the necessary
plates in their mutual reproduction [II]. The replicase prerequisites of Darwinian behavior, i.e., of selection
complex, however, does not multiply - to any consid- and evolution [13]. In a similar way, catalytic hypercy-
erable extent - the mess~nger RNA of the host cell. c1es are also selective, but, in addition, they have
A result of infection is the onset of a hyperbolic integrating properties, which allow for cooperation
growth of phage particles, which eventually becomes among otherwise competitive units. Yet, they compete
limited due to the finite resources of the host cell. even more violently than Darwinian species with any
Another natural hypercycle may appear in Mendelian replicative entity not being part of their own. Further-
populations during the initial phase of speciation, as more, they have the ability of establishing global
long as population numbers are low. The reproduc- forms of organization as a consequence of their once-
tion of genes requires the interaction between both forever-selection behavior, which does not permit a
alleles (M and F), i.e., the homologous regions in coexistence with other hypercyclic systems, unless
the male and female chromosome, which then appear these are stabilized by higher-order linkages.
in the offsprings in a rearranged combination. The The simplest type of coupling within the hypercycle
fact that Mendelian population genetics [12] usually is represented by straight-forward promotion or de-
does not reflect the hypercyclic non-linearity in the repression introducing second-order formation terms
rate equations (which leads to hyperbolic rather than into the rate equations. Higher-order coupling terms
exponential growth), is due to a saturation occurring may occur as well and, thus, define the degree p
at relatively low population numbers, where the birth of the hypercyclic organization.
rate (usually) becomes proportional to the population Individual hypercycles may also be linked together
number of females only. to build up hierarchies. However, this demands inter-
As is seen from the comparative schematic illustration cyclic coupling terms which depend critically on the
in Figure 10, hypercycles' represent a new level of or- degree of organization. Hypercycles Hl and H 2, hav-
ganization. This fact is manifested in their unique ing the degrees Pl and P2 of internal organization,
require intercyclic coupling terms of a degree Pl + P2,
in order to establish a stable coexistence.
It is the object of this paper to present a detailed
theoretical treatment of the category of reaction net-
works we have christened hypercycles [4] and to dis-
cuss their importance in biological self-organization,
especially with respect to the origin of translation,
which may be considered the most decisive step of
Catalyst E
precellular evolution.

III. Darwinian Systems

III. 1. The Principle of Natural Selection

Autocatalyst In physics we know of pr;nciples which cannot be


(Self-replicative unit' reduced to any more fundamental laws. As axioms,
they are abstracted from experience, their predictions
being consistent with any consequences that can be
subjected to experimental test. Typical examples are
the first and second law of thermodynamics.
Darwin's principle of natural selection does not fall
into the category of first principles. As was shown
Catalyllc
H in population genetics [14], natural selection is a con-
Hypercycle
sequence of obvious, basic properties of populations
Fig. 10. The hierarchy of cyclic reaction networks is evident from
of living organisms subjected to defined external con-
this comparative representation (---+ chemical transformation, straints. The principle then makes precise assertions
catalytic action) about the meaning of the term fittest in relati~:m to

6
environmental conditions, other than just uncovering The essential requirement for a system to be self-
the mere tautology of 'survival of the survivor.' selective is that it has to stabilize certain structures
Applied to natural populations with their variable at the expense of others. The criteria for such a stabil-
and usually unknown boundary conditions, the prin- ization are of a dynamic nature, because it is the
ciple still provides the clue for the fact of evolution distribution of competitors present at any instant that
and the phylogenetic interrelations among species. decides which species is to be selected. In other words,
This was the main objective of Charles R. Darwin there is no static stability of any structure, once
[15] and his contemporaty Alfred R. Wallace [16], selected; it may become unstable as soon as other
namely, to provide a more satisfactory foundation more' favourable' structures appear, or in a new envi-
of the tenet of descendence. ronment. The criteria for evaluation must involve
Actually, most of the work in population genetics some feedback property, which ensures the indentity
nowadays is concerned with more practical problems of value and dynamic stability. An advantageous mu-
regarding the spread of genetic information among tant, once produced as a consequence of some fluctua-
Mendelian populations, leaving aside such academic tion, must be able to amplify itself in the presence
questions as whether' being alive' really is a necessary of a large excess of less advantageous competitors.
prerequisite of selective and evolutive behavior. The Therefore, advantage must be indentical with at least
fact that obvious attributes of living organisms, such some of those dynamic properties which are responsi-
as metabolism, self-reproduction, and finite life span, ble for amplification. Only in this way can the system
as well as mutability, suffice to explain selective and selectively organize itself in absence of an 'external
evolutive behavior under appropriate constraints, has selector'. The feedback property required is rep-
led many geneticists of our day to believe that these resented by inherent autocatalysis, i.e., self-reproduc-
properties are unique to the phenomenon of life and tive behavior.
cannot be found in the inanimate world [14]. Test- In a general analysis using game models [18], we have
tube experiments [7], which clearly resemble the ef- specified those properties of matter which are neces-
fects of natural selection and evolution in vitro, were sary to yield Darwinian behavior at the molecular
interpreted as post-biological findings rather than as level. They can be listed as follows:
a demonstration of a typical and specific behavior
of matter. Here one should state that even laser modes
exhibit the phenomenon of natural selection and an 1) Metabolism. Both formation and degradation of
analysis of their amplification mechanism reveals the molecular species have to be independent of each
more than formal analogies. Yet, nobody would call other and spontaneous, i.e., driven by positive affin-
a laser mode 'alive' by any standard of definition. ities. This cannot be achieved in any equilibrated sys-
Wsuch questions may not have much appeal to those tem, in which both processes are mutually related
who are concerned with the properties of actual living by microscopic reversibility yielding a stable distribu-
organisms, they become of utmost importance in con- tion for all competitors once present in the system.
nection with the question of the origin of life. Here Complexity, i.e., the huge multiplicity of alternative
we must, indeed, ask for the necessary prerequisites structures in combination with time and space limita-
in order to find those molecular systems which are tions simply doesn't allow for such an equilibration,
eligible for an evolutionary self-organization. The un- but rather requires a steady degradation and forma-
derlying complexity we encounter at the level of mac- tion of new structures. Selection can become effective
romolecular organization requires this process to be only for intermediate states which are formed from
guided by similar principles of selection and evolution energy-rich precursors and which are degraded to
as those which apply to the animated worled. some energy-deficient waste. The ability of the system
Recent work (loc. cit.), both theoretical and experi- to utilize the free energy and the matter required
mental, has been concerned with these questions. In for this purpose is called metabolism. The necessity
the following we shall give a brief account of some of maintaining the system far enough from equili-
previous results concerning Darwinian systems. brium by a steady compensation of entropy produc-
tion has been first clearly recognized by Erwin
Schrodinger [19].
III. 2. Necessary Prerequisites of Darwinian Systems
2) Self-reproduction. The competing molecular struc-
What is the molecular basis of selection and evolution? tures must have the inherent ability of instructing
Obviously, such a behavior is not a global attribute their own synthesis. Such an inherent autocatalytic
of any arbitrary form of matter but rather is the conse- function can be shown to be necessary for any mecha-
quence ofpeculiar properties which have to be specified. nism of selection involving the destabilization of a

7
population in the presence of a single copy of a newly III. 3. Dynamics of Selection
occurring advantageous mutant. Furthermore, self-
copying is indispensable for the conservation of infor- The simplest system in accordance with the quoted necessary prere-
mation thus far accumulated in the system. Steady quisites can be described by a system of differential equations
of the following form [4] (x=dxJdt; t=time):
degradation, a necessary prerequisite with respect to
condition 1) and 3), would otherwise lead to a xi=(AiQi-Di)Xi + I Wi.X.+<P i (1)
complete destruction of the information. k:f:i

3) Mutability. The fidelity of any self-reproductive


where i is a running index, attributed to all distinguishable self-
process at finite temperature is limited due to thermal reproductive molecular units, and hence characterizing their partic-
noise. This is especially effective if copying is fast, ular (genetic) information. By Xi we denote the respective popula-
mbre precisely, if it requires for each elementary step tion variable (or concentration). The physical meaning of the other
an energy of interaction not too far above the level parameters will become obvious from a discussion of this equation.
of thermal energy. Hence mutability is always physi- The set of equations first of all involves those self-reproductive
units i, which are present in the sample under consideration and
cally associated with self-reproducibility, but it is also which may be numbered I to N. It may be extended to include
(logically) required for evolution. Errors of copying all possible mutants, part of which appear during the course of
provide the main source of new information. As will evolution.
be seen, there is a threshold-relationship for the rate In these equations describing an open system, metabolism is
reflected by spontaneous formation (AiQix,J and decomposition
of mutation, at which evolution is fastest, but which (DiX,J of the molecular species. 'Spontaneous' means that both
must not be surpassed unless all the information thus reactions proceed with a positive affinity and hence are not mu-
far accumulated in the evolutionary process is to be tually reversible. The term Ai always contains some stoichiometric
lost. function j,(mb m2'" ml) of the concentrations of energy-rich
Only those macromolecular systems which fulfil these building material (Je classes) required for the synthesis of the molec-
ular species i, the precise form of which depends on the particular
three prerequisites are eligible as information carriers mechanism of reaction. This energy-rich building material has to
in a virtually unlimited evolutionary process. The be steadily provided by an influx of matter as have the reaction
properties mentioned have to be inherited by all products to be removed by a corresponding outflux (<P,). For a
members of the corresponding macromolecular class, spontaneous decomposition, the Di-term is linearly related to Xi
reflecting a common first-order-rate law. In more complex systems
i.e., by all possible alternatives .or mutants of a given both Ai and Di may include further concentration functions if
structure and, furthermore, they have to be effective the corresponding reactions are enzyme-catalyzed or if further
within a wide range of concentration, i.e., from one couplings among the reactions are present.
single copy up to a macroscopically detectable abun- Self-reproduction, the second prerequisite, manifests itself in the
x,-dependence of the formation rate term. A straightforward linear
dance. The' prerequisite of realizibility' excludes sys-
dependence represents only the simplest form of inherent autocata-
tems of a complicated composition and structure, in lysis. Other more complicated, yet still linear mechanisms, such
which the features mentioned would result from a as complementary instruction or cyclic catalysis, can be treated
particular coincidence of molecular interactions in an analogous way as will be shown Nonlinear autocatalysis,
rather than from a general principle of physical inter- on the other hand, is the main object of this paper.
Mutability is reflected by the quality factor Qi' which may assume
action. As an example, consider the nucleic acids as any value between zero and one. This factor denotes the fraction
compared with proteins. Reproduction in nucleic of reproductions that take place at a given template i and result
acids is a general property based on the physical in an exact copy of i. There is, of course, a complementary term
forces associated with the unique complementarities related to imprecise reproduction of the template i; Ai(l- Qi) Xi.
It means the production of a large variety of 'error copies' which
among the four bases. Proteins, on the other hand,
in most cases are quite closely related to the species i. The produc-
have a much larger functional capacity, including in- tion of error copies of i will then show up with corresponding
structive and reproductive properties. Each individual terms in the rate equations of each of its' relatives' k. Correspond-
function, however, is the consequence of a very spe- ingly, the copy i will also receive contributions from those relatives
cific folding of the polypeptide chain and cannot be due to errors in their replication. These are taken into account
by the sum term; I Wi.X •. The individual mutation rate parameter
attributed to the class of proteins in general. It might i=l=k
even be lost completely by a single mutation. w. io will usually be small compared with the reproduction rate
parameter Ai Q, - the smaller the more distant the 'relative' k.
If all species present and their possible mutants are taken into
Systems of matter, in order to be eligible for selective account by the indices i and k (running from I to N), the following
self-organization, have to inherit physical properties conservation relation for the error copies holds:
which allow for metabolism, i.e., the turnover of energy-
rich reactants to energy-deficient products, and for I Ai(l- Qi)Xi = I I Wi. X• (2)
('noisy'J self-reproduction. These prerequisites are in- i k:f:i

dispensible. Under suitable external conditions they also The individual flow or transport term <Pi' finally, describes any sup-
prove to be sufficient for selective and evolutive behav- ply or removal of species i other than by chemical reaction. It
ior. is required due to the metabolic turnover (cf. above). In most

8
cases each species contributes to the total flow <P, in proportion by B.L. Jones, R.H. Enns, and S.S. Rangnekar [21,22]. The explicit
to its presence: expressions obtained from the exact solutions by second-order per-
turbation theory are in agreement with the formerly [4] reported
(3) approximations *. The following discussion is based on the exact
solutions given by B.L. Jones et al. [21] which offers an elegant
quantitative representation of the selection problem.
In evolution experiments the overall flow can be adjusted in order
to provide reproducible global conditions, such as constant overall
population densities: III. 4. The Concept "Quasi-Species"
Lxk=const",cn (4)
k The single species is not an independent entity because
In this case, the flow <P, has to be steadily regulated In order of the presence of couplings. Conservation of the total
to compensate for the excess overall production, i.e. population number forces all species into mutual
competition, while mutations still allow for some co-
W, = L Akxk- LDkxk'" L Ekxk (5) operation, especially among closely related species
, k

(i.e., species i and k with non-vanishing Wik and Wki


where we call Ei ",Ai -Di the 'excess productivity' of the template
terms).
i. Notice that the error production does not show up explicitly
in this sum as a consequence of the conservation relation (2). Let us, therefore, reorganize our system in the follow-
If, in addition, the individual fluxes of the energy-rich building ing way. Instead of subdividing the total population
material are also regulated, in order to provide for each of the into N species we define a new set of N quasi-species,
A classes a constantly buffered level (m, ... m)), the stoichiometric for which the population variables Yi are linear combi-
functions f,(m, ... m)) appearing in the rate parameters Ai are
constant and as such do not have to be specified explicitly. We nations of the original population variables Xi'
shall refer to this constraint, in which, via flux control, both the whereby, of course, the total sums are conserved:
non-organized, as well as the total organized material is regulated
N N
to a constant level, as 'constant overall organization '. It is usually
maintained in evolution experiments, e.g., in a flow reactor [9], I 1 x = I 1 Yk
k~
k
k~
(9)
or- on average - in a serial transfer experiment [7]. An alternative
straightforward constraint would be that of 'constant fluxes'. In How to carry out this new subdivision is suggested
this case, the concentration levels are variable, adjusting to the
turnover at given in- and outfluxes. Both constraints will cause by the structure of the differential equations (6). It
the system to approach a steady state with sharp selection behavior. corresponds actually to an affine transformation of
The quantitative results may show differences for both constraints, the coordinate system, well known from the theory
but the qualitative behavior turns out to be very similar [4]. It of linear differential equations. One obtains a new
is, therefore, sufficient to consider here just one of both limiting
cases. The constraints to be met in nature may vary with time
set of equations for the transformed population vari-
and, hence, will usually not correspond to either of the simple ables Yi which reads:
extremes - just as little as weather conditions usually resemble sim-
ple thermodynamic constraints (e.g., constant pressure, tempera- (10)
ture, etc.). However, the essential principles of natural selection
can only be studied under controlled and reproducible experimental An application of this procedure to the non-linear
conditions. equations (6) is possible because the term causing
For the constraint of constant overall organization the rate equa- the non-linearity, E(t) according to Eq. (8), remains
tions (I) in combination with the auxiliary conditions (2) to (5)
reduce to:
* Jones et al. [21] pointed out that a neglection of the backflow
xi=(Wii-£(I))Xi+ L W"Xk (6) term L Wi,X k in [4] is not valid for the approach to the steady
k*i k*i
state because the term Wmm-E(t) becomes very small. They re-
where ferred to Eq. II-49 in [4], where any error rate was deliberately
neglected (i.e. Q= I) for the purpose of demonstrating the nature
(7)
of solutions typical for selection. They overlooked, however, our
may be called the (intrinsic) selective value and explicit statement (p. 482 in [4]) that such an assumption may
apply approximately only to a dominant species with a well estab-
£(1)= LEkxk!Lxk (8) lished selective advantage, while cell mutants owe their existence
, k
solely to the presence of the Wik terms. The approximations ob-
the average excess productivity, which is a function of time. Only tained previously (Eq. II-33a; II-43; II-59; II-69; JI-72 in [4]; cf.
when the population variables Xk(t) become stationary, will E(t) also [22]) indeed agree quantitatively with those following from
reach a constant steady-state value which is metastable since it the exact solution by application of perturbation theory (Eq. (21)
depends on the population of the spectrum of mutants. For con- and (22) in [21] and Eq. (13), (18) and (19) in this paper).
stant (i.e., time-invariant) values of W" and wik the non-linear On the other hand, we should like to state that we appreciate
system of differential equations (6) can be solved in a closed form. very much the availability of the exact solutions, as obtained by
Approximate solutions of the selection problem have been reported Thompson and McBride [20] as well as by Jones et al. [21) which
in earlier papers. In recent years, an exact solution has been worked aid tremendously the presentation of a consistent picture of the
out by c.J. Thompson and J.L. McBride [20] and independently quasi-species.

9
invariant in the transformation and can be expressed molecules, being the replicative units, we just use these
now as the average of the A,'s. differences of their sequences in order to define the
(molecular) species. The differences are, of course,
E(t) = ~)kydIYk (11) expressed also by different phenotypic properties,
k
such as replication rates, life times, error rate, etc.
The A;'s are the eigen-values of the linear dynamic
system. They -as well as the eigen-vectors which The single (molecular) species, however, is not the
correlate the x/s whith the Yi's-can be obtained true target of selection. Eq. (10) tells us that it is
from the matrix, consisting of the coefficients W ii rather the quasi-species, i.e., an organized combination
and Wik. of species with a defined probability distribution which
The solutions of the system (10) are physically ob- emerges via selection. As such it is selected against
vious. Any quasi-species (characterized by an eigen- all other distributions. Under selection strains the popu-
value Ai and a population variable y;), whose Ai-value lations numbers of all but one quasi-species really will
is below the threshold represented by the average, disappear. The quasi-species is closely correlated to
E(t), will die out. (Its rate is negative!) Correspond- what is called the "wild-type" of a population.
ingly, each quasi-species with a Ai above the threshold
will grow. The threshold E(t), then, is a function of The wild-type is often assumed to be the standard-
time, and-due to equation (1l)-will increase, the genotype representing the optimally adapted pheno-
more the system favours quasi-species associated with type within the mutant distribution. The fact that
large eigen-values. This will continue until a steady it is possible to determine a unique sequence for the
state is reached: genome of a phage supports this view of a dominant
representation of the standard copy. Closer inspection
(12) of the wild-type distribution of phage Q{3 (in the labo-
i.e., the mean productivity will increase until it equals ratory of Ch. Weissmann) [24], however, clearly de-
the maximum eigen-value. By then all quasi-species monstrated that only a small fraction of the sequences
but one, namely the one associated with the maximum actually is exactly identical with that assigned to the
eigen-value - will have died out. Their population wild-type, while the majority represents a distribution
variables have become zero. of single and multiple error copies whose average
only resembles the wild-type sequence. In other
Darwinian selection and evolution can, thus, be charac- words, the standard copies might be present to an
terized by an extremum principle. It defines a category extent of (sometimes much) less than a few percent
of behavior of self-replicative entities under stated selec- of the total population. However, although the pre-
tion constraints. dominant part of the popUlation consists of non-stan-
dard types, each individual mutant in this distribution
Such a process, for instance, can be seen in analogy is present to a very small extent (as compared with
to equilibration, which represents a fundamental type the standard copy). The total distribution, within the
of beha vior of systems of matter under the constraint limits of detection, then exhibits an average sequence,
of isolation and which is characterized by a general which is exactly identical with the standard and,
extremum principle. The extremum principle (12) is hence, defines the wild-type. The quasi-species, in-
related to the stability criteria of I. Prigogine and troduced above in precise terms, represents such an
P. Glansdorff [23]. As an optimization principle it organized distribution, characterized by one (or more)
holds also for certain classes of non-linear dynamical average sequences. Typical examples of distributions
systems [21]. Furthermore, the validity of the solu- (related to the RNA-phage Q(3) are given in Table 2.
tions of the quasi-linear system (10) is not restricted One unique (average) sequence is present only if the
to the neighborhood of the steady state. copy which exactly resembles the standard is clearly
the dominant one, i.e., if it has the highest selective
What is the physical meaning of a quasi-species? value within the distribution. Mutants, whose W ii are
very close to the maximum values, will on average
In biology, a species is a class of individuals character- be present in correspondingly high abundance (cf.
ized by a certain phenotypic behavior. On the genoty- Table 2). They will cause the wild-type sequence to
pic level, the individuals of a given species may differ be somewhat blurred at certain positions. If two
somewhat, but, nevertheless, all species are rep- closely related mutants actually have (almost) identi-
resented by DNA-chains of a very uniform structure. cal selective values, they may both appear in the
What distinguishes them individually is the very se- quasi-species with (almost) equal statistical weights.
quence of their nucleotides. In dealing now with such How closely the Wi;-values have to resemble each

10
Table 2.
The abundance of the standard sequence in the wild-type distribution is determined by its quality function Qm and its superiority ITm'
At given number of nucleotides Vm the quality function can be calculated from the average digit quality iim of the nucleotides referring to
a particular enzymic read-off mechanism. Both iim and ITm also determine the maximum number of nucleotides VrnaX ' which a standard
sequence must never exceed, otherwise the quasi-species distribution becomes unstable. The data refer to RNA sequences consisting of
4500 nucleotides (phage Qp).

The values in the dark fields (a) show the relative abundance of assumed relative population number
the standard sequence within the wild-type distribution (in per- degeneracy selective value of individual mutant
cent) according to Eq. (18) and (25). Negative values mean that the mu tant class of class Wkk/Wmm I x degeneracy)
distribution is unstable. The light fields show the threshold numbers error - free ~ 1 8.9 x 10' I Xl)
Vrnax for given iim and ITm values. The data clearly demonstrate
one - error
the sensitivity of Vrnax towards the parameter iim. For a well-adapted 1 0.99 4 x 10' Ix 1)
M'a
species, I-iim should be slightly larger than I/v m (e.g., = I-ijm= 4 0.9 5 x 105 Ix 4)
M'b
0.0005 for Vm =4500 nucleotides requiring ITm values ~ 10). 495 03 6.3 x 10' Ix 495)
M"
M" 2000 0.1 4.9 x 10' (x 2000)
qm average digit copying quality M,. 2000 -0 4.3 x 10' (x 2000)
2:M, 4500 2.2 x 10' Ix 1)
multiple - error
V mox
M, - 10' -0 < 30 Ix 107 )
_ 2'500
LM k >, -0 6.88 x 10' Ix 1)
b
one percent. Class M Ib contains four degenerate mutants possess-
E ing selective values within 10% of that of the standard while 495
o mutants of class M Ic show Wkk values 30% of W mm . A bulk of
2000 mutants is by one order of magnitude lower in their Wkk
.~
o
.~
values and an equal amount of mutants is not viable at all, i.e.,
they do not reproduce with any speed comparable to that of the
a. standard. Furthermore all the copies with more than two errors
;,
III have been assigned Wkk values ~ W mm . Although this may not be
an realistic assumption, it is of no serious consequence with respect
to the population numbers of individual sequences which are extre-
mely small because of the large multiplicity of different error copies.
Despite this fact, the sum of all multiple error copies represents
a
the largest group in this example, followed by the total of one-error
In part b a more realistic example of a quasi-species distribution copies. On the other hand, the standard is by far the most abundant
comprising 1.10 9 individuals is presented. A sequence of 4500 individual in the quasi-species distribution.
nucleotides would have 13500 olJe-error mutants, supposed that An alternative calculation has been made in which the relative
for each correct nucleotide (A, U, G, or C) there are three incorrect selective value of the one-error mutant I a has been raised from
alternatives. Experiments with RNA-replicases, however, show that 0.99 to 0.9995. While the gros of the distribution changes only
purine -> purine and pyrimidine -> pyrimidine substitutions are slightly, the population number of the particular mutant I a rises
by far more frequent than any cross-type substitutions: purine to the value found for the standard type (i.e., both result to
<-> pyrimidine. Hence-in order to be more realistic-we have 8.4 x 10 7 ). This example shows the limitation of the approximations
assumed only one incorrect alternative for any position. Accord- behind Eqs. (18) and (19) requiring wkm~ W kk - W mm . A more rig-
ingly the multiplicity of any k-error copy is just G). The total orous numerical evaluation yields a population number of mutant
1 a amounting to only about 60% of that of the standard. Even
of 4500 different one-error mutants have been subdivided with for small differences of selective values the standard clearly remains
respect to their degenerate (average) selective values into five the dominant species. Only if a one-error mutant resembles the
classes. There is one mutant in class MIa which resembles the standard within limits of Wmm - Wkk~ 1/1\nit may be considered
standard quite closely. Its selective value (Wkk ) differs by only to be a degenerate and hence undistinguishable individual.

other for both mutants to become selectively indis- ent quasi-species being degenerate in their eigen-
tinguishable, depends on their 'degree of affinity.' values Ai' Most of these neutral mutants die out after
For distant relatives, the correspondence has to be appearance but a minor part may spread through
much more precise than for one-error copies. A spe- the population and coexist with, or displace, the for-
cial class of 'reversible neutral' mutants, hence, can merly established quasi-species. This diffusional
be quantitatively defined. There is, of course, a second spread of neutral mutants can be understood only
wider class of neutral mutants which belong to differ- on the basis of stochastic theory (cf. below).

11
Ill. 5. Realistic Approximations of the distribution. This provides a great adaptive and evolutive flexi-
bility of the quasi-species and enables it to react quickly to environ-
mental changes.
An explicit representation of the eigen-value of the selected quasi-
species can be obtained with the help of perturbation theory. The
The approximations break down only in the case of the presence
result of second-order perturbation theory resembles the previously
of two or more dominant species (cf. Table 2) which are (almost
reported expression for Wmax ([4], Eq. II-33a):
exactly) neutral mutants. However, those reversible neutral mutants
can be combined to a selectively indistinguishable subclass of
(13) species and as such will determine the dynamic behavior like a
single dominant species, according to the relations given above.
Here the index m refers to that (molecular) species which is dis- It is interesting to note the fact that within the quasi-species there
tinguished by the largest selective value. The approximation holds is no selection against reversible neutral mutants (' reversible' being
only if no other Wkk approaches this value too closely and the defined as sufficiently large W ik and W ki to guarantee a reproducible
dominant copy m can be considered as representative of the wild- representation). These reversible neutral mutants being part of the
type. Table 2 shows, how effective the approximation indeed is quasi-species have to be distinguished from unrelated neutral mu-
tants, (Wik and W ki too small to provide a reproducible representa-
for any system of realistic importance. The larger the information
tion according to Eq. (IS». Those unrelated neutral mutants can
content the smaller the individual w-values. The approximation
still coexist, to a minor extent, as a consequence of random fluctua-
thereby reveals a very important fact; selection (under strain) is
tions [25]. The stochastic treatment shows that competition among
extremely sharp with respect to distant relatives (the smaller the
those neutral species is a random drift phenomenon leading to
Wmk- and wkm-values the closer may W kk resemble Wmm without
extinction with an indeterminate' survival of the survivor' as well
being of any restriction to m). However, selection is smooth with
respect to very close relatives. These are always present in the as to a certain upgrowth and spread of new mutants, a phenomenon
distribution if their selective value W kk is much smaller than Wmm to which geneticists [26] refer as non-Darwinian behavior (i.e.,
(or even zero). If the sum term in Eq. (13) can be numerically survival without selective advantage). It should be realized that
neglected (cf. values in Table 2), the extremum principle (Eq. (12» this stochastic behavior of unrelated neutral mutants, although
can be expressed as: it was not anticipated by Darwin and his followers, is not in
contradiction with those properties which lead to the deterministic
(14) Darwinian behavior. The selection of reversible neutral mutants
is even in accordance with the Darwinian principle, if this is inter-
or preted in the correct way as a derivable physical principle, where
it then applies to the concept of quasi-species.
(15)

where
III. 6. Generalizations
EHm = L Ekxk / L X k (16)
k*m k*m In the quantitative representation of Darwinian system by Eqs.
(2) and (6) we have made a number of special assumptions in
represents the average productivity of all competitors of the selected
connection with the structural prerequisites and external con-
wild-type m and
straints. In this section we want to find out how far we can general-
ize those assumptions without losing the characteristic features
(17) of Darwinian behavior.

is a superiority parameter of the dominant species. I) Rate Terms. The linear rate terms for both autocatalytic forma-
With the same approximation the relative stationary population tion and first-order decomposition may be substituted by more
numbers can be calculated, yielding for the dominant copy general expressions. Most common for enzymic mechanisms is
the Michaelis-Menten form:
Wmm-Ek=Fm Qm- u,;l
(IS) rate,..",.._X_i_ or Xi
Em-EHm l-um l
l+a,xi
and for the one-error copy
which replaces the simple Xi-dependence. It has been shown [4]
(19) that for autocatalytic mechanisms of this kind, selection remains
effective for low population numbers and, hence, in the range
which is critical for selection. Saturation will not prevent the up-
which is valid, as long as wkm<ii W mm - W kk (cf. Table 2). growth of advantageous mutants, but may allow for some coexis-
Higher approximations could be obtained using Amax in which-ever tence due to a change from exponential to linear growth in the
form it is expressed. Eqs. (l6)-{IS) would change accordingly. unconstrained mechanism.
In general, if the reaction order is defined by a term x{', Darwinian
On the basis of these approximations we can quantitatively character- behavior may be found for exponents:
ize Darwinian behavior of macromolecular systems. Eq. (13) shows
O<k;£l
to which extent the dynamics of selection is determined by the individ-
ual properties of the dominant (standard) species (m), while For k=O coexistence would result in a growth-limited system.
Eqs. (18) and (19) indicate the relative weights of representation Under the constraint of constant fluxes, such a situation may occur
of the standard species and its mutants (cf also Table 2). It is for self-reproductive species if their formation rate is limited by
surprising how small a fraction of the standard species is actually the constant rate of supply of energy-rich building material. Species
present within the wild-type distribution, despite the fact that its which feed on different (mutually independent) sources will not
physical parameters almost entirely determine the dynamic behavior compete with each other. The independent sources then provide

12
'niches' for coexistence. The multiple varieties of different species species k belonging to a different class comprising only fragments
often owe their existence to such or similar devices, the consequence of i. Again, those processes do not change the formal structure
of which is in complete accord with the scope of Darwin's theory. of the differential equations, if the corresponding conservation
The behavior for exponents k> I is analyzed in more detail in relations are appropriately taken into account.
part B of this paper. It leads to extremely sharp selection with
some consequences which were not compatible with Darwin's view, 5) External Constraints. The explicit form of the solutions of the
especially regarding descendence. selection equations depends on the constraints to be imposed. We
have discussed in detail the case of constant overall organization.
2) Autocatalysis. According to our discussion in section II, straight- Similar, though quantitatively different, results are obtained for
forward self-reproduction is only the simplest example among a the constraint of constant fluxes [4, 28, 29]. The externally regulated
whole class of linear autocatalytic mechanisms. Self-reproduction parameters may, of course, involve temporal (e.g., any type of
may generally be effected via a cyclic catalytic process. Single- periodical) variations. This may lead to mechanistic advantages,
stranded RNA-phages, for instance, reproduce via mutual instruc- but does not alter the essential prerequisites and consequences
tion through the two complementary strands. The rate equations of Darwinian behavior. The extremum principle (12) then assumes
for such a two-membered catalytic cycle [4] yield two eigen-values the general form:
for the dominant species:
1' _
lim- JE(t)dt=A m (21)
t __ OO T 0
(20)
A further generalization of the extremum principle has been
These expressions are based on similar approximations as Eq. (13)
achieved by Jones et al. [21].
neglecting the mutation terms. One of these eigen-values, if it is Selection of a quasi-species relative to its competitors may also
positive (i.e., A+A_ Q+ Q_ >D+D_), replaces the Wmm referring be considered in a growing system. It will be shown that a simple
to the self-replicative unit. Here, the kinetic parameters of both normalization procedure is applicable, which allows a generalized
strands contribute with equal weight (geometric mean) to the selec-
treatment of non-steady-state systems.
tive value. They both have to be optimized in order to yield optimal
performance. Wherever phenotypic properties of the RNA strands
6) Stochastic Treatment. A final generalization is of a more princi-
are of importance, equivalence can be most suitably reached by
pal nature. Deterministic rate equations describe generally the a ver-
structural symmetry (cf. t-RNA, midi-variant of Qp-RNA [27]).
age behavior of ensembles consisting of a large number of individ-
The second always negative eigen-value refers to an 'equilibration'
uals. The elementary processes, however, can be represented only
between plus- and minus-strands, the concentrations of which then
by reaction probabilities. Game models which have been developed
assume a fixed ratio. Whenever this equilibration is reached, plus- together with R. Winkler-Oswatitsch (18] demonstrate clearly three
and minus-strand will act like one replicative ann competitive
basic types of behavior which can be treated by stochastic theory:
unit. a) Internal self-control of fluctuations as found around stable
The general treatment of catalytic cycles has been shown [4, 20-22],
steady states and, in particular, at thermodynamic equilibrium,
to resemble the results for simple self-instructive systems. A n-
b) self-amplification of fluctuations characterizing an instability,
membered cycle again is characterized by one positive eigen-value and
which corresponds to the selective value of the single self-reproduc-
c) indifference towards fluctuations yielding random drift behav-
tive unit. The catalytic properties of all members contribute to
IOr.
this eigen-value, in the simplest case, in the form of the geometric
In the first case, fluctuations are of importance only for small
mean of their AQ-values, hence, requiring finite AQ-values for
population numbers and simply mean an uncertainty of any mo-
all members of the cycle. Furthermore, a n-membered cycle is
mentary microstate. For the macrostates, which are accessible to
characterized by (n-I) negative eigen-values, which are representa-
experimental tests, they yield expectation values within specifiable
tive of the internal equilibration of the concentration ratios of
average fluctuation limits.
all members of the cycle.
In the second case deterministic behavior is restricted to the re-
sponse to a given fluctuation. In other words, this' if-then' determi-
3) Mutations. The main source of mutations, especially in the early nacy will predict what happens if a certain fluctuation occurs and
stages of evolution, is mis-copying, i.e., the inclusion of a nucleotide the accuracy of the prediction will increase with the extent of
with a non-complementary base during the process of replication. the fluctuation. The occurrence of the fluctuation itself, however,
The experiments with Qp-phage show that error rates for replacing is uncertain and this microscopic uncertainty is mapped macroscop-
a given purine or pyrimidine by its homologue differ considerably ically via the finally deterministic amplification process. This case
from those for exchanging a purine by one of the pyrimidines is of particular relevance for Darwinian systems. Most mutations
or vice versa [24]. In the formal treatment, using the parameters represent fluctuations of the first type, i.e., they are not of any
Q and w, no distinction has to be made regarding the kind of selective advantage and do not endanger the stability of the wild-
mutation, such as point mutation or frame shifts resulting from type. After occurrence, they cease deterministically as in the case
deletion or insertion. Those distinctions, of course, are important of equilibrium. However, there are also mutations which bring
if the functional properties of the mutants are to be studied. The along a selective advantage, and they have the tendency to amplify
formal representation is also invariant to the causes of mutation, themselves, hence, causing an instability. Whether or not they are
such as misreading in replication, chemically induced changes, or successful in reaching dominance depends on the magnitude of
radiation damage. It may be necessary to correlate some of the their selective advantage and the extent of the fluctuation. A single
mutations more closely with the decomposition term (cf. below) copy still has a fairly high chance of dying out before it is re-
which, however, has no influence on the formal structure of the produced, especially if its W-value is only slightly larger than £(1).
equations. The stochastic theory shows that for small advantages, i.e. (Wm+ 1 -
Wm ) ~ Wm , the fluctuation has to reach a certain extent, i.e., a
4) Decomposition. Mutations as a consequence of external in- number of copies which corresponds to the magnitude of Wml
fluences (e.g. radiation) should be attributed to the decomposition (Wm+ 1 - Wm), before the probability of growing up becomes larger
term. In general, decomposition of the individual i may lead to than l-e- 1 . This is equivalent to saying that only mutants

13
identified by distinct advantages will deterministically influence the ment. We, therefore, now introduce more specifically
evolutionary behavior. Nearly neutral mutants behave stochasti- the concept of information.
cally almost like truly neutral mutants, and, hence, refer to the
third category of games which resembles random drift behavior. In the theory of communication, the information content of a
Neutral mutants of high frequency, of course, are part of a given message consisting of Vk symbols can be expressed as
quasi-species and as such are somewhat stabilized due to a finite
mutation rate. They thereby utilize a fluctuation response which (22)
was characteristic of the first category. Since such a coupling is
rather weak, there may be quite large fluctuations in the relative where i is the average information content of a single symbol.
representation of neutral relatives. Unrelated (i.e., very rare) neu- According to Shannon i can be correlated with the probability
tral mutants, on the other hand, may be considered as different distribution of the symbols [30, 31]:
quasi-species whose eigen-values have the same magnitude as that
(23)
of the wild-type. Most of those neutral quasi-species will have
to die out, but if they happen to grow up they may become persis-
tent and even replace the former wild-type (' survival of the survi- with
vor'). This kind of behavior can be deduced only from stochastic
theory. Corresponding calculations have been carried out for the (24)
spread of genes in Mendelian populations, especially by M. Kimura
[25] and his school. The constant K usually is taken to be l/ln 2 in order to yield
the unit' bits/symbol'. The alphabet generally includes classes of
In conclusion, evolution is a deterministic process with symbols (e.g., A=4 for nucleic acids). The practical use of Eq. (23)
respect to its progressive character. There will always is limited to those cases where the a-priori probabilities of all
symbols are known and where the number of symbols in the mes-
be favorable competition of the wild-type with less ad- sage is large enough that the averages apply. In order to account
vantageous mutants, coexistence of neutral or nearly for all cooperative effects or redundancies influencing the probabil-
neutral, closely related mutants, and upgrowth of new ity distribution, it might be necessary to know the probabilities
clearly advantageous quasi-species. However, evolution of all AV possible alternatives of symbol combinations.
In our case we are actually not so much interested in any statistical
is indeterminate with respect to the temporal sequence
a-priori probability of a symbol, but rather in the probability that
of the appearance of l11utants, as well as with respect a given symbol is correctly reproduced by the genetic mechanism
to genetic drift caused by unrelated neutral mutants. however sophisticated the machinery may lie at the various levels
Only a small fraction of these neutral quasi-species of organization. This probability refers to the dynamical process
actually can grow up. Evolution via rare neutral muta- of information transfer and, therefore, must be determined experi-
mentally from kinetic data (wherever it is possible; cf. below).
tions may, therefore, be more important in the later Let us call these probabilities for correct symbol reproduction
than in the earlier stages of evolution, where many qj. A message consisting of Vi (molecular) symbols then will be
advantageous alterations are still possible and, hence, reproduced correctly with the probability or quality factor:
occur with relatively high frequency.
n qij=qi'
v,
Qi= (25)
j= 1

Even if the symbols consist of only A classes, the quality factor


III. 7. Information Content of the Quasi-species for each symbol of the message might be dependent on its particular
environment so that the determination of the geometric mean iii
may require the consideration of various cooperative effects, specif-
In our approach to molecular evolution we have not ically associated with the message' t. Nevertheless, this average
yet dealt explicitly with the concept of genetic infor- iii for any given message i can be determined and it turns out
mation. We have defined the (molecular) species as that for a particular enzymic reproduction machinery those aver-
the replicative unit with a distinct information con- ages apply quite universally, whenever the message is sufficiently
long. Moreover, the individual q-values in general are so close
tent, represented by a particular arrangement of mo- to one that the geometric mean can be replaced by the arithmetic
lecular symbols. We have also taken into account mean, i.e.,
the similarity relations among different such symbol
arrangements, which led to the concept of the quasi-
species. In deriving the criteria of selection and evolu- (26)
tion, it proved sufficient, just as in population gen-
Eq. (25) then comprises the information-theoretical aspect of repro-
etics, to notice the individual differences in genotypic
duction where ii, however, refers to a dynamic rather than to
information and correlate them with their characteris- a static probability. The numerical values of ii may take into ac-
tic dynamic properties as expressed by the selective count all mechanistic features of symbol reproduction including
value W ii • any static redundancy which reduce the error rate of the copying
On the other hand, questions such as, "How much process. Nature actually has invented ingenious copying devices
ranging from complementary base recognition to sophisticated en-
information can be accumulated in a given quasi- zymic checking- and proof-reading mechanisms.
species?" or, "Where is the limit of reproducibility
and, hence, of the evolutionary power of a quasi- Genetic reproduction is a continuously self-repeating
species?" would remain unanswered in such a treat- process, and as such differs from a simple transfer

14
ofa message through a noisy channel. For each single of 99%) is just sufficient to collect and maintain re-
transfer it requires more than just recovery of the producibly an information content not larger than
meaning of the message, which, given some redun- a few hundred symbols (depending on the value of
dancy, would always allow a fraction of the symbols In(Jm) or that the maintainance of the information
to be reproduced incorrectly. It is also necessary to content of the genome as large as that of E. coli
prevent any further accumulation of mistakes in suc- requires an error rate not exceeding one in 10 6 to
cessive reproduction rounds. In other words, a frac- 10 7 nucIeotides. It is a relation which lends itself to
tion of precisely correct wild-type copies must be able experimental testing, and we shall report correspond-
to compete favorably with the total of their error ing measurements below. Eq. (28) also gives quantita-
copies. Only in this way can the wild-type be main- tive account of what has been called in population
tained in a stable distribution. Otherwise the informa- genetics the' genetic load,' the importance of which
tion (now in a semantic sense, i.e., the copy with has been stressed long ago.
optimum Wii-value) would slowly seep away until
it finally is entirely lost. The results of this section can be summarized as fol-
The condition which guarantees the stable conserva- lows: Any mechanism of selective accumulation of in-
tion of information is the selection criterion Eq. (14) formation involves an upper limit for the amount of
or Eq. (15). This criterion can be expressed in a gen- digits to be assembled in a particular order. If this
eral form as: limit is surpassed, the order, i.e., the equivalent of infor-
mation, willfade away during successive reproductions.
f17) Stability of information is equivalent to internal stabil-
ity of the quasi-species. It is as much based on competi-
and as such applies to any reproduction mechanism, tion as is selection of the quasi-species. However, two
even if (Jm cannot be expressed in as simple a form quasi-species can be brought to coexistence, while viola-
as valid for the linear mechanism (cf. Eq. (17». If tion of the threshold relation will result in a total loss
we combine the selection criterion, as derived from of genetic information. Hence internal stability of the
dynamics theory, with the information aspect, as
quasi-species distribution, more than its 'struggle for
expressed by Eq. (25), we obtain the important thresh- existence' is the characteristic attribute of Darwinian
old relationship for the maximum information con- behavior.
tent of a quasi-species:

In (Jm
vmax = - 1- (28) IV. Error Threshold and Evolution
-qm
IV. I. Computer Test of the Error Catastrophe
The number of molecular symbols of a self-reproducible
unit is restricted, the limit being inversely proportional
The physical content of the threshold relation CEq. 28)
to the average error rate per symbol: l-iim
may be exemplified with a little computer game (cf.
There is another way of formulating this important Table 3). The goal is to create a meaningful message
from a more or less random sequence of letters. For
relationship. The expectation value of an error in
this purpose the computer is initially given a set of
a sequence ofv m symbols; sm=vm(l-iim) must always
remain below a sharply defined threshold: N random sequences and programmed:
a) to remove each sequence from its memory after
ee~ <(Jm (29) a defined (average) lifetime,
b) to reproduce each sequence which is present in
otherwise, the information accumulated in the evolu- the storage with a characteristic rate, and
tionary process is lost due to an error catastrophe. c) to introduce random errors in the reproduced
Table 2 contains examples which demonstrate the rel- copies, again with a chosen average rate of substitu-
evance of Eq. (28). The threshold is not sensitively tions per symbol.
dependent on the magnitude of the superiority func- The average rates for a) and b) are matched in such
tion, but (J m must be larger than one, i.e. In (J m > 0, a way that a steady representation of N copies of
in order to guarantee finite values for vrnax ' In practice sentences is maintained in the store, each sentence
(cf. below), In (Jm is usually between one and ten. Rela- having a finite lifetime. Hence any information gained
tion (28) allows a quantitative estimate of the evolu- during the game can be preserved only via faithful
tionary potential, which any particular reproduction reproduction of the sequences present. The gain of
mechanisms can provide. It states, for instance, that information, on the other hand, must result from
an error rate of I % (or a symbol-copying accuracy a selective evaluation of the various mutant sequences

15
Table 3. Self-correction of sentences is the result of the evolution conditions the information is not stable any more. For small selec-
game, exemplified in this table. tive values (as in this example), however, disintegration (or accumu-
The target sentence reads: lation) of information is a comparatively slow process.

TAKE ADVANTAGE OF MISTAKE INITIAL SENTENCE: TAKE ADVANTAGE OF MISTAKE


It has been chosen because it provides' selectively advantageous'
information with respect to the mechanism of evolution. Its special
DIGIT QUALITY 9m : 0.985
form permits a cyclic closure, whenever functional links among SELECTIVE ADVANTAGE PER BIT: 2.5
the single words are introduced (as will be done in part B).
Using a code, in which each letter (and word spacing) is represented
by a quintet of binary symbols, the information content amounts NUMBER OF BEST SENTENCE NUMBER OF
to Vm = 125 bits, allowing for about 4 x 10 37 alternatives. This GENERATION MI STAKES
number excludes appearance of information by mere chance. The
sequences of letters shown in this tables for given generations
have been sampled as being representative for the total population
of sequences in the computer store. 1 TAKE ADVANTAGE OF MISTAKE o
5 TAKF !DVALTAGE OF MISTAKE 3
INITIAL SEQUENCE: BAK GEVLNT GUPIF LESTKKM
10 TALF ADVALTACE OF MISTAKI 5
DIGIT QUALITY 9rn: 0.995 20 DAKE ADUAVEAGE OF MJUTAKE 6
SELECTIVE ADVANTAGE PER BIT: 10
40 TAKE ADVONTQCU OF MFST!ME 7

1. GENERATION: RAK GEVNNT GUPQF KESTKKM 71 TAKEB ?VALTAGI LV MIST!KE 8

5. GENERATION: NAK AEZ,NS GEPOF MESTMKU


71 GENERATION FOR9m~ 0.97
10. GENERATION: VAKF ADV!NT.GE OF MISD!KE
?AMEBADTIMOACFHQEBA!STBMF 18
16. GENERATION: TAKE ADVANTAGE OF MISTAKE
(GOAL REACHED) Comparison of the last two rows (referring to generation 71) shows
that disintegration is much faster at an error rate of 3% (ilm=
0.97).
The first example demonstrates that evolution is very efficient For the other example (selective advantage per bit= 10) the thresh-
old is not yet passed at ilm=0.985; so that information is stable,
near the critical value l-il~l/vm' which with vm=125 amounts
to ilm=0.992. Starting with a random sequence of letters the target as seen below, where the process starts with the correct sentence.
sentence is usually reached within 20(±6) generations for any INITIAL SENTENCE: TAKE ADVANTAGE OF MISTAKE
value of il between 0.995 and 0.990. This efficiency near the thresh-
old is even more evident if we compare the evolutionary progress
at a given generation for various values of ilm:
DIGIT QUALITY 9m:
0.985
SELECTIVE ADVANTAGE PER BIT: 10
INITIAL SEQUENCE: BAK GEVLNT GUPIF LESTKKM
71 GENERATION
SELECTIVE ADVANTAGE PER BIT : 10 NUMBER OF
OUTPRINT OF 8 REPRESENTATIVE SENTENCES MISTAKES
BEST SEQUENCE AFTER 11 GENERATIONS NUMBER OF
9rn MISTAKES
TAKE ADVANTAGE OF MISTAKE o
TAKE ADVANTAGIPOF MISTAKE 2
0.999 LAKD AEV,NTAGU AF KISTQKM 9
TAKE ADVANTAGE OF MISTAKE o
0.995 TAKE ADV!NT GE OF MISTAKE 2
0.990 TAKEBADV!NTAGE OF MISXAKE TBKE !DVANTAGE OF MISTAKE 2
3
0.985 VATA ADBKMDI DHOD ?CSYBKE 18 SAKE ADVANTAGE OF MGSTAME 3
TAOE ADVANVAGE OF MISTAKE 2

Analogous behavior is found for the disintegration of information


TAKE ADVAVTAGE OF MISTAKE 1
for Vm > vrnax ' At an error rate (I-ilm) = \.5%, a selective advantage
per bit of 2.5 corresponds to a rrm value of about 5. Under these
TAKE .DVANTAGE OF MISTAKE 1

16
according to their meaning, or better, according to error rates (I-gm) which are of the same order of
their more or less close relationship to any meaning. magnitude as I/v m (e.g., for 100 bits: g::::::0.99).
This evaluation is to be effected by intrinsic meaning- For sufficiently large O'm-values (> 3) the target sen-
dependent properties of the sequences, which in- tence is then obtained within a number of generations
fluence their rates of reproduction and (or) removal which corresponds to the order of magnitude of the
as expressed by the selective value. evolutionary distance between the target and the ini-
In natural selection, the target of evolution is always tial (more or less random) sequence (e.g., 100 gener-
the genotype which represents the phenotype with ations). However, as soon as the threshold for I-gm
the optimum selective value. Evaluation then is = InO'm/vm is surpassed, no more information can be
effected via the phenotypic, i.e., physical and chemical gained, regardless of how large a selective advantage
properties of the particular individual which deter- per bit is chosen. If one starts out with a nearly
mine the reproduction rate and quality, as well as correct sentence, the information disintegrates to a
the lifetime of the genotype in relation to the average random mixture o(]etters, rather than to evolve to
of its competitors present in the population. Likewise, an error-free copy. The threshold is very sharp but
in our psychic memory we can associate with any the rate of disintegration varies near the threshold.
sequence of letters a reproductive value which is re- There is only a weak dependence of the threshold
lated to its meaning. In our game we could, thus, value on the magnitude of O'm, unless this parameter
evaluate any sequence of letters according to its rela- gets very close to unity. The superiority O'm is calcu-
tion to meaning, using our imagination. The com- lated from the relative selective advantages, and,
puter, of course, can achieve such a goal only via hence, some knowledge about the error distribution
a particular program, in which the evolving sentences (relative to the respective optimal copy) is required.
are compared with one or several possible target sen- This distribution of course depends on the magnitudes
tences. of the selective advantages. The computer experiment
Let us then assume, that each sequence is reproduced closely resembles the expected error distribution,
with a rate which depends on the number of symbols which near the critical value I-gm:::::: I/v m(with In O'm
that coincide in their position with those of a (mean- :::::: 1) yields an almost equal representation of the
ingful) target sentence. Using binary coding we may optimum copy, all one-error copies (relative to opti-
define, that with each bit closer to the target, we mum), and the sum of all multiple-error copies (in
enhance the reproduction rate by a certain factor; which distribution the two-error copies again are
with each bit more distant we slow it down corre- dominantly represented, with strongly decreasing ten-
spondingly. dency for copies with more errors). For smaller selec-
The information about possible target sentences tive advantages (e.g., Wmm - W kk < 3) this representa-
which thereby has to be supplied to the computer tion shifts in favor of the error copies and in disfavor
in advance, however, is not used for any other pur- of the (relative) optimum, which for In 0'", = I is al-
pose than to provide the computer with a value ready present with less than 10% of the total.
scheme. The evaluation procedure could easily be
made more sophisticated, i.e., more closely resem-
bling our mental evaluation of 'meaning,' up to a IV. 2. Experimental Studies with RNA-Phages
level that the particular target finally reached is not
at all predetermined. However, these mechanistic de- As trivial as this game may appear-after one has
tails of simulation are not of so much importance rationalized its results - as relevant has it turned out
for exemplifying the physical meaning of the thresh- in nature in determining the information gained at
old relation, after we can well define the intrinsic the various levels of precellular and cellular self-or-
evaluation procedure of molecular evolution (an ganization. An experiment resembling almost exactly
example is provided by a game model demonstrating the above game has been carried out with phage Qp
the evolution of t-RNA molecules [18]). The results by Ch. Weissmann and his coworkers [32, 33].
of the computer experiment, according to Table 3, An error copy of the phage genome has been
can be summarized as follows: produced by site-directed mutagenesis. The procedure
At high symbol-reproduction quality, e.g., for a sen- consists of in vitro synthesis of the minus strand of
tence of 100 bits with average error rates per symbol the phage RNA containing at the position 39 from
the 5'-end the mutagenic base analog N4-hydroxy
l-gm~1O-2
CMP, instead of the original nucleotide UMP. Using
the evolutionary progress is very slow, even if large this strand as template with the polymerizing enzyme
O'rn-values, i.e., large selective advantages are involved. Qp-replicase, an infectious plus strand could be ob-
Maximum progress is achieved if we choose average tained in which at position 40 from the 3' -end this

17
position corresponds to position 39 from the 5' -end gion - which does not influence any protein encoded
in the minus strand and is located in an extra-cistronic by the phage RNA - has such a considerable effect
region - an A-residue is substituted by G. E. coli upon the replication rate. S. Spiegelmann was the
spheroplasts then were infected with this mutant plus- first in stressing the importance of phenotypic prop-
strand yielding complete mutant phage particles, erties of the phage RNA molecule with respect to
which could be recovered from single plaques. Serial the mechanism of replication and selection. The (Jrn
transfer experiments in vivo (infection of E. coli with value reported above refers to a particular mutant
complete phage particles) as well as in vitro (rate and its satellites. Other mutants might influence the
studies with isolated RNA strands using Qp-replicase) tertiary structure of Qp-RNA in a different way and,
allowed for a determination of reproduction rate hence, exhibit different replication rates. Moreover,
parameters for both the wild-type and the mutant-40 mutations in intracistronic regions may be lethal and,
including their distributions of satellites. Combined therefore do not contribute to Ek +m at all. If we
fingerprint and sequence analysis, applied to succes- consider the measured value as being representative
sive generations, indicated changes in the mutant pu- for the larger part of mutations we obtain for the
pulation due to the formation of revertants. Studies maximum information content, then, a value only
with different initial distributions of wild-type and slightly larger than the actual size of the Qp genome,
mutant revealed the fact that natural selection in- which comprises about 4500 nucIeotides. One might
volves the competition between one dominant individ- be somewhat suspicious with such a close agreement
ual and a distribution of mutants. The quantitative and we have mentioned our reservations. However,
evaluation shows that the value depends on the partic- they refer mainly to the value of (Jrn which enters
ular selective advantage as well as on distribution only as a logarithmic term. Larger (Jm value would
parameters of the mutant population. The wild-type stiII yield acceptable limits for vmax . Thus the value
as compared with the particular mutant shows a selec- obtained may finally be not too far beyond reality.
tive advantage There is another set of experiments, carried out by
Ch. Weissmann and his coworkers [24], which indi-
Wwild-type - Wmutant ~ 2 to 4 cates the presence of a relatively small fraction of
while the rate of substitution was estimated to be standard phage in the wild-type distribution. These
data suggest that (J~ 1 ~ Qm and that the actual number
l-q~3 x 10 4 . of nucleotides is indeed very close to the threshold
The q-value is based on the rate of revertant forma- value vmax (cf. Eq. 18).
The midi-variant, used in the evolution experiments
tion and hence applies to the particular (complemen-
tary) substitutions of G. Mills and S. Spiegelmann et al. [27] consists of
only 218 nucleotides and, hence, is not as weII adapted
G -+ A or C -+ U, respectively. to environmental changes as Q,rRNA. It is, of course,
optimally adapted to the special environment of the
According to Eq. (20) the quality factors of both the 'standard reaction mixture,' used in the test-tube ex-
plus and the minus strand contribute equivalently to periments (which does not require the RNA particles
the fidelity of reproduction. G -+ A and C -+ U substi- to be infectious). However, its response to changes
tutions are, therefore, equivalent. They may not differ in the environment, e.g., to the addition of the replica-
too much from A -+ G and U -+ C replacements, the tion inhibitor ethidium bromide, is fairly slow. The
main calise being the similarity of wobbling for GU mutant obtained after twenty transfers, each aIIowing
and UG interactions. for a hundred thousand-fold amplification differs in
Since the replicating enzyme requires the template only three positions from the wild-type of the midi-
to unfold in order to bind to the active site, the q- variant and shows a relative small selective advantage
values should not further depend on the secondary in the new environment. The reason for the slow
or tertiary structure of the template region. In vitro response is that 218 nucleotides with an average single
studies with a midi-variant of Qp-RNA [27] yield digit quality of 0.9995 yield Q values close to one
rates for C -+ U substitutions which are consistent and lead to wild-type sequences, that are very faith-
with the values reported above. Purine ~ pyrimidine fully replicated, carrying along only a small fraction
and pyrimidine -+ purine substitutions seem to occur (;$ 10%) of mutants in their error distribution.
much less frequently and, hence, do not contribute The remarkable result of these studies in the light
materially to the magnitude of q. of theory is not the fact that the threshold relation
A determination of (Jrn is more difficult, since it de- as an inequality is fulfilled. Since its derivation is
pends on the magnitude of Ek +m • First of all, it is based on quite general logical inferences, any major
noteworthy that modification of an extracistronic re- disagreement would have indicated serious mis-

18
conceptions in our understanding of Darwinian sys- Even more important is to realize that in nature no
tems. There is not the slightest reason for any such (single-stranded) RNA phage exists which comprises
discrepancy, since we know quite well the molecular more than about 10000 nucleotides in its genome. This
mechanism of self-replication in such a 'lucid' system suggests that the enzymic mechanism of RNA replica-
as phage Qp. The truly surprising result is that the tion, especially with respect to the discrimination of
actual value of v not only remains below the threshold the bases A and G or U and C has reached its optimum
vrnax , but, in fact, resembles it so closely. The number and could not be improved further. It is not possible
of nucleotides could easily have been restricted by for any single-stranded RNA to maintain reproducibly
factors other than symbol quality ij, thereby yielding more information than is equivalent to the order of
v values far below the threshold allowing for a repro- magnitude of 1000 to 10000 nucleotides (the precise
ducible accumulation of information. number depending on the value of am).

Hence , we are forced to conclude that these RNA Larger molecules could exist, of course, according
phages during their evolution, indeed, tried to accumu- to chemical criteria, but they would be of no evolu-
late as much information as was possible, utilizing also tionary value. Moreover, the requirements for selec-
large extracistronic, but phenotypically active regions tive conservation of information must be fulfilled by
in their genome. This fact does not exclude that under both the plus and the minus strand, as prescribed
other (e.g., artificial) conditions much smaller RNA by Eq. (20), although only one of the strands needs
molecules, such as the mentioned midi-variant, could to carry the genetic information to be translated by
win the competition, or that under different natural the host mechanism. These conclusions apply only
circumstances also much smaller viable phages exist. to RNA molecules which in their replication phase
act as single-stranded templates and for which the
mechanism depicted in Figure 11 has been proposed
[11].

IV. 3. DNA-Replication

3' With double-stranded molecules, especially with


DNA, we encounter a quite different situation. They
generally reduplicate in the form of double-stranded
units, i.e., they may be considered to be truly self-
reproductive, at least in a phenomenological sense
r s· (even if the instruction conveyed is based again on
the complementarity of the nucleotides).

¥
Let us briefly summarize what is known [10] about
reproduction of such double-stranded DNA mole-
cules (cf. Fig. 12):

4e s·
a) Replication is a semi-conservative process. Each
of the two strands of the DNA duplex is copied during
::f~ 3'
the reproduction phase, leading to two (essentially
identical) duplices, each of which contains one paren-

~
tal strand.
b) Replication starts at a defined growing point and
5'
may proceed in both directions of the strand. The
Fig. II. The replication cycle encountered in RNA phages leads unwinding of the double strand is aided by so-called
to single-stranded units of RNA with highly specific secondary unwinding proteins, some of which have been isolated
and tertiary structures utilized as phenotypic targets [II, 34]. The and identified. They enhance the rate of unwinding
formation of complete or partial duplices between plus and minus
as much as thousand-fold, yielding a relatively fast
strands (the so-called Hofschneider or Franklin pairs, resp.) is
prevented by an immediate internal folding of the newly synthesized movement of the replication fork. At the same time
strand. Using a midi-variant of the phage Qp, S. Spiegelmann it is necessary to relieve the torque caused by the
and coworkers [35] were able to demonstrate the eXIstence of inhib- unwinding in some part of the molecule. It is
itory effects due to duplex formation. Single-strand replication suggested, that a chain break and repair mechanism,
is based on an efficient interaction of the replicase with both the
plus and the minus strand, requiring a certain symmetry in those
effected by endonucleases and ligases, may permit
regions of the tertiary structure which are phenotypically impor- intermediate rotation of chain sections around a phos-
tant. phodiester bond.

19
5' 3' e) The various functions required in DNA replication
have been identified by isolation of the particular
enzymes and by demonstration of their activity. In
particular, several polymerase complexes (I, II and
III) have been characterized, which comprise poly-
merizing as well as several chain-decomposing func-
tions. Of special interest here is the 3' -+ 5' exonuclease
activity of polymerase I. It allows for a preferential
excision of a non-base-paired nucleotide at the 3'-
terminus of the growing chain. Since chain growth
occurs only in the 5' -> 3' direction this exonuclease
function allows for a proofreading of the newly syn-
thetized chain fragments. Its optimal activity is about
2% of that of polymerizing functions. The 3' -+ S'
exonuclease is to be distinguished from a 5' -+3' exo-
nuclease, which also is part of the DNA-polymerase
I complex and probably involved in excision repair.
It acts only at the S' -terminus and cleaves the di-ester
Fig. 12. The semi-conservative replication of double-stranded DNA bond at a base-paired region, possibly up to 10 re-
is a highly sophisticated process including many steps of reaction sidues apart from the 5'-end. It, hence, can remove
and control of which the most important ones are indicated here oligonucleotides, while the proofreading 3' -+ 5' en-
[10]. Both daughter strands are polymerized in the 5' -+ 3' direction.
The unwinding of the parental double helix is effected concomi- zyme only removes single non-base-paired nucleotides
tantly by an unwinding protein (U). The synthesis of new fragments at the end of the growing chain.
is initiated by RNA primers formed with the help of an enzymic
system (I) and later hydrolyzed away presumably by the nuclease
We may conclude now an important difference be-
function of polymerase-I (PI)' Chain elongation up to fragments tween RNA and DNA replication, which is expressed
with 1000 to 2000 nucleotides is believed to be effected mainly in the average symbol quality factors for both mecha-
by the polymerase-III complex (Pm). Those nascent so-called Oka- nisms. In RNA replication the accuracy of informa-
zaki fragments have to be linked together by a ligase (L). Mispaired tion transfer has to be established in the continuous
nucleotides at the 3' -end of the fragments (and only those) are
excised by the 3' -+ 5' -exonuclease function, most likely of the poly- polymerization. However the RNA-replicase solves
merase-I complex (PI)' whose activity is predominantly associated the problem, it achieves apparently a limiting value
with gap filling and repair. Other features, such as repair by 5' -+ 3'- of ij between 0.9990 and 0.9999. Approximately the
exonuclease action, through which whole fragments of DNA can same fidelity should be reached by any continuous
be removed, are not included in this scheme since they may not
be as important for the synthesis of new strands.
DNA-polymerizing mechanism.
Mutant bacteriophage DNA-polymerases devoid of
3' -+ 5' -exonuclease activity have been tested in vitro
and shown to incorporate errors with the relatively
c) Replication of both strands proceeds by inclusion high frequency of about one for every thousand nu-
of nucleotide residues in the 5'-3' direction. The cleotides. Similar results have been reported for
DNA-polymerases can include the monomers only purified avian myoblastosis virus DNA-polymerase.
in this unique vectorial way, which cannot take place However, also lower error rates have been found.
concomitantly at both strands. Electron microscopy For instance, studies with small eukaryotic DNA-
with a resolution of about 100 A has revealed the polymerases, lacking proofreading exonuclease activ-
existence of single-stranded regions at only one side ity, yielded values one order of magnitude lower than
of the growing fork, suggesting that the other strand in the cases mentioned above (i.e., one for every five-
is completed only after a larger stretch, sufficient for to tenthousand nucleotides) [36-39].
a 5'-3' progression, has been created. The observed DNA fragment of 1000 to 2000 nucleo-
d) Replication occurs in short, discontinuous pulses. tides, appearing during DNA polymerization (in pro-
In prokaryotes, the fragments produced in a single karyotic cells) may also directly refer to the limited
pulse are about 1000 to 2000 nucleotides long. They fidelity of the polymerase function. Apparently, the
are initiated by the formation of primers, for which polymerase cannot easily extend a mispaired terminus
very short segments of RNA serve. The fragments generated by itself ([10], p. 88), although this has been
of copied DNA occurring along both strands behind observed in the absence of exonucleases. On the other
the replication fork are later sealed together by li- hand, 3'-5' -exonuclease if present will recognize the
gases. mismatch and excise the wrong nucleotide. There is

20
no reason to assume that the optimal resolving power Correction of errors, on the other hand, cannot be
at this step is much different from that in polymeriza- postponed to any later stage, i.e., after both chains
tion. Hence, proofreading may reduce the error rate have beeR completed. Although repair systems using
(optimally) by another three orders of magnitude. 5' --> 3'-nuclease activities do exist, they cannot deter-

a b

1IIIIIIIIImllllllllllllllllii 1IIIIIIIIImllllllllllllllllli
Two HOMOLOGOUS DNA MOLECULES

111111111111111111111111111111 111111111111111111111111111111

+
3'
5' tmmrrnT ]1111111111111
~~
5'
3,
3'
5' MIDI +j!!@!!!@ 5'
3'
AN ENDONUCLEASE MAKES A NIO'
IN ONE STRAND OF EACH MOLECULE.

II 3' ,. 5' 3' , 5' S' - 31 EXONUCLEASE REMOVES

5,1111111Jii"1_3' 5, lIlliiil!iilllllii .3'


MI SPA I RED TERMl NAL NUCLEaT I DE,

+ 3' + 5'
5,11I11II11I(~> )!MOO 3'
3' 5'
5' 11I1II1I1Im l> jMID 3'
DNA POLYMERASE SYNTHESIZES ON
ONE S! DE OF EACH CUT 5TRAt:D THUS

~: rmnnr: J!I!l ~: 3'~ 1IIIIIIIIIIl5' EXPOSING TWO SINGLE-STRANDED FREE

III 5'~_3'
REGION TAILS.

+ 3'~+ 5'
5' 3' Two
IV CROSSING OVER WITH
CORRECTED PAl RS
SUCH SINGLE-STRANDED REGIONS.
IF HOMOLOGOUS. CAN BASE PAIR GIVING
3' 5' A SHORT DOUBLE-STRANDED BRIDGE.

5' 3'

3' ~ 5'

'::::::::II~'
AN ENDONUCLEASE NICKS THE OTHER
STRANDS GIVING ONE RECOMliINANT
MOLECULE AND TWO MOLECUL.AR fRAG-
V
3' l!IIIItIIIIl 5' MENTS WITH OVERLAPPING TERMINAL.
SEQUENCES,
5' ~_3'

VI
3'
5' _ III !iffiiji] 3'
5'
~: 111111111111"" ""'''''''''''If!
.l1li111l1li 1l1li 11 3'
5'

+ +
EXONUCL.EASE EATS AWAY ONE
DNA POLYMERASE SYNTHESIZES
STRAND Of EACH HAL.F MOL.ECUL.E
THE MISSING PORTIONS,
REVEALING HOMOLOGOUS REGIONS,
3' ., 5'
VII 5·_JiiiIM3'
3'
+ 5' 3'
+ 5' BASE PAIRING GIVES DOUBLE-

III IIII III III III 1111111111 3'


POL¥NUCLEOTIDE LiGASE S~ALS
THE TWO STRANDS GIVING DOUBLE
STRANDED RECOMBINANT ~10L£CULE.
VIII 5' II l1li I IIH I1111 1111 111111111 I 3' 5' 11111 STRANDED RECOMB I NANT WH I CH
IS CDMPLE TED BY GAP FILL I NG
t } USING DNA POLYMERASE AND
LIGASE,

Two DOUBLE STRANN.D RECOMBI-


NANT DNA MOLECULES

Fig. 13. Genetic recombination allows for error detection in completed double strands of DNA. This model was originally proposed to
explain the mechanism of crossing over. It can be applied to error correction as well. The symbol • designates a genetically correct,
the symbol 0 an erroneous nucleotide. Accordingly: always resembles the correct complementary, ~ the mismatched (non-complementary)
and 6the complementary, but erroneous nucleotide pair, regardless of which of the four nucleotides is involved. Assume that strand
nicking is triggered by a mismatched pair (stage II). Then 3' .... Y-exonuclease action will correct the error: 6. . 6in 50% of the cases
(stage III), while in the other 50% the wrong nucleotide will complement itself: ~ .... g. The incorrect (though complementary) pair,
however, is not fixed as in a simple repair mechanism. Recombination with the correct copy (stage VI, VII) will restore the original
situation (stage I and VIII) in which only one of four homologous positions is occupied by an incorrect nucleotide. Hence iteration
of the procedure can lead to a steady reduction, rather than to a 50%-irreversible fixation of errors. This scheme points out that
crossing over is associated with error checking in completed strands. The scheme (copied from [45]) can be understood on the basis of
known functions of DNA-polymerase, which does not exclude the existence of other hypothetical and, even more efficient mechanisms.
A complete understanding of the fidelity problem, which has to include a consideration of vegetative multiplication processes, requires
a more detailed knowledge of the mechanism than is available hitherto

21
mine which of the two strands contains the mis- IV. 4. The First Replicative Units
matched member of the incorrect pair (cf. [36]). More
detailed mechanisms of kinetic proofreading have For a discussion of the origin of biological informa-
been proposed [40] and experimentally tested [41, 42] tion we have to start at the other end of the evolution-
(for a review cf. [43]). ary scale and analyze those mechanisms which led
We may therefore conclude: The optimum average to the first reproducible genetic structures. The physi-
symbol quality for DNA replication reaches values cal properties inherent to the nucleotides effect a dis-
of 0.999999 or somewhat higher, thus allowing for crimination of complementary from non-complemen-
an accumulation of information of up to an equiva- tary nucleotides with a quality factor ij not exceeding
lent of one to ten million nucleotides (depending on
a value of 0.90 to 0.99. The more detailed analysis
the magnitude of O"rn). It is gratifying to notice that based on rate and equilibrium studies of cooperative
this number coincides with known sizes of genomes interactions among oligonucleotides has been
in prokaryotic cells (e.g. E. coli: 4 x 10 6 base pairs). presented elsewhere [4, 44]. In order to achieve a
Again there is no need at all for any individual to discrimination between complementary and non-com-
reach this'limit. Other restrictions, such as packing
plementary base pairs according to the known differ-
requirements in the case of DNA phages, etc., may
ences in free energies, the abundant presence of cata-
limit the actual size of a genome. As for RNA phages,
lytically active, but otherwise uncommitted proteins
any intermediate size below the threshold may, thus,
as environmental factors might have helped. How-
be observed.
ever, uncommitted protein precursors in some cases
will favor the complementary, in other cases the non-
There is an upper limit for the genetic information complementary, interaction. Any preference of one
content of a prokaryotic cell. Just as any extension over the other can only be limited to the difference
beyond the single-strand information capacity of 104 of free energies of the various kinds of pair interac-
nucleotides requires a new mechanism involving double- tion. Any specific enhancement of the complementary
stranded templates and proofreading enzymes, the new pair interaction would require a convergent evolution
limit of about 10 7 nucleotides set by the prokaryotic of those particular enzymes which favor this kind
DNA-reproduction mechanism could not have been ex- of interaction. In order to achieve this goal they must
ceeded until another mechanism for further reduction themselves become part of the self-reproducing sys-
of errors was available. Such a mechanism, namely tem which in turn requires the evolution of a transla-
genetic recombination was invented by nature at the tion mechanism.
prokaryotic level. However, it took about two to three The first self-reproductive nucleic acid structures with
billion (10 9 ) years before it reached perfection in order stable information content - given optimal ij values
to give rise to another extension of the genetic informa- of 0.90 to 0.99-were t-RNA-like molecules. For any
tion content of single individuals. reproducible translation system, however, an infor-
mation content larger by at least one order of magni-
tude would be required. As we know from the analysis
The process of genetic recombination utilized by all
of RNA-phage replication, such a requirement can
eukaryotic cells requires two alleles to be identified
be matched only by optimally adapted replicases,
at their homologous positions. Since the error rate
which could not have evolved without a perfect trans-
for the enzymic DNA reproduction is below 10- 6
lation mechanism. The phages, we encounter today,
per nucleotide, uncorrected mistakes are very rare
are late products of evolution whose existence is based
and cannot be present in more than one of the four
on the availability of such a mechanism, without
equivalent sites of the two alleles. Hence, there is
which nature could not afford to accumulate as much
a further opportunity to identify and correct those
information in one single nucleic acid molecule.
errors in the recombinants, even if they occur in for-
Hence, there was a barrier for molecular evolution
merly completed duplices. A possible scheme is
of nucleic acids at the level of t-RNA-like structures
depicted in Figure 13. However, the mechanism of
similar to those barriers we find at later stages of
recombination is neither yet known in sufficient de-
evolution, requiring some new kind of mechanism
tail, nor is it clear how many steps finally are responsi-
for enlarging the information capacity.
ble for the further reduction of the error rate. The
fact is that such a reduction has been achieved, as
is revealed by an analysis of evolutionary trees, and The t-RNA's or their precursors, then, seem to be the
that it is an important prerequisite for the expansion 'oldest' replicative units which started to accumulate
of genetic information capacity up to the level of information and were selected as a quasi-species, i.e.,
man. as variants of the same basic structure.

22
The first requirement was stability towards hydro-
lysis. It has been shown by a game model, similar
to the one described in IV. 1., that the presently known
secondary (and tertiary) structure of t-RNA (cf.
Figs. 14a and b) is a direct evolutionary consequence
of this requirement. The symmetry of this structure,
furthermore, reflects the optimization of its replicative
mechanism which, according to Eq. (20), supposes
equivalent behavior of the plus and the minus strand

3'
5'
3'
5' +

p 'OH
p
p

Fig. 15. 'Flower' model of Spiegelmann's midi-variant of Qp-RNA


(plus strand). Symmetry requirements are less important where
the information is mapped in genotypes which are reproduced
via standardized polymerization mechanisms. The midi-variant of
a phage Qp is selected solely for its phenotypic information, in that
it exhibits an optimal target structure for recognition by the enzyme
ac Qp-replicase. This property must be inherited by both the plus
,--,
Qugmented D-helix and the minus strand. The symmetry of the structure becomes
I la-steml I most obvious in the 'flower' model, although this arrangement
probably does not represent the natural structure of the active
molecule. According to the mechanistic conditions of single-strand
replication shown in Figure II, a model admitting immediate chain
folding during synthesis [27] should be advantageous

in order to yield optimal performance. This symmetry


r
TWCstem
~
ac stem
can also be found at the level of RNA phages, espe-
cially for variants which are selected for being pheno-
L extra loop
typically most efficient with respect to in vitro replica-
tion, but otherwise not carrying genetic information
T\j! C loop
(Fig. 15).
plus G'8 - G'9
b
Fig. 14. Symmetry of functional RNA molecules, as exemplified IV. 5. The Need for Hypercycles
with t-RNAphe, aids single-strand replication by specifically
adapted enzymes. The plus and minus strands of the symmetrical
structure are distinguished by common phenotypic features. Al- It is the object of this paper to show, first that the
though t-RNA's in present organisms are genotypically encoded, breakthrough in molecular evolution must have been
their symmetry might still reflect the ancestrial mechanism of brought about by an integration of several self-repro-
single-stranded RNA reproduction, for which plus and minus
ducing units to a cooperative system and, second that
strand are equally important. The symmetry is most obvious in
the secondary structure (a), but shows up accordingly also in the a mechanism capable of such an integration can be
tertiary structure (b) (reproduced from [46]) provided only by the class of hypercycles. This conclu-

23
sion again can be drawn from logical inferences, based ation of information. Its prerequisite is integration of
on the following arguments: self-reproductive symbols into self-reproductive units
The information content of the first reproductive which are able to stabilize themselves against the accu-
units was limited to Vmax ;:S 100 nucleotides. Several mulation of errors. The same requirement holds for
of those units representing similar functions but dif- the integration of self-reproductive and selectively sta-
ferent specificities were required to build up a transla- ble units into the next higher form of organization,
tion system. Such a system might have emerged from in order to yield again selectively stable behavior. Only
one quasi-species, but the equivalent partners had the cyclic linkage -as an equivalent of autocatalytic
to evolve simultaneously. This is neither possible by reinforcement at this level (cf II.) -is able to achieve
linking them up into a larger self-reproductive unit this goal.
(because.of the error threshold), nor could it result
from compartmentation, because of the strong com-
petition among the equivalent self-reproductive units Table 4. The essential stages of information storage in Darwinian
within the compartment. Such a process rather re- systems
quires functional linkages among all self-reproductive
Digit Super- Maximum Molecular mechanism
units, to be distinguished by the following qualities:
error iority digit and example in biology
a) The linkage must still permit competition of each rate content
self-reproductive unit with its error copies, otherwise I ~qm U m vrnax
these units cannot maintain their information.
b) The linkage must' switch off' competition among 5 x 10- 2 2 14 enzyme-free RNA
20 60 replica tion '
those self-reproductive units which should be inte- t-RNA precursor, v=80
200 106
grated to a new functional system and allow for their
5 x 10- 4 2 1386 single-stranded RNA replica-
cooperation. 20 5991 tion via specific replicases
c) The integrated functional system then must be able 200 10597 phage Qp, v=4500
to compete favorably with any other less efficient I x 10- 6 2 0.7 X 10 6 DNA replication via poly-
system or unit. 20 3.0 X 10 6 merases including proofread-
These three requirements can be fulfilled only by a 200 5.3 X 10 6 ing by exonuclease
cyclic linkage among self-reproductive units or, in E. coli, v=4 x 10 6
other words, the functional linkage among autono- I X 10- 9 2 0.7x10 9 DNA replication and recombi-
mous self-reproductive units itself has to be of a self- 20 3.0 X 10 9 nation in eukaryotic cells
enhancing cyclic nature, otherwise their total informa- 200 5.3 X 10 9 vertebrates (man), v = 3 X 10 9
tion content cannot be maintained reproducibly. Hy- Uncatalyzed replication of RNA never has been observed to
percyclic organization, thus, appears to be a necessary any satisfactory extent; however, catalysis at surfaces or via not
prerequisite for the nucleation of integrated self-re- specifically adapted proteinoids (as proposed by S. W. Fox) may
productive systems of larger information content, as involve error rates corresponding to the values quoted.
were required for the origin of translation. This state-
ment is the conclusion of what is to be shown in
the subsequent parts by a more detailed analysis of The results of section IV are summed up in Table 4,
linked systems. showing the essential stages of information storage
in Darwinian systems, which could be facilitated by
If we are asked, "What is particular to hypercycles? ", various storage mechanisms of reproduction.
our answer is, "They are the analogue of Darwinian This table will be useful for a discussion of a model
systems at the next higher level of organization." Dar- of continuous evolution from single molecules to inte-
winian behavior was recognized to be the basis of gener- grated cellular systems, as presented in part C.

24
B. The Abstract Hypercycle

Topologic methods are used to characterize a particu- necessary to reach a stable information content of a few
lar class of self-replicative reaction networks: the thousand nucleotides. Such an amount would be just
hypercycles. The results show that the properties of sufficient to code for a few protein molecules, as we find
hypercycles are sufficient for a stable integration of the in present RNA phages. The physical properties in-
information contained in several self-replicative units. herent in the nucleic acids allow for a reproducible
Among the catalytic networks studied, hypercyclic accumulation of information of no more than 50 to 100
organization proves t6 be a necessary prerequisite for nucleotides.
maintaining the stability of information and for pro- The last of these three statements may be questioned on
moting its further evolution. The techniques used in the basis of the argument that environmental factors
this paper, though familiar to mathematicians, are - such as suitable catalytic surfaces or even protein-
introduced in detail in order to make the logical like enzyme precursors [47] - may cause a consider-
arguments accessible to the nonmathematician. able shift of those numbers. In fact, the figures given
were derived from equilibrium data, namely, from the
free energies for (cooperative) complementary versus
noncomplementary nucleotide interactions. Neverthe-
v. The Concrete Problem less, we still consider them upper limits which in nature
may actually be reached only in the presence of suitable
In Part A of this trilogy on hypercycles we have arrived catalysts or via annealing procedures. Laboratory
at some essential conclusions about Darwinian systems experiments on enzyme-free template-induced polyme-
at the molecular level, which may be summarized as rization lead to considerably lower numbers. On the
follows: other hand, environmental catalysts cannot yield fide-
1. The target of selection and evolution is the quasi- lities of symbol recognition exceeding the equilibrium
species, which consists of a distribution of (genotypi- figures, unless they themselves become part of the
cally) closely related replicative units, centered around selectively optimizing system. There is no way of
the copy (or a degenerate set of copies) corresponding systematically favoring the functionally advantageous
to the phe.notype of maximum selective value. over the nonadvantageous interactions, other than via
2. The information content of this master copy - ex- a stepwise selective optimization. The phage genomes
pressed as the number v of symbols (nucleotides) could evolve in the form of single-stranded RNA
· · umt-Is
per rep1IcatIve . . l'ImIte
. d to Vm
In am were
<--_-, h molecules, only because a quite advanced replication
l-q,,; and translation machinery was provided by the host
a m( > 1) is the superiority of the master copy, i.e., an cell. They are postcellular rather than precellular
average selective advantage oyer the rest of the distri- evolution products. Something like the magnitude of
bution, and lim' the average quality of symbol copying. the information content of their genomes is just what
Exceeding this threshold of information content will would be required at the beginning of translation,
cause an error catastrophe, i.e., a disintegration of namely, the reproducible information for a set of
information due to a steady accumulation of errors. enzymes that could start a primitive translation mecha-
3. A highly evolved enzymic replication machinery is nism. Hence the essential conclusion from Part A is:

25
The start of translation requires an integration of Let us aid our intuition again by playing another
several replicative units into a cooperative system, in version of the computer game introduced in Part A.
order to provide a sufficient amount of information for In the first part of the game the objective was to
the build-up of a translation and replication machinery. demonstrate the need for adapting the symbol-
Only such an integrated machinery can bring about a reproduction quality to the information content of
further increase of fidelity and hence allow for a the sentence to be reproduced. In the second part we
corresponding expansion of the information content. assume now that the average quality factor iim is not
sufficient for a stable reproduction of the whole sen-
How can one envisage an integration of competitive
tence in the form of a replicativ-:: unit, but suffices for
molecules, other than by ligation to one large re-
copying units as small as single words. It refers to a
plicative unit, which is prohibitive due to the threshold
relation for vmax ' (Note that the units to be integrated natural situation in early evolution, where the physi-
cal forces inherent in the nucleotides may have been
have to remain competitive with respect to their
sufficient for an evolution of stable t-RNA-like mol-
mutants in order to evolve further and not to lose their
specific information.) Let us briefly investigate three ecules (= single words), but did not admit the build-
possible choices: up of an - even primitive - translation apparatus ( = a
whole 'meaningful' sentence). Accordingly, the com-
1. Coexistence. Stable mutual tolerance of self-
puter is programmed just to reproduce single words
replicative units in the absence of stabilizing in-
using error rates sufficient to guarantee their stability
teractions is possible only for individuals belonging to
against accumulation of errors.
the same quasi-species. The quasi-species distribution
As a first variant of the game let us try to establish a
could well provide favorable starting conditions for the
plain coexistence of the four words. For this purpose we
evolution of a cooperative system. However, it does not
attribute to all correct words in the sentence the same
favor the evolution of functional features. The coupling
selective value, while a mistake in any word is of
stabilizing the quasi-species is solely dictated by the
disadvantage with respect to the correct word by a
genotypic kinship relations, which usually do not
given factor (per bit). As before, the words are allowed
coincide with functional needs. Required is a set of
to reproduce, the total number being limited to N
selectively equivalent genotypes that complement each
copies. This variant, however, differs from the original
other at the phenotypic level. The quasi-species distri-
game in that the individual words now behave as
butions as such does not meet these selection criteria.
independent replicative units. Table 5 shows some
2. Compartmentation. Enclosure of a Darwinian sys- typical results: Despite the fact that all words have the
tem in a compartment will not provide a solution of this same selective value and are able to compete favorably
problem either. The main consequence of compartmen- with their error copies, the sentence as a whole is
tation is an enhancement of competition due to the unstable. Only one of the four words can win the
restriction of living space and metabolic supply. Hence competition, but it cannot be predicted by any means
a compartment will only stabilize further a given which of the four words actually wins. One may
selectively advantageous quasi-species; it will not favor characterize this situation by the tautology: 'survival of
the evolution of equivalent partners according to the survivor'. The term 'fittest' means nothing but the
functional criteria, which requires the cooperating mere result of the contest.
partners to diverge genotypically. A compartment,
In the next variant of the game we introduce a
however, may offer advantages for a system that has functional linkage between related words: A given
already established a stable cooperation via functional
word provides catalytic help for the reproduction ofthe
linkages (cf. Part C). More sophisticated compartments
next word whenever it forms a meaningful sequence:
such as' present living cells, which comprise only one (or
a few) copies of each replicative subunit together with a
machinery for reproduction of the whole compartment
require, of course, a symbol quality iim which is adapted
to the total information content according to the
relationship for vmax' In other words: They are subject
to the same limitations as a fully ligated unit. The coupling is proportional to the popUlation number
3. Functional linkages. Selection of functionally of the catalyst (i.e., to the representation of the particu-
cooperating partners may be effected via the functional lar word in the computer store). In other words,
linkages, which provide either a mutual catalytic reproduction is facilitated according to a rate law:
enhancement of reproduction or a structural stabili-
zation. A closer inspection of such linkages is the main k1x 1 and
topic of this paper. kiXi+k;XiXi_l for i=2,3,4

26
Table 5. A game representing the competition of selectively equivalent replicative units

The aim of this game is to preserve the information of the sentence: Below typical results often games are listed. The' X' indicates which
word is selected, while all the others die out. The number denotes

8 08
the generation after which selection is complete.

Game TAKE ADVANTAGE OF MISTAKE Generation


1 X 12
2 X 15
3 X 19
4 X 23
5 X 10
6 X 20
Each word symbolizes a replicative unit. All words have exactly the 7 X 9
same selective value. The selective advantage per bit is 2.7. Each letter 8 X 13
consists of 5 binary digits. 9 X 22
10 X 26
Digit Digit Word Error
mutation number quality expectation Error distribution of the selected word ADVANTAGE. The solid
_ c;ke-r
probability factor value line resembles the Poisson distribution -~; where B=v(l-q) is the
(I-ij) Q=q' k
[%J expectation value for an error in the word (v=45 bits).
(The errors refer to one single digit. All wrong letters differ from the
TAKE 3.15 20 0.53 0.63
correct ones in only one of their five digits.)

ADVANTAGE 1.4 45 0.53 0.63 o errors 1 error 2 errors 3 errors

OF 6.3 10 0.53 0.63 ADVANTAGE

MISTAKE 1.8 35 0.53 0.63 ADVANTAGE


ADVANTAGE
ADVANTAGE ADVANTAG!
Since there is no coupling among the words every game ends with the ADVANTAGE ADVANDAGE
selection of one word. All words are degenerate with respect to their ADVANTAGE ADVARTAGE
selective values; therefore, each of the four words has an equal chance ADVANTAGE ADVINTAGE
to be the survivor. Due to the high average error probability ( ~ 2 % ADVANTAGE ADFANTAGE
per bit) the sentence as a whole (125 bits) is not a stable replicative
ADVANTAGE ADZANTAGE
unit.
ADVANTAGE AHVANTAGE
ADVANTAGE AHVANTAGE ADVANDACE
ADVANTAGE
ADVANTAGE
ADVANTAGE
AHVANTAGE
AFVANTAGE
AFVANTAGE
ADVANDAIE
ADVARXAGE
ADVINTRGE
l lTVANTAGU I

Xi or Xi _ l' resp. being population numbers, in this case the sequence. However, fixed-point analysis as carried
referring to the words in the computer store. The result out in Section VII will show that, even under those
of this game variant is usually fixation of the last word special conditions, only the last member in the chain
of the sentence, i.e., 'mistake', while all other words die will grow in proportion to the total population, while
out. Only if the coupling is relatively weak and a all other members assume essentially constant popu-
particular k i value is chosen large enough do we find lation numbers, irrespective of the size of the total
that the corresponding word (i) may outgrow the population. Hence, in a growing population, the re-
others, representing selection among (essentially) inde- lative abundance of the last memberchangesdrastically
pendent competitors. The result that the last word in until the system again reaches a range where only the
the sequence receives all the benefit of coupling (when- abundant member remains stable. In the process of
ever the coupling terms are predominant) may be molecular evolution population numbers of indi-
astonishing. One would expect that there must at least viduals usuaIIy show those drastic changes, e.g., from
exist a range of stability for the whole sentence. This is one single mutant up to a detectable magnitude of
certainly true for a certain magnitude of the population (more than) billions of copies. Thus the result obtained
numbers, if the values of the rate parameters obey a in our game turns out to be quite representative of what
certain order with respect to the position of the words in actually would happen in nature.
27
The fact that linear coupling - if it works at all- feeds do not have to be the same - which would seem very
all the advantage forward to the last member in the improbable for any realistic system. Each word, fur-
sequence provides a strong hint for a possible solution thermore, is represented by a stable distribution of
of the problem: The couplings should form a closed mutants. Unless one of the words is wiped out by a
loop: fluctuation catastrophe (which becomes very improb-
able at a sufficiently large number of copies) the
population numbers will continue to oscillate. In other
words: The information of the whole sentence is stable.

VI. General Classification of Dynamic Systems

V I.1. Definitions

In the following sections we shall carry out a more


rigorous mathematical analysis of dynamic systems,
especially of those which are of importance in pre-
cellular self-organization. To determine which systems
are relevant we shall have to inspect different classes of
reaction networks including both noncyclic and cyclic.
Evolutionary processes can be described phenome-
Then the enhancement due to coupling will cyclically nologically by systems of differential equations, as has
fluctuate through all words of the sequence. Our sen- been shown for a particular case in Part A. The term
tence actually was chosen as to provide automati- dynamical system then refers to the complete manifold
cally such a cyclic overlap through the word 'mistake'. of solution curves of a given set of differential
Since each word is a catalytic cycle (i.e., a self- equations.
replicative unit) the system represents a hypercycle of Let us consider a general dynamic system that is
second degree according to our definitions introduced described by n ordinary, first-order, and autonomous
in Part A. The result of the game is represented in differential equations;
Figure 16. All four words show a stable steady-state
representation with a periodic variation of their popu-
i= 1, 2, ... , n (30)
lation numbers. The selective values of different words

Fig. 16. Each word of the sentence TAKE ADV ANT AGE OF MISTAKE represents a self-reproducing unit. The information of the sentence
is stabilized by hypercyclic coupling among the words. In the graph, each printed word is representative of to copies in the computer store.
All words in a vertical row refer to the same time, the intervals of which change discontinuously along the horizontal axis. The
oscillation builds up from an initial equipartition of words and maintains a phase shift from word to word. The error distribution for
each of the four words is stable and of the same kind as shown in Table 5

2R
Later on we shall extend our analysis also to some Assume we can express 1'; as a polynomial in the various
nonautonomous systems for which Ai = Ai(t). concentrations Xi (which as an approximation may also
As before, the Xi represent population variables that apply to irrational expressions or ratios of poly-
usually will refer to self-replicating macromolecular nomials), then it will usually be possible to find leading
assemblies. The constants ki(i = 1, 2, ... , m) enter as terms in 1';, which dominate in certain ranges of
parameters and may be composed of rate constants of concentration. These leading terms usually are simple
elementary processes, of equilibrium constants for monomials of a given power of Xi' As such they
reversible and rapidly established reaction steps and of determine the dynamic behavior of the system.
concentrations of those molecules that serve as the The simple case X = kxP is illustrated in Figure 17. The
(energy-rich) building material for the synthesis of the textbook solutions have been normalized to x(O) = 1
macromolecules, assuming that these concentrations and x(O) = 1. As outlined in the Figure's legend, the
are buffered and hence can be included as time- whole family of solution curves can be subdivided into
independent values. Both the sets of X and k values can three classes, which are restricted to different regions of
be represented as column vectors in a concentration the concentration/time diagram. Let us consider three
space, or in a parameter space, respectively, representative examples, which will be of particular

(XI)
interest in our forthcoming discussion (cf. Table 6).

X= ~2. and k= (~l)


k.2
.
x(t)
. .
Xn km 8

By B we denote the initial conditions for a given set of


solution curves, which in our case are represented by 7
the set of initial concentrations Xo'
According to the procedure employed in part A we split
the functions Ai into three terms: 6

(31)

The Ais comprise all posltIve contributions to the


chemical rate, representing an •amplification' of the Xi
4
variables, while the Llis include all negative rate terms
resembling 'd~composition' of the macromolecular
species. <Pi finally refers to a flux which may effect either 3
dilution or buffering of the component i, depending on
the external constraints applied to the system. The
difference Ai - Ll i may be called a net growth function 2
1';. Referring to the Darwinian system (cf. part A), 1';, in
I
particular, is given by H-iixi + wikx k' and if summed
k*i
over all species k = 1 to n, it resembles the excess growth
function E= I Ekx k · 2 3
k~ I
time

Fig. 17. Different categories of growth can be related to single-term


VI.2. Unlimited Growth
growth functions r(x)=dx/dt (normalized to r= 1 and x= 1 for
t = 0). Region A does not include any growth function which could be
Removal of selection constraints leads to a new system represented by a simple monomial r = x p • In this region all popu-
of differential equations lation numbers x(t) remain finite at infinite time. The borderline
between region A and B is given by the growth function r(x) = e'-x
Xi = 1';(x, k, B) (32) (curve 4). Region B is spanned by all monomials r(x) = x P with
- w <p < I. Curve 1 in this region exemplifies constant growth rate
describing a situation which in the following is called (p = 0) equivalent to linear growth. Exponential growth (p = 1)
provides the borderline between regions Band C (curve 2). While
'unlimited growth '. This terminology is representative population numbers in region B reach infinity only after infinite time,
for the system as a whole; for individual members it they show singularities at finite times in region C. As an example,
may also include decay or stationary behavior. hyperbolic growth (p =2, singularity at t = I, = 1) is shown by curve 3

29
i) Solution curve 1 represents a system with constant therefore necessary to formalize these conditions and
(positive) growth rate. The population variable x(t) include them in the theoretical treatment.
increases linearly with time. The solution curve also In irreversible thermodynamics we would prefer selec-
represents an example for the family of curves in tion constraints that facilitate a thermodynamic de-
region B of Figure 17, which grow to infinity at infinite scription, e.g., constant generalized forces or constant
time. An irreversible formation reaction with totally generalized fluxes. For the analysis presented here, we
buffered concentrations of reactants mav serve as the have to adjust these to conditions for selection and
most common example. Self-reproducing species in evolution that can be materialized in nature. The
ecologic niches, feeding on independent sources, may constraints qJ;, as used in Equation (31), are too general
adjust their growth rates to the constant influx or for any straightforward analysis. In general we may
production rate of food and then constitute another distinguish between specific and nonspecific selection
example for a growth behavior which is independent constraints. In the first case, the constraints act specifi-
of the population size. cally on a single species or on a few species whereas the
ii) Solution curve 2 results from growth rates linear in second case refers to regulation of a global flux ¢. Then
the popUlation variable and exhibits an exponential changes in all population variables are proportional to
increase of x with t, typical of Darwinian behavior, as their actual values Xi:
was shown in Part A. The curve 2 furthermore estab-
lishes the borderline between regions Band C, i.e., (34)
between functions that reach infinity at infinite and at
finite time. In practice, nonspecific selection constraints can be
iii) Solution curve 3 finally represents an exampfe for introduced into a dynamic system by the application of
functions with a singularity at finite time [tc = (kx o)- 1]. a continuous dilution flux. Thereby the total con-
In this particular case, the growth rate was assumed to centration, c = I Xi' can be controlled. The correspond-
be proportional to the square of the population ing differential equation for c:
variable.
n n
The whole range C may be characterized as 'hyperbolic c= I Xj = I I](x)-¢ (35)
growth'. Of course, in any real and finite world a j~ I j~ I
population can never grow to infinity, because the
fulfils the condition of stationarity: c= 0, when the flux
available resources are finite and hence constraints will
is adjusted to compensate the net excess production:
always tak.e care of growth limitations. The phenomena
giving rise to the hypothetical existence of a singularity
will still cause a behavior quite different from that ¢=¢o= II](x) (36)
j~ 1
encountered in Darwinian systems.
This selection constraint, referred to as 'constant
At this point we may define the 'degree' P of the growth
organization', has been introduced previously and was
functions in a more general way, which will turn out to
also used in Part A. Condition (36) will be used
be useful for classification. As before, Pi is the power of
frequently in the following sections to facilitate a
the leading term in the growth function rio An n-
general analysis of selection processes. Other con-
dimensional dynamic system then may be character-
straints have been investigated as well [53]. As will be
ized by a set of Pi values: (PI P2 ... pJ. When we have a
seen in the next section, the important features of
uniform distribution of powers Pi'
selective and evolutive processes are fairly insensitive
Pi=P2="'=Pn=P, (33) to the constraints applied. (These, of course, are always
reflected in the quantitative results.)
we shall call the system 'pure'. Otherwise we are The condition of constant organization leads to the
dealing with 'mixed' systems, which may be classified following differential equations for the dynamic
by their distributions of Pi values. Obviously, 'pure' system:
systems can be analyzed much more easily than 'mixed' X. n
systems. Xi=r;(X)----'- II](x), i=1,2, ... ,n (37)
Co j~ 1

Here Co denotes the stationary value of the total


VI.3. Constrained Growth and Selection concentration which may be maintained by regulation
of the flux to the value ¢o'
In reality we shall always encounter constraints which The individual selection behavior for the three simple
provide certain limits for growth. For experimental growth functions: P = 0, 1, and 2, as discussed III
studies, we must insure reproducible conditions. It is connection with Figure 17, is detailed in Table 6:

30
Table 6. Growth rates and selection behavior under the selection constraints of constant overall organization in the dynamic system
.x=f-q,
p Unlimited growth Long-term behavior under constraints of constant organization

Growth rate Solution curve Type of growth x Type of selection behavior


r(x)

1
2 ° k
kx
x=xo+kt
x=xo·exp(kt)
linear
exponential
x,=k,co/Ik j
xk=CO,Xi=O
Coexistence of species with no selection
Competition leading to selection
of the globally 'fittest' species
kk-k,>O,i+k
3 2 kx 2 X = xo(1- kXot)-1 hyperbolic xk=CO,xj=O Competition aiming at local optimization
k=1,2, ... ,n;i+k 'once-for-ever' decision

i) Constant growth rates - corresponding to a linear


increase of the population with time - yield under the (38)
constraint of constant organization a stable coexistence
of all partners present in the system. Upgrowth of Either e(t) or 4>(t) can be chosen freely. The other
advantageous mutants shifts the stationarity ratios function, however, is determined then by the following
without causing the total system to become unstable. differential or integral equation, respectively.
ii) Linear growth rates, corresponding to an exponen-
de
I
n
tial increase of the population size, result in com- 4>(t) = T;(x) - - or (39)
petition and selection of the 'fittest'. Advantageous i~ I dt
mutants, upon appearance, destabilize and replace an
established population.
iii) Nonlinear growth rates (p> I), characterized by
e(t)=eo + ittl T;(X)-4>("t)}d"t (40)

hyperbolic growth, also lead to selection, more sharply It is appropriate now to introduce normalized popu-
than in the Darwinian system mentioned under ii).
Mutants with advantageous rate parameters, however, lation variables ~ = ~ x. The differential equations then
e
in general will not be able to grow up and destabilize an
can be brought into the form:
established population, since the selective value is a
function of the population number (e.g., for p=2,
W ~ x). The advantage of any established popUlation (41)
with finite x hence is so large that it can hardly be
challenged by any single mutant copy. Selection then As we see immediately, ~i does not depend explicitly on
represents a 'once-for-ever' decision. Coexistence of the selection constraint 4>(t). There is, however, an
several species here requires a very special form of implicit dependence through e(t). We therefore push
cooperative coupling. our general analysis one step further by considering
The examples mentioned are quite representative. We some obvious examples: Let us assume that the net
may classify systems according to their selection be- growth functions T;(x) are homogeneous of degree A in
havior as coexistent or competitive. In a given system x. Although this condition seems to be very restrictive
we may encounter more than one type of behavior. we shall see that almost all our important model
systems will correspond to it, at least under certain
boundary conditions. Homogeneity in x leads to the
VI.4. Internal Equilibration in Growing Systems same condition as the requirement of a defined degree
p(A = p) in the unlimited growth system (see Sec. 1.5).
While the condition of constant organization simplifies Now, the transformation of variables is rather trivial:
the analysis of dynamic system considerably, it is (42)
limited to systems with zero net growth. In this section
we shall try to extend the range of applicability. The and we obtain for the rate equation:
main problem is to find out in which way and under
which conditions predictions on growing systems can
(43)
be made, given the results obtained from an analysis of
the corresponding stationary states. For this purpose
we introduce nonspecific and time-dependent selection Two important conclusions can be drawn from a
constraints (Eq. 34): simple inspection of this equation: If A= p = 1, i.e., for a

31
Darwinian system as discussed in Part A, the de- dimensional map provide us with a vague feeling for the
pendence on c vanishes and not only the long-term three-dimensional scenery. It is this kind of problem
behavior but also the solution curves are identical in that fixed-point analysis deals with. The landscape
growing and stationary systems as far as relative corresponds to a potential surface along which the
population variables ¢i are concerned. dynamic system is moving. In most cases a complete
If A= p =1= 1, the long term behavior of ¢ will be identical knowledge of this potential surface is not required, and
with that for the stationary system at constant organi- therefore a 'fixed-point map' will turn out to be much
zation, provided c(t) becomes neither zero/nor infinite. simpler than a survey map we use to orient ourselves in
Thus for all realistic systems with homogeneous net an unknown region. In general, the ' fixed-point map'
growth functions T;, the results offixed-point analysis in shows exclusively the positions of locally highest and
~ space, as obtained in the next section, will be valid lowest points, such as mountain peaks, passes, and
also for the case of growing populations. valleys, which are called sources, saddles, and sinks.
It is possible to generalize the latter result also to other Such special points are the fixed points of the potential
classes of growth functions, as will be shown in the field. Often it is necessary to include also the ridges as
section on fixed-point analysis. Internal equilibration
simplifies analysis of complex dynamic systems tre-
mendously. In many cases the results become identical a
or similar to those for stationary conditions. If we ana-
lyze for the selective behavior of a system, these are the
conditions which count. In the following section we
shall inspect more closely various dynamic systems
under these conditions.

VII. Fixed-Point Analysis


of Self-Organizing Reaction Networks

VI 1.1. The Appropriate Method of Analysis

In analyzing various molecular processes of self-


organization we are naturally more interested in the
final outcome of selection than in a detailed resolution
of the dynamic process. Accordingly, in this section we
do not need all the information that is provided by the
complete set of solution curves satisfying a system of
differential equations. Fixed-point analysis, therefore,
is our method of choice, because it serves best the
purposes of a comparative analysis of selective be-
havior. Only in some cases shall we also consult more
sophisticated techniques, such as the inspection of the
complete vector fields.
Nowadays, fixed-point analysis is a routine technique
for studying the long-term behavior of dynamic sys-
tems. It can be found in mathematical textbooks or
treatises (see, e.g., [48J). Fixed-point analysis has also
been applied to problems of economics and to ecologic
models as well as to chemical reactions far from
equilibrium [49]. A summary of the present stage of b
development was given recently in a progress report
Fig. 18. a) A topographic map provides an abstract representation of
[50].
a landscape. The lines drawn connect points of equal altitude. The
picture shows a region in the Eastern Alps. (reprinted from
"Osterreichische Karte" I: 50000 Blatt Nr.177 (1962) by courtesy of
VII.2. Topologic Features Bundesamt fUr Eich- und Vermessungswesen Abt. Landesaufnahme).
b) The fixed-point map is a further abstraction of the topographic
Let us imagine a mountainous country for which we map. The drawing records the fixed points of a): 0 sources or peaks,
have a map (cf. Fig. 18). The contour lines in the two- E8 saddle points, • sinks; the solid lines here mark the separatices

32
lines which separate one valley from another (Fig. 18). CLASS W, W2
Characteristically, they are called 'separatrices'. A

+•
fixed-point map including separatrices is sufficient to
predict where a trajectory starting from a given point <0 <0 NODE }
on the map will lead. Trajectories are the lines of <0 W,=W 2 FOCUS SINKS
'i' -a+ib
<0
steepest descent, which in a landscape will be followed -a-ib a,b>O SPIRAL
by flowing water. The gravitational potential field on
the surface of the earth, on the other hand, is less 2 ED >0 <0 SADDLE
complicated than the fields we encounter in self-
organizing dynamic systems. Whereas water flowing on 3 0 >0 >0 SOURCE
earth always approaches a sink, such as a lake, self-
4 (I) >0 =0
organizing dynamic systems may show a more complex
behavior. For instance, there are situations called limit 4 e =0 <0
cycles where - in the language of our illustration- 4 @ +ib -ib CENTER
water would never stop flowing at a certain point but
rather would circulate forever along a closed line Fig. 19. Symbols are used to classify various fixed points: Class 1:
stable fixed points or sinks; Class 2: saddle points; Class 3: sources;
determined by the shape of the potential field. Even
Class 4: unstable fixed points including eigenvalues OJ with zero real
stranger situations have been described, to which parts. The examples refer to a two-dimensional dynamic system
mathematicians actually refer as 'strange attractors',
representing something like non periodic orbits. Attrac-
tor is a more general expression than sink. It includes
(1) Stable fixed points or sinks, i.e., locally lowest points.
not only sinks, but also stable closed and nonperiodic
All eigenvalues W k have negative real parts and hence
orbits.
fluctuations along all possible directions in concen-
In a fixed-point map, the whole area under con-
tration space are compensated by an internal coun-
sideration can be separated into a number of regions
teracting force. In chemistry, sinks correspond to
usually called basins, belonging to individual attrac-
chemical equilibria in closed and to stable stationary
tors. The boundaries of these regions are the separat-
states in open thermodynamic systems.
rices. Thus, from all points of a basin the water flows to
the same attractor, which of course has to lie inside that (2) Saddle points with at least one direction of in-
region. stability. Here one w k value at least will have a positive
Now let us be more precise and characterize the real part. Consequently, a small perturbation or fluc-
quantities and expressions that are necessary for fur- tuation in this direction introduces a force that tends to
ther discussion in mathematical terms. Fixed points or increase the fluctuation. As a result the dynamic system
invariant points of dynamic systems are defined as will move away from the saddle.
those points at which all concentrations or population
variables, Xi' are constant in time. Hence, the first time (3) A source representing a locally highest point. It
derivatives vanish differs from the saddle only by the fact that it is unstable
with respect to all directions. All W k values have
positive real parts.
Xi=O, i=1,2, ... ,n (44)
(4) Another class of fixed points, which cannot be
analyzed completely within the linear approach. Some
thereby determining the positions of all fixed points
of the frequencies W k show zero real parts and the
belonging to a given dynamic system. When all random
nonlinear contributions may change their nature. An
fluctuations in population variables are strictly sup-
example is provided by centers that are defined by
pressed, integration of the dynamic system starting at a
purely imaginary eigenvalues, and whose trajectorial
fixed point trivially leads to time-independent, constant
representations are manifolds of concentric orbits. We
populations. The response of the system to small
shall encounter such situations in this paper.
changes in concentration at given fixed points provides
an excellent tool for a classification of these points. It After 'long enough' time - which means a period much
can be described by a set of normal modes with longer than the largest time constant of the dynamic
reciprocal time constants wk , which are obtained as the system - every realistic dynamic system (i.e., a system
eigenvalues of a system of linear differential equations without external suppression of fluctuations) will ap-
representing the best fit of the nonlinear system around proach an attractor. Thus the result of selection will
the point of reference (cf. VIl.4). Accordingly we can always coincide with an attractor in concentration
distinguish four main classes of fixed points. space.

33
The final result of a selection process corresponds either (CD'0,O) =(1,0.0)
to a stable stationary state or to a continuously and 1
periodically changingfamily of states. In some very rare
situations nonperiodic changes within a defined set of
states may occur as well. For all these stable or quasi-
stable final situations a common, general expression is
a
used in differential topology: the 'attractor' of the
dynamic system, which includes the stable point, the
closed orbit, and the aperiodic line. Within a given basin,
the result of a selection process is approach to an 01
attractor, which is independent of the particular initial
conditions. ......
- - x]_
..
.. .." ..... 3
(O.O.C o)': (0,0.11

VII.3. An Appropriate Space:


the Concentration Simplex
co----- 3=(O,O,Co)=IO,O,1l
The concentration variables or population numbers
span the n-dimensional open space IRn : {Xl' X 2 , 00., Xn; Sl__
-oo<Xi<oo, i=I,2,oo.,n}, only part of which is 2
physically meaningful: b 2 = (D,CO'O) =10,1,0)
~~~--~~--?X2
)l(ncIRn; )l(n: {Xl' X2, 00., Xn; Xi~O, i= 1, 2, 00., n} (45)

All concentration variables can be summed to give a


non-negative and finite total concentration c:
1= (CQlO,O) =(1,0,0)
n

c= I Xi' O~C< 00
i= 1
Fig. 20. Diagram a) illustrates the simplex S3 while diagram b) shows
which is used for normalization: how it is embedded in the physically accessible concentration space.
For some of the points the total concentrations Co = l: x" or the
,
I 1 ~i=I (46) coordinates x" x 2 , X3 and e!, e e are given in parenthesis
2, 3
i=

According to the properties of the variables )l(n can be Finally, we would like to stress a difference between
mapped now isomorphically onto a unit simplex (Sn) maps on )l(n and §n which becomes apparent when we
for any given value of c = co. (The corresponding space compare results obtained for different values of co' Due
will be denoted by §n): to normalization, the size of the simplex Sn is fixed,
whereas the physically accessible region of)l(n varies
(47) with Co' The positions and the normal modes of fixed
points, in general, will depend on Co too. For a complete
A unit simplex Sn is a regular polyhedron with n corners description of the long-term behavior of dynamic
in the corresponding (n -I)-dimensional subspace de- systems, it is necessary to evaluate fixed-point maps
n
fined by I ~i = 1. The edges of a simplex are of unit which themselves are 'functions' of the total con-
centration co. Many fixed points, as we shall see later,
length and represent coordinate axes for the variables show a simple concentration dependence: Their coor-
~i' As an illustrative example S 3 is shown in Figure 20. dinates are proportional to co. Upon changes of the
Diagrams on S 3 are familiar to chemists from the total concentration co' these points move along lines
representations of ternary systems. passing through the origin of )l(" (see Fig. 21) and
As a consequence of Equation (46) the dynamic system consequently are mapped as single points on Sn.
on the unit simplex has lost one degree of freedom Accordingly the fixed-point map as a whole becomes
compared to )l(n. In other words: Due to normali- much simpler. This formal dependence of fixed-point
zation, the variables ~i always refer to a fixed value of maps on the values of total concentration Co will be of
c = Co and thereby one linear dependence is introduced particular importance in the analysis of growing
among the variables. systems.

34
while the coefficients Aij are the elements of an n x n Jacobian matrix
(A) defined at the fixed point x:

(50

°
Since A,(x) = by definition of the fixed point, the linearized system of
differential equations is given by

z=A·z (51)

The reciprocal time constants referring to the normal modes are


obtained now as eigenvalues of the matrix A. The eigenvectors ~i
determine the corresponding linear combinations of concentration
XI variables.
Fig. 21. Illustration of some points with positions exhibiting charac- (52)
teristic dependence on total concentration Co in concentration space
)1(3 (a) and on the simplex 53 (b). A = (c o/3, c o/3, c o/3), 8=(0, 0, co), The w)' in general, are complex quantities and determine the nature
C=(I, co-I, 0) and D=(co-l, co-I, 2-c o). The arrows in of the fixed points, the most important ones of which have been
a) indicate where the points migrate with increasing total concen- summarized already in Figure 19.
tration (note that those points for which all coordinates are propor- Provided the matrix A is not singular, a stable fixed point of the
tional to Co like A and 8 are mapped into single points on 53) linearized system (51) corresponds to a stable fixed point of the
nonlinear problem in almost all cases [51 J. There are, however, some
important exceptions (Rew)=O): A center in the linear system may
appear as a spiral sink in the nonlinear case and vice versa. The
A highly symmetric part of a particular (n -1)- famous Latka-Volterra model system represents one example for this
dimensional hyperplane embedded in n-dimrnsional con- kind of behavior [52]. We shall encounter another one, the hyper-
centration space is called the uni't simplex. An illustration cycle of dimension n = 4, in Section VIII.1.
If more than one stable fixed point, limit cycle, or other attractor is
of a simplex, which can be described in three-dimensional
obtained for a given dynamic system, we would also like to know the
space and therefore is easy to visualize, is given in Figure basins for which the attractors represent the infinite time limits of the
20. The unit simplex includes the total physically mean- trajectories. Individual basins are separated by separatrices, which
ingful range of concentrations and is best suited for a can be determined in principle by backward integration (t -> - t)
diagrammatic representation of selective processes. starting from saddle points and following the lines of steepest descent.
If all stable fixed points and other attractors for a given dynamic
system as well as their basins are known, we can predict the result of a
selection process starting from any point in the given concentration
VIl.4. Normal Mode Analysis space.
In some cases we shall obtain Re Wj = 0. Linearization around the
Starting from the general system of nonlinear differen- fixed point then does not provide enough information, and one has to
go back to the nonlinear dynamic system for a complete characteri-
tial equations we first determine the fixed points zation. Often, direct inspection of the vector field around the fixed
according to Xi = O. For a straightforward analysis of a point is not too involved and yields the desired results.
dynamic system, it is important to know all the fixed
points in the region under investigation. In general, Determination of normal modes is an intrinsic part of
however, this information will not be sufficient. Trajec- fixed-point analysis. It represents an inspection of the
tories of the n-dimensional dynamic system will often trajectories of the dynamic system in the close vicinity of
end in sinks. However, there may be stable closed orbits the fixed point. In most cases it is sufficient to character-
or strange attractors, the existence of which can be ize the stability properties of the fixed point. The linear
guessed by a careful inspection of the nature of the fixed approximations involved, however, may not always
points in the surrounding region and an analysis of the suffice to provide enough information, requiring more
vector fields. For instance, stable limit cycles in two sophisticated methods of analysis.
dimensions can be identified by Poincare maps. Infor-
mation on the nature of the fixed points can be obtained
by normal mode analysis. VII.5. Growing Systems

For this purpose the dynamic system is linearized in the neigh- From Equation (37) it is easy to deduce a differential
borhood of a given fixed point x: equation for the total concentration c:

z,=Ai(x)+
n
L A,)zj+O(lzI2)
j= 1
(48)
c= ±
j~ 1
lj(x) (1 -~)
Co
(53)

The new variables z, are defined by


Co represents the stationary value of the total con-
(49) centration which is controlled by the unspecific flux 4>0'

35
Apparently, this equation has a fixed point at c=c o' systems describing transitions between different levels of organi-
The eigenvalue of the normal mode zation have to pass through certain critical stages or periods. To be
more concrete we shall consider one example representing an
important problem in self-organization of biologic macromolecules:
the transition from independent competitors to a functional unit
(54)
consisting of cooperating polynuc1eotides and proteins. According to
the definition given in Section 1.4, only one species is selected in a
is negative as long as the sum of all net growth terms r; competitive system and hence there is no stable attract or in the
interior of Sn' Any cooperative system, on the other hand, has to have
is positive. Thus we find a stable stationary state at such an attract or, otherwise at least one of the cooperating macromo-
c=c o' lecules would die out after long enough time. Consequently, a
In certain systems the fixed-point maps referring to dynamic system, which in principle is able to simulate the desired
development from a more random to a more organized state, must
internal organization also depend on the values of the
contain a critical instability at certain values of its parameters.
total concentrations co. Now, we are in a position to
attribute some physical meaning to the former purely
mathematical treatment. For this purpose we assume a VJI.6. Analysis of Concrete Systems
nonstationary dynamic system, which starts to evolve
a) Independent Competitors
at t = to with a corresponding initial value of total
concentration, c(to) = co' Selection constraints will be As a lucid example for the application of the method of
adjusted in such a way that the total concentration c(t) fixed-point analysis we consider the problem of selec-
changes slowly in comparison to the internal processes tion of a quasi-species, treated in Part A. The mathe-
of the dynamic system, i.e., all changes due to external matical framework is compiled in Table 7. The coor-
processes are much slower than changes due to internal dinates of the concentration space are given by the
organization. The system approaches a stable solution normal variables Yk; the eigenvalues Ak are the growth
(i.e., a sink, a stable closed orbit or another kind of parameters of the functions' Ii.. The analysis refers
attractor) at every instant. When the preceding con- to a given distribution of mutants. Appearance of
ditions are fulfilled the system comes closely enough to new mutants that provide any contribution to the
the long-term solution and the time-dependent process selected quasi-species will change the meaning of the
can be described as a sequence of stationary solutions concentration coordinates Yk' i.e., their correlations
with continuously changing total concentration. In with the true concentration variables X k . The results in
more physical terms we may say, the dynamic system Table 7 are self-explanatory. We shall use them in the
develops under established internal equilibrium. As following for a comparative discussion of the three
expected, the analysis of a system can be simplified growth functions r; = kixf which appear in Table 6, i.e.:
enormously if the condition of internal equilibration is
1. Constant growth rate: p=o
fulfilled.
2. Linear growth rate: p=l
Internal equilibration in dynamic systems with homogeneous growth 3. Quadratic growth rate: p=2
functions r, is easy to analyze, because in this case the fixed-point
maps S" do not depend on the total concentrations co. From low to I. The first case yields one stable fixed point, a focal sink inside the
high values of Co no change in the selective behavior will occur. unit simplex S":
Moreover, in growing homogeneous system the long-term devel-

x=+ (~.:)
opment does not depend on the degree of internal equilibration.
(55)
The ultimate result of a selection process, thus, will be the same in.
systems of this type, independent of whether internal equilibrium has "k
L... J :•
been established during the growth period or not There are, however, J= 1 kn
situations to which the concept of internal equilibration must not be 'Inside' the unit simplex means for all coordinates of x: 0 <x, < co.
applied without careful analysis. At certain critical total con- The (negative) eigenvalue of the Jacobian matrix is n-fold degenerate
centrations, C = C,n discontinuous changes may occur in fixed-point
maps, e.g., sinks may become unstable, stable limit cycles may
disappear, etc. A well-known instability ofthis kind is represented by "I k j
(0= _i= 1
a 'Hopf bifurcation , [58]. An internally equilibrated dynamic system (56)
Co
which reaches such a point from one side, e.g., a growing system
approaching the critical concentration from lower values, is essen- holding also for w" which refers to the variation of the total
tially off equilibrium after it passes the critical point For the analysis concentration c.
of dynamic systems in the surroundings of such points, special care is The result is stable coexistence of all species.
needed. We shall encounter some such examples in Section VII. A· 2. The second case is treated in Table 7. As we recall there is only one
very general study of similar situations has been pursued by R. Thom stable fixed point The fact that it is situated at the corner of the
[59] in his catastrophe theory. simplex indicates competitive behavior. Only one of the con-
These complicated dynamic systems, of course, are more interesting centration coordinates of the nodal sink is positive ( = co), all others
from the biophysical point of view. In fact, the emergence of being zero. As in the first case, the map does not depend on the overall
organized structures requires drastic changes like the discontinuities concentration co' nor is the final result dependent on initial
mentioned above in the fixed-point maps. Inevitably, dynamic conditions.

36
Table 7. Fixed-point analysis of the selection of a quasi-species (cf. part A)

The rate equation reads: Wjl)=A J-).! wj2)=A j -A2 II Wj")=AJ-A"


j=2,3, ... ,n-l,n j=1,3, ... ,n-l,n ... j=I,2, ... ,n-2,n-l
W~l)= -A 1 w~2) = - .1.2 UJ~n) = - An

With respect to the degrees of freedom of the simplex S", each fixed
point Yk has n -1 normal modes with the reciprocal time constants
The long-term behavior IS determined by n fixed points at the wjk) describing the process of internal organization of the distribution
corners of the simplex S" resulting from competition among different quasi-species. Further-
more the simplex S" has one normal mode w;kl which corresponds to a
variation of the total concentration c. All Internal modes wjk) are
represented by differences of eigenvalues A. Hence there is only one
stable fixed point for the largest eigenvalue: Am> Aj , j = 1, 2, ... , n,
'*'
j m. It is a nodal sink, i.e., all wt) values are different and negative.
Accordingly, the quasi-species with the smallest eigenvalue is
described by a source, owing to its positive w} values. The remaining
Normal mode analysis yields for every fixed point Yk a spectrum of n- 2 fixed points then are saddle points, because they involve positive
n wj') values. as well as negative normal-mode rate constants wjk)

3. The third case finally shows a total of2" -1 fixed points, which can These are the only stable fixed points. Being at the corners of the unit
be grouped in three classes. simplex they indicate again a competitive behavior, allowing for only
The first class includes n focal sinks, one at each of the corners of S" one survivor, i.e., a pure state. In this case of nonlinear growth rates,
however, the result of the competition depends on initial conditions,
since there are n stable fixed points (in contrast to only one stable
fixed point for linear autocatalysis). This means that each of the n
with wjk)= -kkCO j= 1,2, ... ,n-l (57) competitors can decide the contest in its own favor, depending on
W~k)= -kkC O initial population numbers. Once the winner is established, there is no
easy way for any competitor to grow up and replace it. We therefore

El

11,0,0 )
1

+ 3 2
(0,0,1) (0),0 )
a b c
Fig. 22. Three-dimensional fixed-point maps for different types of b) Linear growth rate (p = 1),
independent competitors at constant organization. (The symbols E,
CD, and ® have been introduced in Fig. 10).

A pure state consisting of species 3 represents the only stable long-


a) Constant growth rate (p=O), time-range solution of the system. With the exception of the two
edges 12 and TI all trajectories start in point 1 and end in point 3.
c) Quadratic growth rate (p = 2),

The map shows a focus inside the unit simplex S 3 which means stable The simplex S 3 is split into three regions, each being a basin for a
and coexistent behavior of all three species. It is easy to visualize the stable fixed point. The size of the basin is correlated directly with the
whole manifold of trajectories approaching the stable focus along values of the corresponding rate constants. Since k3 is largest the fixed
straight lines through every point in S". point "3
has the largest basin

37
call this situation 'once-for-ever selection'. As in the two preceding required to facilitate phenotypic diversification. The
cases the fixed-point map does not depend on the total concentration third system, finally, is strongly anticooperative, to
Co·
The two other classes of fixed points include one source in the interior such an extent that a species, once established, selects
of the unit simplex (all coordinates being finite) and 2n - n - 2 saddle against any mutant, whether or not it provides a
points, one on each edge and one in each face (including all possible selective advantage.
hyperfaces) of Sn' Both classes of fixed points represent unstable Following up the suggestions which emerged from the
behavior. We dispense with listing their coordinates and normal
modes; they can be obtained by straightforward computations.
comparative review in Section V we shall now in-
Instead we illustrate the typical selection behavior of the different vestigate more closely ensembles with functional link-
growth systems by showing some examples of unit simplices of ages. They will have to include replicative units for
dimension 3 (cf. Fig. 22). the purpose of conservation of the genetic information,
The three relatively simple model cases have been at the same time they will have to be stabilized
chosen to exemplify the method of fixed-point analysis cooperatively via couplings, which will cause the
and to stress those properties we have to watch out for. growth function to be inherently nonlinear. The pro-
The nature of the fixed point, especially whether it perties to be expected for the linked system hence will
provides stable or unstable solutions, is of utmost bear some relation to the third example of independent
importance for problems of selection and evolution. Of competitors.
no less significance is the position of the fixed points in
the unit simplex. Cooperative selection of a set of b) Catalytic Chains
replicative units requires the fixed point to lie in the The most direct way of establishing a connection
interior of the unit simplex Sk referring to a subspace XC k among all members of an ensemble is to build up a
formed by the concentration coordinates of the k chain via reactive couplings, much as we link words
cooperating units. On the other hand, the position of into sentences in our language (Fig. 23).
a sink at one of the corners of Sk is representative 'of
competition, leading to selection of only one com- The rate terms referring to these couplings will cause the net growth
functions r; for all but the first member to be nonhomogeneous:
ponent, while positions at edges, faces, or hyperfaces
indicate partial competition and selection.
The build-up of a translation apparatus, for instance, Co
i (kjXj+kjXjXj_l)]
Xl =klx l -~ [klXl +
J= 2

requires the concomitant selection of several repli-


cative units as precursors of different genes. None of the xi=k,x,+k;XiXi_l-~ [klXl + i (kjXj+kjXjXj_l)]
Co j= 2
three systems discussed above fulfils the requirements for i=2,3, ".,n. (58)
for such a concomitant selection. The first system
appears to ~e coexistent, but it is not selective and Due to the lack of homogeneity the fixed-point maps will be of a more
complicated form than in the cases discussed thus far.
therefore cannot evolve to optimal function. The
To keep the procedure lucid we start with a three-dimensional system
second system allows for coexistence only within and extend our analysis later to higher dimensions. Table 8 contains a
narrow limits of the quasi-species distribution; it does compilation of the pertinent relations of dimension three together
not tolerate divergence of the genotypes, which is with a brief characterization of the fixed-point map. According to this

(b) (c) (d)

Fig. 23. Fixed-point maps of a catalytic chain of self-replicative units At low concentrations (a) the stable solution corresponds to selection
@ under the constraint of constant organization: of species 1. If the two other species, however, have not yet been
extinguished when the total concentration reaches a critical value, a
r l =klx l ; new stationary state emerges, at which all three species become stable
r;=k,x, +k;xix,_l (for i=2, 3) (b). With a further increase of the total concentration (c), only species
3 is favored so that the final situation (d) is equivalent to a selection of
kl =3; k 2 =2; k3=1; k~=2; k~=l
species 3. The underlying mechanism, however, differs from that for
l=x l ; 2=x 2 ,,·6=x 6 independent competitors

38
Table 8. Fixed-point analysis of catalytic chains of dimension three
The fixed-point map shows six fixed points with the coordinates and normal modes as given below:

w\j)=k 3 -k l w\2)=k j -k2 w\3)=k l -k3


wi l ) = k~ Co - k j + k2 w~2)=k~co-k2+k3 wh3) k2 - k3

_
X6
( kl~k2)
k j -k3
~k-'-
3

k~k~co-k~(kl -k2)-k~(kl-k3)
K
k~k~

(k~co - k2 + k3Hk3 - k 2)
W\6) and w~6) are the eigenvalues
k~co
of the Jacobian matrix A(x = X6)'

The three fixed points Xj' X2 , and X3 coincide with the corners of the the position of the fixed point X4 , X5 , or X6 , respectively, lies outside
unit simplex S3 (ef. Fig. 23) and hence signify competitive behavior the simplex S3' which means outside a physically meaningful region
- irrespective of their nature. The positions of the three other fixed of the concentration space. (At least one concentration coordinate is
points depend (linearly) on the total concentration co' The two fixed negative.) For Co -> 0 the positions of these fixed points even approach
points x4 and X5 move along the edges 12 and 23 of the simplex, infinity. The dynamic system becomes asymptotically identical with
thereby showing partial competition. Solely the fixed point X6 may the system of exponentially growing (non coupled) competitors,
pass through the interior of S 3 yielding cooperative selection of all characterized by the fixed points Xj' X2 , and x3 •
chain members. If k j > kz, k3 and Co is above a threshold given by the sum of
[(k j - k2)/k~] + [(k j- k3)/k~], the fixed point x6 , indicating coopera-
At low total concentration: tive behavior, enters the u~it simplex. However, it does not ap-
proach any point in the interior of S3, but rather migrates toward
the corner 3.

analysis, the three members (II to 13 ) of the linear chain of self- Co below the critical value given by Equation (60), the three fixed
reproductive units can be selected concomitantly only under very points X4 , x5 ' and X6 lie outside the unit simplex (Fig. 23a). If Co
special conditions, namely equals the critical value, the fixed point X6 reaches the boundary of
the simplex (Fig. 23b) and, with increasing co' migrates through its
(59) interior. At the same time it has changed its nature, now representing
and a stable fixed point (Fig. 23c), which in this particular case is a spiral
sink. (A more detailed presentation of fixed-point analysis with
inhomogeneous growth functions will be the subject of a forthcoming
(60) paper [53]). Figure 23d indicates the final fate of this stable fixed
point, namely, migration to the corner 3. The system thereby
It seems very unlikely that partners which happen to fulfill condition approaches the pure state X3 =c o·
(59) can maintain it over long phases of evolution (which means that The relevant results obtained for three dimensions can be generalized
mutations that change relation (59) must never occur). Even if they easily for the n-dimensional system. The role of species 3 is now taken
are able to do so, the system will then develop in a highly asymmetric by species D. Instead of six we find 2n fixed points. The most
manner, whereby - at least under selection constraints - only the interesting fixed point is x2n • Its position can easily be determined:
population number ofthe last member in the chain increases with Co.
Being aware that this soon means a divergence of population k j -k2
numbers by orders of magnitude, we may conclude that such a system
k~
will not be able to stabilize a joint function, since it cannot control the k j -k3
relative values of population numbers over a large range of total
k~ (61)
concentrations.
This behavior is illustrated with some examples in Figure 23,
presenting some snapshots of a continuous process in a system c - I kj-k J

growing in a stage close to internal equilibrium. For concentrations o j= 2 kj

39
If and only if the rate constants fulfil the relations k1 > k),j = 2,3, ... , n networks does not reveal any unexpected, new features. At very low
and the total concentration exceeds the critical value: total concentrations the three species behave like independent
competitors. There are now two critical values of Co' at which either
c
cr
= I
J= 2
k1 -k j
k~
(62)
II and I2 or II and I, become coexistent. This finally depends on
whether I2 or I, is more efficiently favored by II. One of the two fixed
points turns out to be a stable node, the other a saddle point. At
the fixed point x2n lies inside the simplex Sn. Then, x 2n corresponds higher total concentration the stable fixed point again migrates
to a stable stationary state. All concentrations besides xn are toward one of the corners 2 or 3, respectively. An illustration of this
constant at this state and hence the system approaches the pure behavior is given in Figure 24.
state xn = Co at large total concentrations. The three-dimensional system investigated here can be generalized in
two ways:
1. More than two branches may start out from a given point.
We may summarize the behavior of catalytic chains:
2. The individual branches.may contain more than one member. The
1) Statile sationary states exist only when the rate results offixed-point analysis of these many-dimensional systems are
constants and the total concentration fulfil certain essentially the same as those obtained in three dimensions and can be
relations: summarized as follows:

Branched systems of self-replicative units are not stable


over long time spans. The branch which is most efficient
The system must be subject to selection constraints in in growing will be selected while other branches will
order to select against other nonfunctional units, and disappear. What remains finally is the most efficient
the required order of rate constants must not be linear chain and thereby the whole problem is reduced
changed by selection of favorable mutants. to a dynamic system of type (58), which we have
2) Provided the conditions given in (1) are fulfilled, the discussed in the previous section.
concentrations of individual species are of a compara-
ble magnitude only in a rather small range of total
concentrations. With increasing values of Co the last
member ofthe chain, In' grows under (quasi-)stationary VII.7. Fixed-Point Analysis of Hypercycles
conditions and finally will dominate exclusively.
The catalytic chain therefore is not likely to be useful as a) Classification
an information-integrating system.
Ring closure in dynamic systems leads to entirely new
properties of the system as a whole, as we have seen in
c) Branched systems Part A. The set of molecules which are formed in a
closed loop of chemical reactions represents a catalyst.
Wherever coupled systems evolve, branching of couplings as depicted A cycle of catalysts (Fig. 4) in turn has autocatalytic
in Figure 24 will be inevitable. Fixed-point analysis of such branched properties and may be regarded as a self-replicative
system. After finding that straightforward or branch-
ing couplings among self-replicative units do not lead
to a joint selection of the functionally linked system,
we may ask whether any ring closure in the chain of
couplings will bring about a change in the nature of
the selective behavior of the total ensemble. We might
argue that this must be the case, since we remember
that in open chains the recipient of all the benefits of
coupling was always the last member.
Hypercycles have been generally classified in Part A.
The simplest constituents of this class of networks are
obtained by a straightforward functional link among
self-replicative units as shown in Figure 25.
This section on hypercycles will consist of three dif-
ferent parts. First we present some definitions and
useful criteria for classification of this new kind of
Fig. 24. Fixed-point map of a dynamic system representing a
branching point in a catalytic network of self-replicative units © catalytic system. Then the results of fixed-point analysis
for the most important 'pure' types of hyper cycles are
under the constraints of constant organization described. Finally, we shall study one example of a self-
r; =k 1 x,; T,=k,x,+k;x,x 1 (for i=2, 3) organizing system which represents a realistic catalytic
k1=3; k2=k3=O; k~=l; k~=2; co =3.5 hypercycle.

40
Fig. 25. Catalytic hypercycles, a) degree p=2, n=6, b) degree p=3, n=6, and c) degree p=n=6

Primarily, hypercycles differ from ordinary catalytic cycles by Hypercycles with cyclic symmetry and homogeneous growth func-
nonlinear terms in the growth rates. In simple cases, the functions r; tions r; thus are completely determined by the values of nand P and
will be products of concentrations as shown in Equation (63). The the vector k.
exponents PA, according to
, Schematic diagrams for three examples of hypercycles
r; = ki fl x P).' (63) with n = 6 and p = 2,3 and n are shown in Figure 25.
A~ 1
Cases with p = 1 must be excluded from the general
can be regarded as elements of a matrix P. The indices A and i denote class of catalytic systems called hypercycles, since they
which population variable (x A) has to be raised to the power PAi in the fall into the family of systems with linear growth rates
function r;. The dynamic system is then determined completely by the r;.
matrix of exponents P, by the vector ofrate constants k=(kl ... k,),
and by a set of initial conditions. At first we shall study the 'pure'
cases only, which are characterized by homogeneous growth terms r;. b) General Analysis
The requirement of homogeneity leads to a first restriction for the
exponents in the matrix P: A summary of fixed-point analysis of hypercyclic
systems is given in Table 9.
I PA'=P; i=I,2, ... ,n (64) We discuss two cases which are most important in the
A= 1
context of this paper.
'P' is now common for all n differential equations and represents the 1. The simplest hypercyc1e possible with p = 2
degree of the growth functions introduced in Section V. In addition to 2. The hypercycle, which utilizes catalytic'links among
the restriction of homogeneity we shall allow individual con-
all members, i.e., PAi = 1 for i = 1, ... , n and A= 1, ... , n,
centrations to appear only as first-order terms in r;. Some important
cases with higher-order dependences will be discussed below. Ac- and hence, p=n
cordingly, the exponents PAi are restricted to just two possible values: The first system we christen simply 'elementary hyper-
PA'={O, I}. cycle', the second - in accordance with its most com-
Finally, we shall introduce cyclic symmetry into the net growth mon physical realization as a cooperatively behaving
function:
complex -' compound hypercycle'.
I; = kzXIXjXkXl'" xr
j=i-l+n(oil); l=i-3+n(oil +iii2+ 0i3);'" c) The Elementary Hypercycle
p-1
k=i-2+n(0,J +Oi2); r=i-p+n I 0," (65) Depending on the dimension of the dynamic system, we
Il= 1
observe interesting changes in the nature of the fixed
The assumption of cyclic symmetry is not essential for the most point in the center of the simplex. For this purpose we
important features of the solutions. It is a reasonable assumption,
however, if no further information on structural differences in the
inspect more closely the sets of eigenvalues obtained for
kinetic equations for the individual members of the cyclic system is different values of n, which are described appropriately
available. The matrix P is of general and simple form now. A concrete as vectors, ill = Re ill e1 + i 1m ill e z in the complex Gau-
example, the matrix P with n = 6 and P = 3 is shown below: ssian plane (Fig. 26). The fixed point in the center is a
focus for n = 2, a spiral sink for n = 3, a center for n = 4.
100011)
I 10 0 0 1 For n ~ 5 we obtain saddle points with spiral com-
( I 1 1 000 (66) ponents in some planes. These characteristic changes in
P(n=6,p=3)= 0 1 I 1 00
001110 the nature of a fixed.J?oint are reminiscent of a Hopf
000111 bifurcation despite the fact that our parameter is a

41
Table 9. The fixed-peint map of a hypercycle
Subjecting the dynamic system (65) to the condition of constant 3) In many cases there are also one-, two-, three-, or even higher-
organization we find: dimensional manifolds of fixed points, e.g., fixed-point edges, tri-
angles, tetrahedra, and higher-dimensional simplices [54]. These
X. n manifolds always occur in the boundaries of the corresponding
Xl=kiXiXJ ... Xl-~ L krx,xs···x t
simplices Sn, for example, fixed-point edges are found in the
s
Co r= 1
p-I boundaries of Sn, n 4, fixed-point triangles in the boundaries of Sn,
j=i-l+no il ,···,l=i-p+l+n L 0;" n S 6, and fixed-point tetrahedra on Sn, n 8. s
Jt= 1
Normal-mode analysis around the central fixed point "0' which is
p-I
responsible for cooperative selection, yields:
s=r-l+no,j, ... ,t=r-p+l+n L 0,"; p:;;,n (T.9.l)
11= 1
(0) l-y-(p-I) (Co )P-I
Fixed-point analysis can be carried out analytically for any value ofn w· =- -·k
) l-y n
if all the rate constants' are equal:
2n:i .
-}

kl =k 2 =···=k n =k (T.9.2) j=1,2, ... ,n-l; y=e n

The results obtained are: (T.9.3)


1) One fixed point, which we denote by "0' is always positioned in the
center of the concentration simplex. For p=2 there are n or n-l distinct eigenvalues, while for p=n
2) n additional fixed points occur at the corners of the simplex Sn: all eigenvalues are equal to OJ~o). The first case is the usual situation.
n -I single and one double-degenerate eigenvalues w~o) = OJj~n/2 =
X 1 'X 2 '···,x n •
- k(co/n)P-1 are obtained for p = 2 and even n, whereas for odd n all
the eigenvalues are distinct. The negative value of OJ)O) again indicates
, Variations in the individual rate constants on the solutions will be that the dynamic system on the simplex Sn is stable against
discussed in Section VIII. fluctuations in total concentration c.

rapidly approach Coin (for equal k i values), which is just


the same value as in the case of stable fixed points.
For the fixed point at any corner k (Xk = co) of Sn we find
one positive and n -1 zero OJY) values. In Section VIII
we shall analyze the nonlinear contributions and
n=2 n:3 n:4
identify these fixed points as saddle points. The cor-
responding long-term solutions hence do not contrib-
ute to the selection behavior.
The fixed-point map for a hypercycle with p = 2 and
n = 3 is shown in Figure 27 for a concrete example.

Fig. 26. Normal modes OJ for the central fixed point (x o) in


hypercyc\es of type (65) with p =2 and dimension n. ReOJ and 1m OJ
stand for imaginary and real part of the frequency OJ, respectively

discretely varying quantity, the dimension n of the


dynamic system. As we shall show by a more general
analysis in Section VIII the central fixed point is
asymptotically stable for n = 2,3, and 4. In the case of
higher dimensions n ~ 5 we find a more complex
attractor, namely, a stable closed orbit or limit cycle,
which always remains inside the simplex and therefore
never reaches the boundary. In the latter case, time
Fig. 27. Fixed-point map of a dynamic system (65) consisting of self-
averages of concentrations Xi:
replicative units © forming a hypercycle under th.e constraint of
1t constant organization
XJt)=-SxJr) dr, Xi = lim Xi(t) (67)
to t~oo

42
In genera\, the net growth functions for the individual self-replicative (1.0.0 )
units which form the dynamic system of a hypercycle will contain not 1
only catalytic terms but also first-order growth terms:

Subjecting a dynamic system with these growth functions to the


constraints of constant organization we obtain:
(68)

101012~"O~-----
u
/
I 3 \
(0.0.1) \
?O--
...:.:.----

47
1I ', - - . . . . . . .

Xi =kiXi +k;XiXj---'- L (kkXk + k~XkX,)



(69) 1
\,
Co k 1 ,

j=i-l+n<5 il , l=k-l+n<5kl ; i=I,2, ... ,n 1 "


,
\
\
\
From a mathematical point of view the catalytic chain (Fig. 23) differs Q \
\
\
from the hypercycIe just by a single rate constant and results from the \

latter by putting k; =0. We may therefore expect some similarities


\
\
\
between the two types of dynamic systems. Consistent with the
inhomogeneity of the growth functions, the fixed-point maps depend
on the total concentration. At the low concentration limit both ~~
systems become identical with the system of exponentially growing,
indepedent competitors (Fig. 22). At high concentrations, on the (1.0,0)
other hand, the two systems will differ. The dynamic system (69) 1
asymptotically resembles that of the corresponding elementary
hypercycle (p = 2).
As a concrete example we consider again a system of dimension n = 3.
There are seven fixed points: Three coincide with the corners of the
simplex S" three other fixed points lie on the edges, and the seventh
is in the interior of S,.
Numerical results were calculated for a given set of parameters k and
are shown in Figure 28. As for the catalytic chain in Figure 23 we (0,1,0) 2
jII------~&-
present fixed-point maps for three different values of total con-
centration Co' which represent low and high concentration limits (a
and c) as well as the critical point

(b, Co = Co. = k,(k;-' + k~-I) - k, k;-I -k2k~-I).

(1,0,0)
Considering the development of the dynamic systems
1+6
(58) and (69) close to internal equilibrium, we realize a
very important difference between the cyclic and
non cyclic systems: The cyclic system leads to an
asymptotic high concentration limit which is character-
ized by constant relative concentrations of the in-
dividual species, whereas the open chain approaches
the pure state (xn = co) at high total concentration.
Summing up the whole development from low to high
concentration limits we realize that a hypercycle, as
described by the dynamic system (69), is an appropriate
example of self-organization. Starting from compe-
Fig. 28. Fixed-point map of a dynamic system (69) consisting of self-
tition among individual species the growing system replicative units forming a catalytic hypercycle
approaches a final state with dynamically controlled
net production of all members. This internal control (r;=kix, +k;XiXj' j=i-l +n<5iJ;
leads to a stable stationary state or to a state with n=3, p=2, k=(l, 2, 3; 1,2,3);
regular oscillation of population variables about a fixed a) c o =0.5, b) co =2.5, c) lim co -> 00;
point. 1="1,2="2,3=",,4="12,5="23,6="'1> and 7="0)

d) The Compound Hypercycle


The analysis of the case p = n leads to a simple, general the invariant point in the middle (x o) is a focus for all
result: As in the other example treated before, there is values of n, all trajectories starting from the interior of
one fixed point inside the simplex. The whole boundary the simplex, which is the whole physically meaningful
of the simplex, however, consists of unstable fixed domain, will approach this particular point after long
points, fixed-point edges, fixed-point planes, etc. Since enough time. All the eigenvalues wjO) associated with xo

43
ute to the rate of formation of each constituent. A
mechanism leading to such a compound hypercycle
then would need either a - highly improbable-
multimolecular encounter or an intermediate for-
mation of a complex of n different subunits, which is
highly disfavored at low concentrations. Prebiotic
conditions, on the other hand, are characterized by
exceedingly low concentrations of individual macromo-
lecules. For an efficient start of evolution via compound
hypercycles one would have to assume extremely high
association constants far outside the range of experi-
2 ti::::.=====~ 3 mental experience and an inherent linkage between
these. constants and the functional efficiency of the
(0,1,0) (0,0,1) single constituents. The compound hypercycle is thus
Fig. 29. Fixed-point map of a dynamic system (65) consisting of self- likely to be of less importance for the nucleation of a
replicative units ®
forming a compound hypercyc1e under the translation system than any hypercycle oflower degree
constraint of constant organization p. In more advanced phases of precellular evolution

(r;=k,x,x 2 .•. xn; n=3, p=3, k=(l, 1, 1))


compound hypercYcles might have had a chance to
form.
Various systems consisting of catalytically active and
are the same for given values of k, Co, and n. They follow self-reproductive units have been studied by fixed-point
from the expression (3) given in Table 9 if we set p = n. analysis. The results provide clear evidence for the
The fixed-point map for a compound hypercycle with necessity of hypercyclic coupling. Only catalytic hyper-
n = 3 is shown in Figure 29. The complexes, thus, cycles can fulfill the criteria for integration of infor-
represent excellent examples for the control of relative mation listed in Section IV.5.
concentrations of their constituents. 1. Selective stability of each component due to favorable
competition with error copies
e) Comparison of Various Hypercycles 2. Cooperative behavior of the components integrated
into the new functional unit
Hypercycles have an intrinsic capability for integrating
3. Favorable competition of the functional unit with
information. Indeed the simplest members of this class
other less efficient systems
represent the least complicated dynamic structures that
are able to prevent an ensemble of functionally linked
self-replicative units from destroying information by VIII. Dynamics of the Elementary Hypercycle
elimination of some of their members as a result of
selective competition. From the dynamic point of view, Hypercycles, being the relevant systems of prebiotic
all kinds of hypercycles are equivalent with respect to self-organization, deserve a more detailed analysis of
this property. On the other hand, less sophisticated their dynamic behavior. A complete qualitative de-
systems, such as simple catalytic cycles (Fig. 4), are not scription can be given for the class of elementary
eligible as information-integrating systems since they hypercycles (p = 2) up to dimension n = 4. For higher
lack the property of inherent self-reproducibility (cf. [4], dimensions, as well as for hyper cycles of a more
p. SOHf.). complex structure, we have to aid the topologic analy-
A further discrimination within the hierarchy of hyper- sis by numerical integration. We exemplify the methods
cycles can be made according to their realizability in with the class of elementary hyper cycles, which reveal
nature, which will be the subject of Part C. To present all the basic properties of hypercyclic self-
one example of such an argument, we compare here the organization. 1
simple type of hyper cycle (p = 2) and the complex (p = n)
with respect to their physical materialization. Simple
VIII.1. Qualitative Analysis
hypercycles require bimolecular encounters of macro-
molecules according to their growth law. These bimole- Since we are concerned with dynamic systems of cooperating
cular terms can easily .be provided by various me- constituents, the stable attractors in the interior of the physically
chanisms and also result from realistic assumptions accessible range of concentrations are of primary interest. More
about nucleic acid replication or messenger-instructed , For a particular case of a hypercyc1e, in which the second-order
protein synthesis (see also Section IX and Part C). A term XkX k _, of the growth function has been substituted by a term of
compound hypercycle requires all partners to contrib- the form X k In X k _" an analytical solution could be provided [21].

44
specifically, we have to study the stability of those fixed points, for o--_e-·..o G ) G ) - - - -.....(J) m m
which some eigenvalues of the Jacobian matrix have zero real parts. 2 2A 26
In Section VII (Table 9) we encountered essentially two cases:
1. Zero eigenvalues (roy) = 0, j = 2,3, ... , nand i = 1, 2, ... , n) for fixed
points Xi at the corners of the simplices Sn
2. Purely imaginary eigenvalues (ro~O)4 = ± i) for the central fixed point
of the four-membered hypercyc1e ~n S/.
Before presenting a general proof for the stability of the central fixed
points in hypercyc1es of low dimensions n ~4, let us inspect the
topology of these systems in more detail.
The 'dynamic systems corresponding to elementary hypercycles can 3 3A
be decomposed into several subsystems each of which is defined on a
globally invariant subspace. A set of points or a subspace will be
called' globally invariant' with respect to a given dynamic system if
Fig. 30. Dynamic systems corresponding to elementary hypercycles
and only if a trajectory that passes through any point of the subspace
of dimensions n = 2, 3, and 4. The individual systems are mapped on
never leaves the subspace.
the simplices Sn and can be decomposed into globally invariant
In particular we find that the dynamic systems on the simplices Sn
dynamic subsystems (Table 10): The 'complete' subsystem 2, 3, and 4
can be subdivided into those on boundaries (BS n) and those in the
are characterized by nonzero values of all population variables and
interiors (IS.). The interior of a simplex, defined as before, is the
thus describe the development in the interiors of the simplices S.(ISn:
region where no population variable vanishes: O<~, < 1, i = 1,2, ... , n.
Clearly, the dynamic systems on IS n are most interesting since they
O>x,>c o, i= 1, 2, ... , n). On the boundaries of the simplices Sn(BS n)
one or more population variables vanish and dynamic subsystems of
describe the development of intact hypercyc1es. We denote them in
lower dimension like the 'flowing edge' 2A, the 'fixed-point edge' 2B,
the following by numbers: 2, 3,4, .,. N.
and the triangle of type 3A are obtained (note that the dynamic
On the boundary, one, two, or more population variables vanish.
system 2A occurs in the boundaries surrounding 3, 3A, and 4, 2B in
Consequently, the dynamic systems on BSn can be subdivided into
dynamic systems on simplices of lower dimension like edges, faces, those surrounding 3A and 4, and 3A finally occurs in the boundary
around 4)
and hyperfaces. To distinguish these systems from complete hyper-
cycles we shall use 2A, 2B, 3A, etc. as short-hand notations. All
dynamic systems corresponding to elementary cycles of dimension
n ~ 4 are shown schematically in Figure 30. As a concrete example, terms this means: Starting from any distribution of population
the decomposition of the four-dimensional system into 11 subsystems variables we end up with the same stable set of stationary con-
is presented in Table 10. centrations. The dynamic systems indeed are characterized by
cooperative behavior of the constituents. This result is of particular
importance for the four-dimensional system where the linear approx-
Table 10. Globally invariant dynamic subsystems of the elementary
hypercyc1e with dimension n=4 imation, used in fixed-point analysis, yielded a center surrounded by
a manifold of concentric closed orbits in the x, y-plane (see Fig. 31 a),
Symbol Condition Dynamic system which does not allow definite conclusions about stability.
The dynamic systems on the boundaries of the simplices (BS.)
determine the behavior of 'broken' hypercycles, i.e., catalytic hyper-
4 ~'=~'~j-~'¢' i=I,2,3,4
cycles which are lacking at least one of their members. In reality, these
j=i-l+nb'l and
systems describe the kinetics of hypercycle extinction. They are also
¢= ~I ~2 + ~2~3 + ~3~4 +~4~1
of some importance in phases of hypercycle formation. On the
3A (1=-~1¢ boundaries of the complete dynamic systems up to dimension 4 we
~'=~i~j-(<P, i=2,3 find two kinds of edges 2A and 2B as well as the face 3A (Fig. 30). All
j=i-I and three dynamic systems can be analyzed in a straightforward way.
¢=~1~2+~2~3 The first kind of edge 2A connects two consecutive pure states or
~3=0'~2=00r~I=0 analogously corners, which we denote by 'i' and 'j' U=i+ I-nb,.). As shown in
2A 1;3=1;4=0 ~I=-I;I</>' </>=1;11;2 Figure 32 there is a steady driving force along the edge, always
~2=~1~2-~2¢ pointing in the direction i -> j. The only trajectory of this system thus
~2=~3=0, ~1 =~2=0 analogously leads from corner i to corner j. Accordingly, we shall call system 2A a
or~4=~1=0 flowing edge. In approaching corner j, the driving force decreases
parabolically (Fig. 32). Hence, the linear term ofthe Taylor expansion
2B ~2=~4=0
~,=O, i= I, 2, 3,4 vanishes at the fixed point Xj' and fixed-point analysis cannot yield
~1 =~3=0
the desired prediction as to the nature of this fixed point.
In elementary hypercyc1es the corners of the simplices are saddle
points: A corner (i) is stable with respect to fluctuations along the
All the dynamic systems up to dimension n=4 can be analyzed by edge hl(bxh >0, h = i -I + nb il ) but unstable along the edge i]U = i + I
Lyapunov's method (Table 11). For the three systems 2, 3, and 4, - n bin). On the boundary of every complete dynamic system we thus
Lyapunov functions are given, and hence, the central fixed point find a closed loop, 12 23 34 ... /i1, along which the system has a
represents a stable attractor. Moreover, the basin of this fixed point defined sense of rotation. This cycle is not a single trajectory. A
extends over the whole interior of the simplices. In more physical particular kind offluctu.ation is required at every corner to allow the
system to proceed to the next pure state. The existence of this loop is
2 Purely imaginary eigenvalues will occur also in elementary equivalent to the cyclic symmetry of the total system. The asymmetry
hypercyc1es of dimension 4k, where k is an integer ;:;2. In these at each single corner reflects the irreversibility of biopolymer
higher-dimensional examples, however, the central fixed point is a synthesis and degradation, assumed in our model.
saddle point independently of the nature of higher-order contri- The physically accessible range of variables in the dynamic system3A
butions to the purely imaginary eigenvalues. is circumscribed by two consecutive flowing edges, i] and Ik U= i + I

45
Table 11. Lyapunov functions [57] for basic hypercycles of dimension n=2, 3, and 4

To prove the stability of a certain fixed point x of a dynamic system 1 . - -


x= A(x), we must find an arbitrary function V(x) which fulfils the Clearly, we find r(~o)=-, which satisfies the equation V(~o)=O. (~o
n
following two criteria: represents the central fixed point of the hypercycle.)
For the two-dimensional system (n=2), condition (T.l1.6) can be
(1) V(x)=O and V(x»O, xeU, (T.ll.1) easily verified:
i.e., the function vanishes at the fixed point and is positive in its (T.l1.7)
neighborhood U. Thus V(x) has a local minimum at the fixed point.
Thefunction r represents a parabola with the maximum at (= 1. Thus
(2) V(x)=-= ~ (OV)dx
. _dV L... -
j
-<0, xeU (T. 11.2) r(';) <1 is fulfilled everywhere except at the fixed point (=1, where
dt j~' oX j dt r=!- In this case V is a strict Lyapunov function and ~o is
asymptotically stable.
i.e., the time derivative of Vex) is negative in the neighborhood of For n = 3 the situation is very similar. The inequality (T.11.3), r <1 is
the fixed point. For trivial reasons V vanishes at x: V(x)=O. Ifit is valid at every point in the interior of the simplex S3' except at the
possible to find such a function Vex) for a given fixed point of a fixed point ~o where r=1. V again represents a strict Lyapunov
dynamic system, it is called a (strict) Lyapunov function and the function and the central fixed point ~o is asymptotically stable.
point x is (asymptotically) stable: All trajectories passing through a In four dimensions the problem is more involved. We realize that
point in the neighborhood of x will end in the fixed point x. condition (T.ll.3) is verified almost everywhere on the simplex 5.:
A Lyapunov function Vex) may also be defined in a less strict way so
as to fulfil the weaker criterion: (T.11.8)

V(x)~O (T.11.3) In its interior we find O~r~i with r=i if and only if S=1. The
equation S =1 determines the plane (, + ~3 =1(see Figs. 31 aand 34b).
Any trajectory entering the neighborhood U of x will remain there. V apparently is a Lyapunov function solely in the weaker sense. This
To give a concrete example; sinks are asymptotically stable in the result suggests that the central fixed point at least is stable. To prove
stronger sense of Lyapunov, whereas centers are stable only with asymptotic stability we introduce new variables x, y, z
respect to the weaker criterion (T.lI.3).
For the sake of convenience we use normalized variables (, and X= -2«(2 +~3)+ I x= -(1 +z)(y-xz)
assume the rate constants to be equal to 1, k, =k2 = ... =k n= 1, when y=2«(,+(2)-1 y=(l-z)(x-yz)
we apply Lyapunov's method to basic hypercycles.
The function z=2(~, +~3)-1 z=z3_ z + x 2_y2

which shift the origin of the coordinate system into the center of the
(T.11.4) simplex 5, and place the coordinate axes through the midpoints of
the edges 23, 34, and D, respectively, (cf. Fig. 31a). The fourth
1 variable (,=1-('-(2-';3 is eliminated. The z-axis thus points
has a minimum and vanishes at the fixed point (,=- and thus meets perpendicular to the critical plane ~'+';3 =1. which is spanned by
n the two variables x and y. In this plane the dynamic system simplifies
condition (T.ll.1). The time derivative of V can be obtained by to X= -y, y=x, and Z=X2_y>.
straightforward differentiation The time derivative of z vanishes only along the two lines x = ± y or
(2 = (, and ~, = ~ 3' respectively. Consequently, there is no trajectory
in this critical plane - except the fixed point ~o - and the system will
pass through it in infinitely short time. Along any given orbit the
r= I (,(,; l=k-1+nDk1 (T.l1.5)
condition V(~(t)) <0 is fulfilled at almost every moment, the only
k= 1
exceptions being the instances when the critical plane ~ 1 + ~ 3 = 1 is
Now we have to check criterion (T.l1.2) for systems with different passed. Along all trajectories, V(~(t)) is monotonically decreasing
values of n. In the interior of the simplex Sn the condition V<0 with t. V is a strict Lyapunov function, and thus the fixed point ~o is
becomes equivalent to the inequality asymptotically stable.
In higher dimensions n ~ 5, V(~) is not a Lyapunov function and
1 therefore no predictions on the stability of the central fixed point can
r@<-. (T.11.6)
n be made by this method.

-nDin and k=j+l-nD in ) and one fixed-point edge [k (bFi-1 development of broken hypercycles. After one species in a hypercycle
+ n<l,.). The trajectories ofthis system are shown in Figure 31 b. They has been extinguished by some external event, the remaining dynamic
start from some point of the fixed-point edge and end at the corner k, system is unstable and approaches a pure state after long enough
which thus represents the only stable attractor of the system. The time. In all cases, a species will be selected which occurs just before
species I k consequently represents the survivor or remnant of this the break in the hypercycle. In other words, species Ii will remain the
fragment of a hypercycle. last remnant of a hypercycle which has been destroyed by extinction
The investigation on the boundaries of basic hypercycles can be of its constituent I j' when i is the precursor of j U= i + 1- D,n)' This
generalized to higher-dimensional systems. From the results ob- behavior is not unexpected in light of the known properties of
tained we can make the desired predictions about the long-term catalytic chains.
46
11,0,0,0) (0,0,1,0)

11,0,0,0 ) 1~=r====~==~r====T======~3
1 z

a
b

2 2
(0.1,0,0 ) (0,1,0,0)

Fig. 31. Dynamic topology of the elementary hypercycle of dimension n = 4. The dynamic system on the simplex consists of the system 4 on
the interior IS 4 and four equivalent systems of type 3A on equilateral triangles (S3)' each of which is circumscribed by two flowing edges 2A
and one fixed-point edge 28. a) The system on the interior is described lippropriately in the variables x, y, and z (see Table II). The
manifold of closed concentric orbits belonging to the center of the linearized system lies in the x,y-plane (hatched regIOn in the drawing).
b) The dynamic system 3A: All trajectories start out from some point on the fixed-point edge (13) and end in the same corner (3).
The dashed line connects all the points at which the trajectories are parallel to the fixed-point edge (13)

VIII.2. Numerical Integration

The systems of differential equations for elementary hypercycles


with dimensions up to n ~ 12 have been integrated by standard
numerical techniques. The corresponding solution curves x(t) have
been presented in a previous paper [4] and need not be repeated,
since we are interested in a different aspect of the problem here.
Our present purpose is to search for stable attractors in the interior
of the simplices S. that guarantee cooperative behavior of the con-
stituents. For this goal an investigation of the manifold of trajec-
tories is straightforward.
Differential equations for trajectories are obtained by elimination of
the explicit time dependence in the original dynamic system:

dX 2 A2
--=-=!2(X j ,X 2, ... ,x.)
dX j Aj
dX3 A3
-=-=!3(X j ,X 2, ... ,x.)
dx, Aj

~----O~.2-5-----0.~50-----0-.7L5----~~g2 dx. A.
-=-=!.(x j ,x 2 , ... ,x.) (70)
dX j A,
Fig. 32. The 'flowing edge' 2A. The tangent vector ~2 =~2(l-~2)2 is
positive inside the whole physically allowed region (0 < ~ 2 < 1) and
vanishes at both ends, which represent the two fixed points of the Integration of this new (n -I)-dimensional dynamic system yields the
system: ~j =(1,0) and ~2=(0, 1). ~2>0 means that ~2 is increasing trajectories as solution curves:
during the next differential interval of time. Hence there is only one
orbit on 2A leading from ~j to ~2' i.e., from corner 1 (~2 =0) toward X2 = g2(X 1, x 2 , ... , xn)
corner 2 (~2 = 1). The dynamic system 'flows' along this edge. Note X3 = g3(X n, x 2, .. " xn)
that d~2/d~2 vanishes at the fixed point ~2 (~2 = 1), leading to an
eigenvalue OJ = 0 in the linearized system. Consequently, fixed-point
analysis fails to make a prediction about the stability of this point X.=g.(X j , x 2 , •.• , x.) (71)

47
The trajectory thus is a curve in the n-dimensional concentration
space. For graphical representation we shallnse projections of these
curves on the planes spanned by one selected coordinate x, and by XI'
Trajectories for hypercycles of low dimension (n = 2, 3, and 4) reflect
the already known properties of these dynamic systems. The case
n = 2 is rather trivial: There are only two orbits which converge to the
central stable focus (Fig. 30). The trajectories of the three-
dimensional hypercycle (n = 3) are spirals which rapidly approach the
central fixed point (Fig. 33). This kind of trajectory corresponds to
strongly damped oscillations of the solution curves x(t). The four-
membered hypercycle deserves further consideration. Again, the
o.s trajectories spiral into the center of the simplex (Fig. 34a, b). In
contrast to the three-dimensional example, the central force is mnch
weaker than the rotational component. Accordingly, convergence

Fig. 33. A trajectory of the dynamic system (3) for the elementary
hypercycle of dimension n = 3 is shown as a projection on the plane
O ~----------------~--------------~~-'·I (XI' x 2 )· Initial conditions: xI(0)=0.98, x 2(0)=X 3 (0)=0.01
0.5

a c
" " "

. L~=========;~ ________ ~~ " L-__________ ~~----~L---~~.,


L-__________~~--------~~_ "

" " "

L-__________~~~~~----~_.,
~----------~~--------~~- .,

b d

Fig. 34. Trajectories of the dynamic systems (4, 5, and 12) for elementary hyper cycles of dimension n = 4,5, and 12, respectively. (1) n =4: initial
conditions: xI(O)=O.97, x 2(0)=x 3 (0)=X 4 (0)=0.01; two projections are shown. a) Projection of the trajectory on the plane (XI' x 2 ). The trajec-
tory spirals into the central fixed point with hardly damped oscillations. b) Projection of the trajectory on the plane (XI' X3)' The plane of the
center manifold (x, y-plane in Fig. 31) intersects the xl> x 3 -plane along the line XI +X3 = 1/2. Perpendicular to it we see the z-axis. Note that the
trajectory crosses this plane (x, y) only at single points and does not stay therein for a longer period (Table 11). (2) n = 5: projections on the
plane (XI' x 2 ). c) Initial conditions: XI(O) = 0.9996, x 2(0)=x 3 (0)=X 4 (0)=x S (0)=0.0001. d) Initial conditions: XI(O) =0.2004, X2(0) =x 3 (0) =x 4 (0)
= xs(O) =0.1999. Note that the dynamic system approaches the same limit cycle from both sets of initial conditions. (3) n = 12: projections on
the plane x I, X2' e) Initial conditions: x 1(0) = 0.9989, X2(0) = .... x dO) =0.0001. f) Initial conditions: x 1(0) =0.0848, X2(0) = .... x 12(0) = 0.0832.
Again both limit cycles are the same and come very close to the loop 12,23 ... II, 12, 12 I

48
toward the central fixed point is extremely slow. A projection of the same kinds of undamped concentration pulses that we have observed
trajectory on the x" x ,-plane nicely illustrates the previously derived in the system with equal k values. The size of the pulses is no longer
result that there is no orbit in the plane x, + X3 = 1/2, x 2 + X4 = 1/2. the same for all subunits. Time-averaged concentrations [as defined
Indeed, as one can see from Figure 34 b, the trajectories follow closely by Equation (67)] fulfil the above equation (72). "hich determines
a saddle-like bent surface. the position of the (unstable) central fixed point. Accordingly, the
For basic hypercycles of dimension n;;; 5 the central fixed point pulses for those species which precede a step with a relatively small
represents an unstable saddle. There is no sink in the boundary and rate constant are broad, whereas those of species preceding a
consequently one expects a stable closed orbit. The analytical relatively fast reaction step are small in width and height. The system
techniques have not yet been developed to a sufficient extent to thus regulates the concentration of its constituents in such a way that
provide the proof of the existence of such an attract or in the interior the overall production rate is optimized.
of the simplices. Therefore, we have to rely on numerical results. Hypercycles of higher dimensions (n;;; 5) do not exist in stable states
Numerical integration indeed provides strong evidence for a limit with constant stationary concentrations but exhibit wave-like oscil-
cycle or closed orbit. Starting from various points very close to the lations around an unstable fixed point in the center. Nevertheless, the
center, to a face, to ali edge, or to a corner of the simplex we always constituents show cooperative behavior since their concentrations
arrive at the same limit cycle after long enough time. Two typical are controlled by the dynamics of the whole system and no
trajectories are shown in Figure 34c - f, for elementary hypercycles of population variable vanishes.
dimensions n = 5 and n = 12, respectively. As we can see from a
comparison of the two Figures, with increasing n the limit cycle Dynamic systems corresponding to elementary hyper-
approaches more closely the loop 12, 23, ... ,"III mentioned in the cycles have one and only one attractor in the interior of
previous section. Consequently the oscillations in the individual
the simplex, the basin of which is extended over the entire
concentrations become more and more like rectangular pulses.
The use of numerical techniques also enables us to remove the region of positive (nonzero) concentrations of all com-
assumption: k, =k 2 ••. = kn • Calculations with arbitrary k values have pounds. At low dimension (n ~ 4) the attractor is an
been performed for. dynamic systems of dimensions n = 4 and n = 5. asymptotically stahle fixed point, namely, a foe us for
No change in the general nature of the solution curves is observed. n = 2 and a spiral sink for n = 3 and n = 4. In systems of
Typical examples are shown in Figures 35 and 36. The individual
concentrations in both systems oscillate. For n =4 the concentration
higher dimensions (n ~ 5) numerical integration provides
waves are damped and the dynamic system approaches the central strong evidence for the existence of a stable limit cycle.
fixed point. Its coordinates are determined by the following All elementary hypercycles thus are characterized by
equations: cooperative behavior of their constituents.
k-' Due to their dynamic features hypercycles of this type
"0: x~= -n~J-CO; j=i+l-nil in (72) hide many yet unexplored potentialities for self-
I ki' organization (dissipative structures, e.g., in case of
superimposed transport). 7h~y may also play an impor-
1= 1

Five-membered hypercycles with unequal rate constants show the tant role in the self-organization of neural networks.

- - l lme _

Fig. 35. Solution curves of the dynamic system for an elementary Fig. 36. Solution curves of the dynamic system for an elementary
hypercycle with dimension n=4 and unequal rate constants (k, hypercycle with dimension n = 5 and unequal rate constants (k,
=0.25, k2 = 1.75, k, = 1.25, k4 = 0.75; initial conditions: x , (0) =25/ 13, k2=1 / 13, k,=19/ 13, k4=1, ks=7/ 13 ; initial conditions:
= 0.9997, x 2(0) =x 3 (0) =x 4 (0) = 0.0001; full concentration scale= x,(O) = 0.9996, x 2 (0)=x 3 (0)=x 4 (0)=X 5 (0)=0.0001; full concen-
1 concentration unit, full time scale = 1000 time units). Note that the tration scale = I concentration unit, full time scale = 1000 time units).
concentration of I, (the component preceding the fastest step) is Note that the concentration of Is (the component before the fastest
smallest whereas that of 14 (the component before the slowest step) is step) is smallest, whereas that of I, (the component before the slowest
largest step) is largest

49
IX. Hypercycles with Translation

IX.1. Ideal Boundary Conditions


and General Simplifications

An appropriate set of boundary conditions can be


realized in a flow reactor [4, 9, 55, 56]. The con-
centrations of all low-molecular-weight compounds
(mi' i = 1, 2, ... , A) are buffered with the help of con-
trolled flow devices, at the same time providing the
energy supply for the system. The concentration vari-
ables Xi refer to the macromolecular species synthesized
in the reactor, while all other compounds of the
'standard reaction mixture' do not show up explicitly
in the differential equations, but appear implicitly in
the effective rate constants of Equation 30.
Because of technical difficulties and also for heuristic
reasons it is impossible to account explicitly for all
elementary steps in the reaction mechanism. We rather
have to apply simplified reaction schemes which lead to Fig. 37. Schematic diagram of a hypercycle with translation. Dimen-
an appropriate 'over-all' kinetics. This strategy is a sion: 2 x n, i.e., n polynucleotides and n polypeptides
common procedure in chemical kinetics. Acid base
reactions in aqueous solution for example are generally
described by phenomenologic equations which do not protein with polymerase actIVIty. Altogether these
account for individual proton jumps, but just reflect primordial proteins provide at least two functions:
changes in protonation states of the molecules specific replication and translation. How such a system
considered. can be envisaged is shown in Part C.
For the mechanism of template-directed polymeri- The couplings between the Ii and Ei have to be of a form
zation and translation, the rate equations contain ~he which allows the closure of a feedback loop (Fig. 37). In
population numbers of the complete macromolecules mathematical terms cyclic symmetry is introduced by
as the only variables. Hence chain initiation and assuming specific complex formation between the
propagation steps are not considered explicitly. A enzyme Ej and the polynucleotide Ii' whereby j = i + 1
justification for these approximations can be taken -n~in'
from experiments. Actually, the kind of 'over-all' The kinetics of polynucleotide synthesis follows a Michaelis-Menten-
kinetics we are using here is well established (cf. Part C). type reaction scheme, although we do not introduce the assumption
of negligibly small complex concentrations.

IX.2. The Kinetic Equations (73)

The catalytic hypercycle shown schematically in Figure The four nucleoside triphosphates and their stoichiometric coef-
37 consists of two sets of macromolecules: n polynuc- ficients are denoted by Mi and vi; A= 1, 2, 3, 4, respectively. No~ we
introduce zJor the concentration of the complex I,Ej and xJ, y? or Xj'
leotides and n polypeptides. The replication of polynuc- y, for the total or free concentrations of polypeptides (E) and
leotides (/;) is catalyzed by the polypeptides (E;) which, polynuc1eotides (IJ Mass conservation requires:
in turn, are the translation products of the former. The
hypercyclic linkage is established by two types of (74)

dynamic correlations: For fast equilibration of the complex the concentration z, is related to
1. Each polynucleotide Ii is translated uniquely into a the total concentrations xJ and y? as:
polypeptide Ei • The possibility of translation evidently
requires the existence of an appropriate machinery
z,
o
y, +Xj +
2
0 K
'(1 - (75)
which is composed of at least some of the translation
products Ei and which uses a defined genetic code.
Polypeptide synthesis is assumed to be unspecific, i.e., translation of
2. Polynucleotides and polypeptides form specific com- the polynucleotide 1, occurs with the help of a common' apparatus':
plexes that are also catalytically active in the synthesis
of polynucleotide copies. The polypeptides may be 1,+LvfMf'::.I,+E, (76)
specific replicases or specific co factors of a common 1

50
M~ and >1 denote the activated amino acids and their stoichiometric to an approach to condition (82). As a consequence,
coefficients, respectively. Selection constraints may be introduced the approximations
properly by controlling total concentrations for both kinds of
biopolymers (I and E) independently. By analogy with the constraints
of constant organization we keep both sums of concentrations (83)
constant:
become valid, leading to a 2n-membered catalytic
IY2=c~; Lx2=c~ (77)
k k
cycle, but not a hypercycle. Thus under saturation
conditions, i.e., at high concentrations of the con-
Under all these conditions our dynamic system consiting of 2n stituents, the hypercycle loses the behavior typical of
coupled differential equations reads:
nonlinear growth rates. As a unified system it simulates
the properties of a simple catalytic cycle, which is
equivalent to an auto catalyst or self-reproducing unit.

i=1,2, ... ,n. (78) IX.3. Numerical Solutions

For our purpose, it is sufficient to discuss two limiting The differential equations derived for catalytic hyper-
cases: cycles with explicit consideration of complex formation
1. The concentration Zo of the complex IiEj becomes between the polynucleotides and polypeptides are
proportional to the product of polynucleotide and difficult to study by analytical methods, because of the
polypeptide concentrations at sufficiently low irrational expressions involved. Numerical integration
concentrations: is time-consuming in these cases, but nevertheless, it
1 0 O. represents the only source of information on the
Zi'" K. Yi Xj, (79)
, properties of these dynamic systems. To illustrate the
dynamics of polynucleotide-polypeptide hypercycles
If we further assume the first-order translation process we shall present computer graphs of solution curves as
to be fast as compared to the second-order replication well as trajectories.
- an assumption that is well justified, at least for low In comparison to elementary hypercycles the
concentrations of polynucleotides - the polypeptide polynucleotide-polypeptide systems contain a new
concentration will assume a stationary value that can class of parameters, namely, the association constants
be included in the rate parameters. The formation of of the complexes, K i • As to be expected from the
polynucleotides then is described by a system of differences in kinetic behavior at the low and high
differential equations that is typical of an elementary concentration limits, the equilibrium constants exhibit
hypercycle of dimension n. a dominating influence on the dynamic properties of
2. At high concentrations, Zj becomes equal to the the system. For the sake of a systematic investigation
smaller of the two variables: 3 we reduce the number of independent parameters. The
(80)
assumptions made are essentially the same as those
used for the elementary hypercycles: All rate constants
Accordingly, we approach two possible limiting for polynucleotide replication, 11 =12 = .. In = f, for
situations their translation into polypeptides k 1 = k2 = ... = kn = k,
and all association constants, K 1 = K 2 = ... = Kn = K
Ki~Y? ~xJ: Zi'" l (81) are assumed equal. Then, we study the influence of K on
(82) the properties of the dynamic systems at fixed values of
Ki~XJ~Y?: Zi"'XJ
I and k and for a constant set of initial concentrations.
In the first of these two cases the polynucleotides For hypercycles of dimensions n ~ 4 the solution curves
behave like independent competitors, while the poly- approach a stable stationary state after long enough
peptides - due to Yi = l- Zi ~ 0 - remain stationary. time. The individual concentrations may exhibit dam-
Under natural conditions, where constraints like ped oscillations. The dynamics of these systems are
'constant total concentrations' usually do not apply essentially the same as for hypercycles with higher
- at least not for the assumed small values of Y - the values of n and small equilibrium constants.
resulting growth of polynucleotides would lead to a The dynamics of higher-dimensional hypercycles are
reversal of the concentration ratios y: x and hence more complicated. The long-term behavior of the
system changes with increasing values of the equilib-
3 inf = infimum is the mathematical term representing the smallest rium constant K. Below a certain critical value (Kcr)
member of a set. the system converges toward stable stationary states,

51
whereas limit cycles are obtained for larger values of
K(K > KeJ According to the appearance of solution
curves and trajectories we distinguish four different
cases, arranged with respect to increasing values of the
equilibrium constant K:
1. At small values of K the dynamic behavior is
qualitatively the same as of hypercycles of lower
dimensions. The solution curves exhibit strongly dam-
pled oscillations (Fig. 38) and the trajectories spiral
quickly into the center, which represents a stable
stationary state (Fig. 39).
2. In principle we find the same general type of
dynamic behavior as in case (1). The oscillations,
Fig. 38. Solution curves of the dynamic system for a hypercycle with however, are damped only slightly and the approach
translation. Dimension: 2 x 6, k = 0.25; initial conditions: Y I (0) = 5.0, toward the stationary state is extremely slow
Y2(0)=···=Y6(0)=0.5; x l (0)=···=x 6(0)=1.0; full concentration
(Fig. 40a, b). The situation is quite different from case
scale = 5 concentration units, full time scale = 1000 time units. The
value of the equilibrium constant K is below the critical value for jhe (1), because the damping terms do not show up in
Hopf bifurcation and hence a damped oscillation is observed normal mode analysis but require consideration of
nonlinear contributions. Phenomenologically this fact
reveals itself in the appearance of initially (almost)
constant amplitudes of oscillation. This situation oc-
curs at values of the equilibrium constant K that are
slightly smaller than the critical value Ken i.e.: K = Ker
-15K.


3. At values of K that are slightly larger than the
critical equilibrium constant (K = Ker + (5 K), we ob-
serve an interesting phenomenon. The dynamic system
first behaves much as in case (2). The individual
concentrations oscillate with relatively small ampli-
.,,-,- - - - - r - - - - -
tudes. In contrast to case (2), the amplitudes increase
slightly during the initial period. After this phase of
sinusoidal oscillation, however, the concentration wa-
ves change abruptly in shape and frequency (Fig. 40c, d)
and then resemble closely the rectangular pulses which
we encountered in basic hypercycles of high dimension.
Finally, the dynamic system approaches a limit cycle.
4. At large values of K the individual concentrations
oscillate with increasing amplitude and the dynamic
system steadily approaches the limit cycle (Fig. 40e, I).
L - - - - - r - - - - - - o - - I, The kind of change in dynamic behavior with a
continuously varying parameter as we have observed
here is known in the literature as 'Hopf bifurcation'
Fig. 39. A trajectory of the dynamic system for a hypercycle with
translation. Dimension: 2 x 5, k= 1.0; initial conditions : YI(O)= 5.0,
[58]. The characteristic retardation in convergence
Y2(0) = Y3(0) = y.(O) = Ys(O)=O.5; x I (0)=X 2(0) =x 3 (0)=x.(0)=x s (0) toward the long-term solution that we have found in
= 1.0. a j Projection of the trajectory on the plane (y., Y2) showing the cases (2) and (3) has been described also for other
concentrations of the polynucleotides I I and 1 2 • b) Projection on the dynamic systems and is usually called the 'critical
plane (YI' XI) showing th e concentrations of the polynucleotide I I
slowing down' at the Hopf bifurcation. In the case of
and its translation product, the enzyme E I. Note that the con-
centration of EI is roughly proportional to that of I I and thus the hypercycles, the 'slowing down' around the critical
condition for simplifying the hypercycle with translation is fulfilled to value of K becomes more pronounced at larger values
a good approximation. c) Projection on the plane (XI' Y2) showing the of n. In the five-membered cycle (n = 5) a situation
concentrations of the polypeptide E I . and the polynucleotide 12 , the corresponding to case (3) is hardly detectable. The
formation of which is catalyzed by the former. d) Projection on the
plane (XI ' Xl) showing the concentrations of the polypeptides EI and
catalytic hypercycle with n = 10, on the other hand,
E 2 . Note that K again is below the critical value of the Hopf shows a much longer initial period, as referred to in case
bifurcation and the trajectory converges to the central fixed point (3), than the six-membered system (Fig. 41). The initial

52
I, a I, c I,

I, '---=---...---~-to.,..--_I,

E,
£, £,

"....

/ b
I, ""-----~3~-----.6-- I ,

d
L:..._ _ _ _~----~-_ I,

Fig. 40. Trajectories of the dynamic systems for hyper cycles with translation. a and b) Dimension 2 x 5, K = 1.1, initial conditions: y, (0) = 5.0,
Y2(0) = Y3(0)= y.(O) = y,(0)=0.5; x,(0)=x 2(0)=X 3(0)=x.(0)=x s(0)= 1.0; projections are shown on the planes for the concentrations of 1,,12,
and I" E" respectively; the value of the equilibrium constant K is slightly below the Hopf bifurcation and we observe very slow convergence
toward the stable central fixed point. c and d) Dimension 2 x 6, K = 0.2784, initial conditions: y, (0) = 5.0, Y2(0) = .. , = Y6(0) = 0.5, x, (0)= ... X6(0)
= 1.0; projections are shown on the planes for the concentrations of 11 ,1 2 , and I" E" respectively; the value of the equilibrium constant K is
slightly above the Hopf bifurcation and we observe a metastable limit cycle before the system finally converges to the stable limit cycle. e and
f) Dimension 2 x 5, K = 1.2, initial conditions: y. (0) = 5.0, Y2(0) = Y3(0) = y.(O) = Ys(O) = 0.5, XI (0) = x 2 (0) = x 3 (0) = x 4 (0)= xs(O)= 1.0; projections
are shown on the planes for the concentrations of 11 ,12 , and I" EI , respectively; the value of the equilibrium constant K is above the Hopf
bifurcation and the system converges steadily toward the stable limit cycle. Note that the proportionality between EI and II is reasonably well
fulfilled in all three cases (b, d and f)

phase of sinusoidal oscillations resembles a metastable


oscillatory state. The transition to the final limit cycle
becomes sharper with increasing value of n and is quite
pronounced for the ten-membered hypercycle.
All polynucleotide-polypeptide hypercycles studied so
far have an attractor in the interior of the physically
accessible range of concentrations. They are character-
ized by cooperative behavior of their constituents.
Depending on the values of the product of total
concentrations (c~ and c~) and of association constants
(K) as well as on the size of the hypercycles, we observe
stable fixed points or limit cycles. Small K values then
are complementary to high concentrations and vice
Fig. 41. Solution curves of the dynamic system for a hypercycle with versa. The long-term behavior at low and high con-
translation. Dimension 2 x 10, K =0.026; initial conditions: y,(O) centration limits, obtained by numerical integration,
=5.0, Y2(0)= .. ·=Yto(0) = 0.5; xI(O)=· · =x IO (0)=1.0; full concen- agrees completely with the predictions based on the
tration scale = 10 concentration units, full time scale = 1000 time analysis given in the last section. One of the basic
units. The value of the equilibrium constant chosen is slightly above
the critical value for the Hopf bifurcation. We observe a metastable
simplifications, which concerned quasi-stationarity of
oscillatory state which changes suddenly into the final limit cycle polypeptide synthesis, can be checked directly by an
with the characteristic concentration waves inspection of the projections of trajectories onto the E l'

53
11 plane. For the stationary-state approximation we
expect to find straight lines. As we can see from Figures
39b and 40b, d, f, proportionality of the two con- Xi
centrations is roughly fulfilled and the simplified
I 0.5
treatment appears to be well justified. It was, actually,
the purpose of the numerical analysis of this complex
reaction mechanism to verify the equivalence of com-
plex and elementary hypercycles as far as their self- ar o1~------------~
organizing properties are concerned. The conclusions
reached with elementary systems therefore are relevant
also for all kinds of realistic hyper cycles of a more
complex structure (cf. Part C). i' 0,5

X. Hypercyc1ic Networks
o 500 - - t i m . _ 1000

X.1. Internal Equilibration and Competition


between Hypercycles

The concept of internal equilibration as introduced in


Section VI seems to be very useful for a straightforward
analysis of more complex networks since it permits a
reduction of the number of independent variables.
At first we investigate the process of equilibration in
elementary hypercycles. For that purpose we calculate
time averages of the individual concentrations X;( t)-
see Equation (67) and compare them with the corre-
sponding solution curves x;(t) (Fig. 42). No matter
whether the final state is stationarily inert or oscillat-
ing, the time averages X;(t) become practically con-
stant after a few cycles. The assumption of established
internal equilibrium therefore seems to be a well-justi- o
500 - - t i m e _ 1000
fied approximation for hypercycles. Nevertheless, we
shall check it in a few cases. Fig. 42. Solution curves of the dynamic systems for elementary
Using the concept of internal equilibration we can hypercycles of dimension n = 4 and n = 5 with equal rate constants
and time-averaged concentrations X(t); (a) n=4 and b) n=5. Note
derive an equation for the net growth rate of entire
that X(t) reaches X after a few oscillations, i.e., internal equilibrium
hypercycles: is established relatively fast in both examples
n n n
c= L x;= L I;(x) = L k;x;xj grow hypothetically to infinity at a certain critical time
i= 1 i= 1 i= 1
(too). In fully equilibrated systems these instabilities
1_ c 2 == kc 2 = r(C) (84)
=_n_ occur at
L k;-l t';,,=[kC(t=O)]-l (85)
j=i+ 1-nb;n The results for equilibrated hypercycles calculated
from Equation (85) are compared with the values
Hypercycles, thus, are characterized by quadratic obtained by numerical integration of systems far off
growth rates and follow a hyperbolic growth law. internal equilibrium (t':,,) in Table 12. In fully equilib-
They represent appropriate examples for the kind of rated systems the instabilities always occur somewhat
non-Darwinian 'once-for-ever' selection discussed earlier, t';" < t':". On the whole, these numerical differ-
in Sections VI and VII. ences are of minor importance only, the general
According to the expression for k in Equation (84) the behavior of the dynamic systems and the relative values
rate constant of an entire hypercyc1e will be ofthe same of too being predicted correctly. The assumption of
order of magnitude as that of its slowest single step. internal equilibration thus appears to be a good
Under the condition of unlimited growth, hypercyc1es approximation for most nonequilibrated systems.

54
Table 12. Instabilities in the dynamic systems for hypercycles under unEmited growth conditions

Dimension Boundary and initial conditions Critical time constants

Rate constant Initial concentration Initial distribution' At equilibrium Far off equilibrium
n k c(O) x(O) t:' t:'
1
2 "2 0.55 (0.5,0.05) 3.64 5.0
1
3 "3 0.60 (0.5, 0.05, 0.05) 5.00 6.8
1
4 4 0.65 (0.5, 0.05, 0.05, 0.05) 6.15 7.3

a The distribution of initial concentrations applied in the numerical integration of the system far off equilibrium x(O) =(x 1 (0), x 2 (0) ... ).

Selection among entire hypercycles as single entities X.2. Parasitic Coupling and Catalytic Networks
can be studied generally under the assumption of
The cyclically closed catalytic link, which connects all
internal equilibrium. The dynamic systems obtained
thereby are, of course, identical with those describing active members 11 ", In of a hypercycle might include
branching points and thereby provide a furthering of
independent competitors that are characterized by
quadratic growth rates. Competition between non- external species Iu 1...n' not being an intrinsic part of
the cooperative unit. We call these external members
equilibrated hypercycles is more difficult to investigate,
since only numerical integration of the systems of parasites. To make an analytical treatment feasible we
differential equations is possible. An example has been shall assume internal equilibrium within the cycle
treated elsewhere [53], demonstrating that the assump- (Table 13). Two dynamic systems describing a hyper-
cycle and a single-membered parasite have been in-
tion of internal equilibration represents a powerful
approximation. vestigated by the fixed-point method.
The first example is represented by a catalytic hyper-
As an example for competing systems we consider the two hyper- cycle and a parasite that is not capable of self-
cycles HA and HB with n A and nBmembers subject to the constraints replication (Fig. 43a). Above a certain threshold value
of constant organization. of total concentration (kA co> k), as we can see from
If there is internal equilibration the system reduces to two com-
Table 13, hypercycle and parasite are present with
petitors with quadratic growth-rate terms. From the results of fixed-
point analysis we recall that hypercycle HA will be selected when its nonzero concentration at the stationary state. The
relative initial concentration cArOl exceeds a critical limit: equilibrium concentration of the hypercycle grows with
increasing co, whereas the concentration of the parasite
lim cA(t)=c o (86) remains constant. At high enough concentration, con-
r-oo
sequently, the parasite will lose its importance for the
Otherwise hypercycle HB wins the competition. dynamics of the cycle completely. At low total con-
It seems illustrative to consider one more special case. We assume the centration (kA Co < k) the system becomes unstable.
individual rate constants to be very similar within a given hypercycle, Within the limits of the assumption of internal equilib-
i.e., k, ~k2 ~ ... ~kn=kA and kn+ 1 ~kn+2 ~ ... ~kn+m=kB' Then the rium the parasite destroys the hypercycle and finally
rate constants for entire hypercycles are obtained as follows:
represents the only remnant of the dynamic system.
(87)
The second case describes the development of a hyper-
cycle with a self-replicative parasite attached to it
(Fig. 43b). This dynamic system is characterized by
As we see, the constants are inversely proportional to the numbers of
sharp selection depending on the relative values of the
members in the hypercycle and consequently, smaller cycles seem to
have a certain selective advantage. If we assume, however, all rate constants k and k A' For k > k A the parasite destroys
macromolecules to be present at roughly the same concentrations (x), the hypercycle whereas the inequality k < kA implies
the disadvantage of the larger cycle is compensated exactly by a that the parasite dies out. It might be of some interest to
larger value of the total concentration, c: consider the dynamic system explicitly on the level of
cA(O)=nA'x, cB(O)=nB·x and cO=(nA+nB)x individual polynucleotides. From Table 13 we obtain
limcA(t)=c o if kA>kB (88)
r-oo k=k Xv =k k;}l (89)
x cA x Ik i- 1
Therefore, the chance of survival is roughly the same for hypercycles
of different sizes or dimension n, provided the initial concentrations
under the condition of established internal equilibrium.
of the individual members and the rate constants for the replication
steps are equal. Using the previously derived expression
The results obtained for two hypercycles can be generalized easily to
N independent competitors. kA =(I k i 1)-1
i

55
we find:
kx 11k (90)
k<k - -k + -"
- .--1
-< - - --+k x < V+ 1
A " -1
v+l Lk; Lk;

Thus the result of selection is determined completely by


the ratio of the two rate constants for the reaction steps
starting out at the branching point, no matter what the
values of the other rate constants in the hypercyc1e are.

Numerical integration of dynamic systems of the types shown in


Q
~ b
Figure (43) has been performed in order to study the influence of Fig. 43. Schematic diagrams for hypercycles with parasitic units,
deviations from the equilibrium distribution. In fact all the con- a) the parasite is not self-reproductive, b) the parasite is self-
clusions drawn here can also be verified for systems far off ~roductive. The branching is assumed to occur at the component
equilibrium.
0J
Table 13. Fixed-point analysis of hypercycles with parasitic couplings

A hypercycle with a parasitic unit Ix attached to it (Fig. 43) is which leads to


described by n + I differential equations, n of which are identical with
those of the isolated hypercycle. For the (n+ l)-th differential
equation, which defines the concentration of the parasite, we obtain:
[lJ=x, [l,]=x" and

x
x=kxx,--¢ (T.I 3. I)
Co
Thus, the fixed point x 2 is stable at concentrations below the critical
for the system depicted in Figure 43a and value and unstable above it. At low concentrations XI lies outside the
physically accessible range, x=c o is the only stable stationary state,
x and the hypercycle is destroyed by the parasite. At high con-
x=kxx,x--¢ (T.13.2)
Co centrations the stable fixed point XI lies on the simplex S2' which
means that hypercycle and parasite are coexistent.
for the one exemplified in Figure 43 b. (2) The parasite is self-reproductive (Fig. 43b):
If an equilibrium is established within the hypercycle then the n + 1
differential equations reduce to two. Here the introduction of new
rate constants turns ou't to be appropriate:

(T.I3.3) (T.13.8)

and kA as defined in Equation (84). The system has two fixed points at the corners of S 2:
(I) The parasite is not self-reproductive (cf. Fig. 43a):
(T.13.9)
(T.13.4)
(T. 13. 10)

The first fixed point is stable, provided that kA > k. For the second
fixed point it is again necessary to check the higher-order terms. At
x=co-bx we find
This dynamic system has two fixed points:
k-k
X= _ _A (bx)2(C O-bx) (T.13.11)
(T.13.5) Co

which now leads to

X>O for k>kA


(T.13.6)
and
XI is stable unless the total concentration meets the critical condition
Co = k/k A •
Stability analysis of x2 requires a detailed inspection of the higher-
order terms. For a point x=co-Dx we find Thus, x2 is stable if the inequality k>kA holds. The system is
competitive, which signifies that hypercycle and parastic unit cannot
(T.13.7) coexist except in the special situation where the rate constants are
equal (k=kA)'

56
The results obtained for single-membered parasites can be extended stants, the only possible remnants of catalytic networks
to arbitrary chains using the results derived in Section VlI.6. In of self-replicative units are independently growing
general, the fate of the entire parasite is strongly coupled to the
development of the species attached to the cycle: The parasite will die
species, catalytic chains, or catalytic hypercyc1es. Thus
out always when the concentration of the species after the branching any catalytic network consisting of self-replicative
point approaches zero. There is one interesting special case: units with uniform coupling terms will disintegrate
kx = k,_I' The differential equations for 1H 1 and I x are identical and either to yield a hypercyc1e which then is superior to the
hence the ratio of the two species always remains constant at its initial
other fragments or to give competitive dynamic sys-
value. Numerical integration of several dynamic systems of this type
showed that in this special situation (k x = k, + 1) all members of the tems that are not suited for cooperative evolution.
parasite besides the species I x will die out.
Chain-like parasites might fold back on the hypercycle, thereby
leading toward a catalytic network with a branching point and a X.3. Hierarchy of Coupling Between Hypercycles
confluent. By numerical integration we found that systems of these
types are unstable: The less efficient branch, i.e., the branch with the
smaller values of the rate constants k dies out and a single, simple In principle, hypercyc1es may be coupled to yield more
hypercycle remains. highly organized systems by introduction of appropri-
ate catalytic terms into the rate equation. We consider
Allowing for arbitrary assignment of catalytic coupling two basic hypercyc1es HA and HB and assume that the
terms to a set of self-reproductive macromolecules we hypercycle HA produces a catalytic growth factor for
shall encounter highly branched systems or com- HB and vice versa. Such a growth factor might be a
plicated networks much more frequently than regular constituent of the hypercyc1e or a substance produced
hypercycles. It is of great importance, therefore, to by it. From our previous experience we would expect
know the further deVelopment of these systems in order that mutual catalytic enhancement will lead to cooper-
to make an estimate of the probabilities of hyper cycle ative behavior.
formation. Analytical methods usually cannot be ap- To simplify a straightforward analysis, we assume in-
plied to this kind of system and hence we have to rely on ternal equilibrium to be established in both hypercycles.
the results of numerical techniques. The catalytic terms are of third order with respect to
Some general results have been derived from a variety molecular concentrations (kA c,~ CB and kBc Ac~, re-
of solution curves obtained by numerical integration of spectively, see also Table 14). Consequently, we may
the differential equations for various catalytic net- neglect the second-order growth functions of the un-
works. As suggested by the previous examples, these catalyzed system at high enough concentrations. Fixed-
systems are not stable and disintegrate to give smaller point analysis is no.! sufficient to study the dynamic
fragments. Apart from complicated dynamic struc- system obtained, since it yields zero eigenvalues for all
tures, which owe their existence to accidental coinci- normal modes. The vector field, however, can be
dence of the numerical values for differem rate con- investigated easily because the system has only one

Table 14. Fixed-point analysis of catalytically coupled hypercycles HA and HB

(I) Coupling terms of third order: (2) Coupling terms of fourth order:

(T.14.4)
(T.14.1)
This dynamic system is characterized by three fixed points:

Fixed-point analysis of the dynamic system yields: (T.14.5)

(T.14.2) (T.14.6)

(T.14.3)

The system is competitive. Analysis of the higher-order terms (Fig.


44) reveals that x1 is stable for kA > k B. The condition kA < kB' on the (T.14.7)
other hand, leads to stability of x2 •
X3 thus represents a stable fixed point indicating cooperative
behavior of the two coupled hypercycles HA and Ho under all
possible conditions. The vector field shown in Figure 44 reveals that
the other two fixed points Xl and Xl are sources.

57
degree of freedom. As we see from Figure 44 the two improbable*. One is tempted therefore to conclude
hypercycles still compete despite the presence of the that further development to more complex structures
catalytic factors. The kind of catalytic coupling in- that consist of hierarchically coupled self-replicative
troduced, thus, was not sufficient to cause cooperative units does not likely occur by introduction of higher-
behavior. order catalytic terms into a system growing in homo-
If we increase the order ofthe catalytic terms by one, the ge.neous solution, but rather leads toward individual-
dynamic system involves fourth-order growth-rate ization of the already existing functional units. This can
terms (kAcl.c~, kBcl.c~). Analyzing the vector field in be achieved, for example, by spatial isolation of all
the same way as before (Fig. 44), we find a stable fixed members of a hypercycle in a compartment. Formation
point at finite concentrations of both hypercycles of prototypes of our present cells may serve as one
(see also Table 14). Thus the quadratic coupling term possible mechanism leading to individualized hyper-
is sufficient to cause cooperativity among catalytic cycles. After isolation is accomplished the indivi-
hypercycles. dualized hypercycle may behave like a simple re-
The physical realization of this type of catalytic cou- plicative unit. Hypercycles therefore are more likely to
pling is difficult to visualize at the level of biologic be intermediates of self-organization than final
macromolecules: The presence of a term like k A c1 c~ or destinations.
kBcl.c~ in the overall rate equations requires either a
complicated many-step mechanism or an encounter of
more than two macromolecules, both of which are Conclusions

The main object of Part B is an abstract comparative


study of various functional links in self-replicative sys-
tems. The methods used are common in differential
topology. Complete analytical solutions - except in spe-
cial cases - are usually not available, since the differen-
tial equations involved are inherently nonlinear. Self-
reproduction always induces a dependence of production
rates on population /'lumbers of the respective species.
a Cooperation among different species via encoded func-
tiona I linkages superimposes further concentration terms,
which lead to higher-order dependences of rates on
population variables.
O~------~~------~~--
A comparative analysis of selective and evolutive be-
havior does not require a knowledge of the complete
solution curves. Usually it is sufficient to find their final
destinations in order to decide whether or not stable
coexistence of all partners of a functionally cooperative
ensemble is possible. Fixed-point analysis, aided by
qapounov's method and - in some cases - by a more
detailed inspection of the complete vector field, serves the
purpose quite well. The results of the combined analysis
b 0~------~~--------~-4- may be summarized as follows:
1.0 Functional integration of an ensemble consisting of
several self-replicative units requires the introduction of
catalytic links among all partners. These linkages, super-
imposed on the individual replication cycles of the
-0.5
subunits, mustform a closed loop, in order to stabilize the
Fig. 44. Coupling between hypercycles. a) Catalytic coupling terms ensemble via mutual control of all population variables.
kA cl CB and kBc A c~, respectively. The tangent vector is positive inside 1ndependent competitors, which under certain spatial
the physically allowed region (0 < cB < 1), except at the two fixed
conditions and for limited time spans may coexist in
points; kB>kA is assumed and consequently the hypercycle cB is
selected. The system is competitive despite the coupling term. 'niches', as well as catalytic chains or branched networks
b) Catalytic coupling terms kAclc~ and kBclc~, respectively. The
system contains two unstable fixed points at the corners and a stable * Artificial dynamic systems that are based on technical devices to
fixed point at the center (cA =cB=0.5 because kA =kB)' The system is introduce catalytic coupling terms like, e.g., electric networks may
cooperative not encounter these difficulties.

58
are devoid of self-organizing properties, typical of hyper- Therefore a hypercycle, once established, can not easily
cycles. Mere coexistence is not sufficient to yield co- be replaced by any newcomer, since new species always
herent growth and evolution of all partners of an emerge as one copy (or a few).
ensemble. In particular, the hypercycle is distinguished All these properties make hypercycles a unique class of
by the following properties: self-organizing chemical networks. This in itselfjustifies
1. It provides stable and controlled coexistence of all a more formal inspection of their properties - which has
species connected via the cyclic linkage. been the object of this Part B. Simple representatives of
2. It allows for coherent growth of all its members. this class can be met in nature, as was shown in Part A.
3. The hypercycle competes with any single replicative This type of functional organization may well be widely
unit not belonging to the cycle, irrespective of whether distributed and play some role in neural networks or in
that entity is independent, or part of a different hyper- social systems. On the other hand, we do not wish to treat
cycle, or even linked to the particular cycle by 'parasitic hypercycles as a fetish. Their role in molecular self-
coupling'. organization is limited. They permit an integration of
4. A hypercycle may enlarge or reduce its size, if this iriformation, as was required in the origin of translation.
modification offers any selective advantage.
5. H ypercycles do not easily link up in networks ofhigher However, the hypercycle may have disappeared as soon
orders. Two hypercycles of degree p need coupling terms as an enzymic machinery with high reproduction fidelity
of degree 2 p in order to stabilize each other. was available, to individualize the integrated system in
6. The internal linkages and cooperative properties of a the form of the living cell. Individualized replicative
hypercycle can evolve to optimal function. 'Phenotypic' systems have a much higher potential for further
advantages, i.e., those variations which are of direct diversification and differentiation.
advantage to the mutant, are immediately stabilized. On There are many forms of hypercyclic organization rang-
the other hand, 'genotypic' advantages, which favor a ing from straightforward second-order coupling to the
subsequent product and hence only indirectly the re- nth order compound hypercycle in which cooperative
plicative unit in which the mutation occurred, require action of all members is required for each reaction step.
spatial separation for competitive fixation. While we do not know of an y form oforganization simpler
7. Selection of a hypercycle is a 'once-for-ever' decision. than a second-order hypercycle that could initiate a
In any common Darwinian system muta'!ts offering a translation apparatus, we are well aware of the com-
selective advantage can easily grow up and become plexity of even this 'simplest possible' system. It will
established. Their growth properties are independent of therefore be our task to show in Part C that realistic
the population size. For hypercycles, selective advan- hypercycles indeed can emerge from simpler precursors
tages are alwaysfunctions of population numbers, due to present in sufficient abundance under primordial
the inherently nonlinear properties of hypercycles. conditions.

59
C. The Realistic Hypercycle

The proposed model for a 'realistic hypercycle' is Let us for the time being assume that a crude replica-
closely associated with the molecular organization of tion and translation machinery, functioning with ade-
a primitive replication and translation apparatus. Hy- quate precision, and adapted to a sufficiently rich
percyclic organization offers selective stabilization alphabet of molecular symbols, has come into exis-
and evolutive adaptation for all geno- and phenotypic tence by some process not further specified, e.g., by
constituents of the functionally linked ensemble. It self-organization or creation, in Nature or in the labo-
originates in a molecular quasi-species and evolves ratory. Let us further suppose an environment which
by way of mutation and gene duplication to greater supplies all the activated, energy-rich material re-
complexity. Its early structure appears to be reflected quired for the synthesis of macromolecules such as
in: the assignment of codons to amino acids, in nucleic acids and proteins, allowing both reproduc-
sequence homologies of tRNAs, in dual enzymic func- tion and translation to be spontaneous processes, i.e.,
tions of replication and translation, and in the struc- driven by positive affinities. Would such an ensemble,
tural and functional organization of the genome of however it came into existence, continue to evolve
the prokaryotic cell. as a Darwinian system? In other words, would the
system preserve indefinitely the information which
it was given initially and improve it further until it
reaches maximal functional efficiency?
In order to apply this question to a more concrete
situation let us consider the model depicted in Figure
45. The plus strands of a given set of RNA molecules
contain the information for a corresponding number
of protein molecules. The products of translation can
XI. How to Start Translation? fulfill at least the following functions: (1) One protein
acts as an RNA-polymerase similar to the specific
.. The origin of protein synthesis is a notoriously diffi- replicases associated with various RNA phages. Its
cult problem. We do not mean by this the formation recognition site is adapted to a specific sequence or
of random polypeptides but the origin of the synthesis structure occurring in all plus and minus strands of
of polypeptides directed, however crudely, by a nu- the RNAs; in other words, it reproduces efficiently
cleic acid template and of such a nature that it could only those RNA molecules which identify themselves
evolve by steps into the present genetic code, the as members of the particular ensemble. (2) The other
expression of which now requires the elaborate ma- translation products function as activating enzymes,
chinery of activating enzymes, transfer RNAs, ribo- which assign and link various amino acids uniquely
somes, factors, etc." to their respective RNA adaptors, each of which
Our subject could not be characterized more aptly carries a defined anticodon. The number of different
than by these introductory phrases, quoted from a amino acids and hence of adaptors is adjusted to
recent paper by F.H.C. Crick, S. Brenner, A. Klug match the variety of codons appearing in the messen-
and G. Pieczenik [3]. ger sequences, i.e., the plus strands of the RNAs,

60
which initially functions quite well, is predestined to
deteriorate, owing to internal competition. A typical
set of solution curves, obtained by numerical integra-
tion of the rate equations, is shown in Figure 46.

10

Fig. 45. A minimum model of primitive translation involves a


messenger 10 encoding a replicase Eo. which is adapted to recog-
nize specifically the sequences 10 to 14, The plus strands of I, to 14
encode four synthetase functions E, to E4 • while the minusstrands
may represent the adapters (tRNAs) for four amino acids. Such a
system. although it includes all functions required for translation
and self-reproduction, is unstable due to internal competition.
Coherent evolution is not possible, unless 10 to 14 are stabilized by
a hypercyclic link
o o.s 1D 15 2D lime
Fig. 46. Solution curves for a system of differential equations
simulating the model represented in Figure 45. In this particular
example, it is assumed that initial concentrations and autocatalyt-
so as to yield a 'closed' translation system with a ic-reproduction-rate constants increase linearly from 10 to 14 , while
defined code. It does not necessarily comprise the the other parameters-such as translation-rate constants (1,"4£,),
amino acid assignments (contribution of E" E 2 , E3 E4 to Ftr )
complete genetic code, as it is known today, but rather
or enzyme-substrate-complex stabilities (I, + Eo ~ I,· Eo), etc.-
may be confined to a - functionally sufficient - smal- are identical for all reaction partners. The time course of the
ler number of amino acids (e.g., four), utilizing certain relative population numbers (y? /c~) reflects the competitive be-
constraints on the codon structure in order to guar- havior. The most efficiently growing template (14) will supersede all
antee an unambiguous read-off. The adaptors may others and finally dominate (y~/c~-+ 1). However, since both re-
plication (represented by Eo) and translation function (contri-
be represented by the minus strands of the RNA con- butions of E" E2 and E3 to Ftr ) disappear, 14 will also die out. The
stituents, or, if this should be too restrictive a condi- total population is bound to deteriorate (c~-+O)
tion, they could be provided along with further ma-
chinery, such as ribosomes, in the form of constant
environmental factors similar to the host factors as-
sisting phage replication and translation inside the
bacterial cell.
At first glance, we might find comfort in the thought
that the system depicted in Figure 45 appears to be
highly functionally interwoven; all Ii are supported
catalytically by the replicase Eo, which in turn owes
its existence to the joint function F, of the translation
enzymes El to E4 without which it could not be trans-
lated from 10 , The enzymes El to E4, of course, utilize
this translation function for their own production too,
but being the translation products of 11 to 14 , they
are finally dependent also upon Eo or 10 respectively.
However, a detailed analysis shows that the couplings
present are not sufficient to guarantee a mutual stabil-
ization of the different genotypic constituents Ii' The
general replicase function exerted by Eo and the gen- Fig. 47. In this alternative model for primitive replication and
translation, the enzymes E I to E4 are assumed to have dual
eral translation function F'r are represented in all dif-
functions, i.e., as specific replicases of their own messengers and as
ferential equations by the same term. The equations synthetases for four amino acid assignments. The fate of the system
then reduce to those for uncoupled competitors, mul- is the same as that of the system depicted in Figure 45, since the
tiplied by a common time function fit). The system, messengers are highly competitive

61
Another example of this kind is represented in Figure XII. The Logic of Primordial Coding
47. Here all messengers produce their own specific
replicases El to E 4 , which also provide synthetase XII. 1. The RRY Code
functions (Ftr ). Again, this coupling by means of a
concomitant translation function does not suffice to A most appealing speculative model for the ongm
stabilize the ensemble. The answer to our question, of template-directed protein synthesis, recently pro-
whether the mere presence of a system of messengers posed f3], is based on a number of logical inferences
for replicase and translation functions and of transla- that are related to the problem of comma-free and
tion products is sufficient for its continuous existence coherent read-off. A primordial code must have a
and evolution, is that unless a particular kind of coup- certain frame structure, otherwise a message cannot
ling among the different replicative constituents Ii be read off consistently. Occasional phase slips would
is introduced, such systems are not stable, despite produce a frame-shifted translation of parts of the
the fact that tliey contain all required properties for message and thereby destroy its meaning. The authors
replication and translation. Even if all partners were therefore propose a particular base sequence to which
selectively equivalent (or nearly equivalent) and hence all codons have to adhere. Or, in other words, only
were to coexist for some time (depending on their those sequences of nucleotides that resemble the par-
population size), they could not evolve in a mutually ticular pattern could become eligible for messenger
controlled fashion and hence would never be able function. Uniformity of pattern could arise through
to optimize their functional interaction. Their final instruction conferred by the exposed anticodon loop
fate would always be deterioration, since an occa- of tRNAs as well as by internal self-copying. Among
sional selective equivalence cannot be coherently the possible patterns that guarantee nonoverlapping
maintained over longer periods of evolution unless read-off, the authors chose the base sequence purine-
it is reinforced by particular couplings. purine-pyrimidine, or, in the usual notation, RRY,
Knowing the results of part B, we are, of course, to be common to all co dons specifying a message.
not surprised by this answer. A closer inspection of The particular choice was biased by a sequence reg-
the particular linkages provided by the functions of ularity found in the anticodon loop of present tRNAs,
replication and translation enzymes does not reveal which reads 3'NRapyUY, apy being the anticodon,
any hypercyclic nature. Therefore these links cannot N any of the four nucleotides, and Rand Y a purine
establish the mutual control of population numbers and a pyrimidine, respectively. Another prerequisite
that is required for the interrelated evolution of of ribosome-free translation is the stability of the
members of an organized system. The couplings pre- complex formed by the messenger and the growing
sent in the two systems studied can be reduced to polypeptide chain. A peptidyl-t-RNA must not fall
two common functions, which, like environmental off before the transfer to the subsequent aminoacyl-
factors, influence all partners in exactly the same way tRNA has been accomplished, that is, until the
and hence do not offer any possibility of mutual con- complete message is translated. Otherwise, only func-
trol. tionally inefficient protein fragments would be ob-
The above examples are typical of what we intend tained. It is obvious from known base-pair stabilities
to demonstrate in this article, namely, that that a simple codon-anticodon interaction does not
guarantee the required stability of the messenger-
I. In the early phases of evolution, characterized by
tRNA complex. Therefore the model was based essen-
low fidelities of replication and translation as well
tially on three auxiliary assumptions.
as by the initially low abundance of efficiently repli-
1. The structure of the anticodon loop of the adaptor
cating units, hypercyclic organization offers large rel-
(tRNA precursor) is such, that - given the particular
ative advantages over any other kind of (structural)
and common codon pattern - an RNA can always
organization (Sect. XV), and
form five base pairs with the messenger. The primitive
2. That hypercyclic models can indeed be built to tRNA is then assigned the general anticodon-loop
provide realistic precursors of the reproduction and sequence
translation apparatus found in present prokaryotic
cells (Sect. XVI).
How could we envisage an origin of translation, given
the possible existence of reproducible RNA molecules where YYR is the anticodon.
as large as tRNA and the prerequisites for the syn- 2. The anticodon loop of each primitive tRNA can
thesis of proteins in a primitive form, utilizing a lim- assume two different conformations, which are
ited number of (sufficiently commonly occurring) detailed in Figure 48. Both configurations had been
amino acids? described in an earlier paper by C. Woese [60] who

62
~U-U-'VV'V'VV5'
G-U ~3'

Fig. 48. Two possible configurations of the anticodon loop of


tRNAs: FH according to Fuller and Hodgson [61] and hf according
to Woese [60]. The anticodon pattern (framed) refers to the model
of Crick et al. [3]

named them FH and hf. (FH refers to Fuller and


Hodgson [61] who originally proposed that five bases
at the 3' -end of the unpaired seven-base sequence
in the anticodon loop are stacked on top of each
other, while hf, according to Woese, designates a com-
plementary configuration keeping the five bases at
the 5' -end of the loop in a stacked position.) Woese
assumed that the transition between both configura-
tions plays an important role in ribosomal protein
synthesis, but also referred to its possible significance
in past, more primitive mechanisms.
3. Which of the two configurations is actually present
depends on whether the tRNA is attached to an
amino acid or to a peptide chain. By transferring
an amino acid to the peptide chain, the tRNA flips
from the hf to the FH configuration (cf. Fig. 49).
An additional, fourth postulate, not absolutely neces-
sary as a prereqnisite of the model, invokes an interac-
tion between two adjacent tRNAs at the messenger,
which assures that the required configration will be
energetically the most favorable and contributes fur-
ther to the stability of the polypeptide-messenger
complex.
Figure 49 shows in more detail how polypeptide syn-
thesis may be facilitated on the basis of the arguments
given. The growing polypeptide chain is transported
along the messenger, utilizing as 'fuel' the free energy
of the transfer reaction. This reaction may be aided
by a general nonspecific catalyst, but the mechanism
does not require any sophisticated machinery, such
as is nowadays provided by the ribosomes. Although
interaction between codon and anticodon is stabilized
by five base pairs, it is essential that the actual code
make use of base triplets. It had been emphasized P".1
previously [62] that a primitive code utilizing anything
but three bases is useless in explaining the present code. Fig. 49. The primitive translation mechanism requires 'sticky' in-
teractions between the messenger and the peptidyl-tRNA. It
The model explains well how in the absence of a thereby allows the growing peptide chain to remain in contact
sophisticated translation apparatus a message can be with the message until translation is completed. According to Crick
et al. [3] the transport is effected by a flip mechanism involving
read off conformational changes of the tRNA (FH~hf). The nascent pep-
tide chain is always connected with the messengers via five base
spontaneously,
pairs with some additional stabilization by the adjacent aminoacyl-
sequentially, tRNA. The partial overlap of base pairing guarantees a consistent
completely, i.e., un fragmented, and reading of a message encoded in base triplets

63
reproducibly, i.e., strictly maintaining a given codon can also develop internally within a single strand,
frame. allowing the formation of symmetric secondary fold-
ing structures. Typical examples of (almost) symmet-
The code is inherently related to certain structural
ric foldings are the present-day tRNAs. Single-
features of the anticodon loop of present tRNAs,
suggesting that these molecules are the descendents stranded phage genomes and their derivatives (such
of the first functionally organized entities. The four as the midi-variant of Qf3-RNA) are also dis-
amino acids assigned by this model are: tinguished by such elements of symmetry. Here the
selective advantage of a symmetric structure is ob-
GGg GAg AGg; AAg vious. If the molecules are to be reproduced by a
glycine aspartic acid serine asparagine polymerase, which recognizes specifically some struc-
tural feature, only a symmetric structure would allow
Some of which were very abundant in the primitive the plus and the minus strands to be equally efficient
soup [63]. templates. Such an equivalence of efficiency is re-
On the other hand, the model also introduces some quired for selection. Thus the symmetry of tRNA
difficulties. A uniform RR Y sequence has a large may well be a relic from a time when these molecules
excess of purine over pyrimidine and therefore does still had to reproduce autonomously.
not easily lend itself to stable internal folding. Internal folding also enhances the molcule's resistance
As a consequence, such sequences to hydrolysis and offers an easy way of instructing
the correct read-off of the message. In an open struc-
are quite labile toward hydrolysis
ture in which many nucleotides remain unpaired (e.g.,
(if present as single strands),
for RRY sequences), replication and translation could
have a greater tendency to form duplices
start at any unpaired position of the sequence, leading
(which do not easily replicate by primitive mecha-
to fragmentary products. In a completely paired struc-
nisms),
ture, unmatched sticky ends are predestined to be
lack internal symmetry, and
the starting-points of replication and translation. In
produce minus strands of a different general code
this way the complete message can be read off, requir-
pattern (i.e., YR YY).
ing only transient partial unfoldings of the template
structure, which may be enforced by interactions with
XII. 2. The RNY Code the growing chain. Symmetry, although not abso-
lutely required, would in this case again be of advan-
Before going into a more detailed discussion of the tage (cf. Fig. 50).
points listed above, let us now offer an alternative From a logical point of view the RNY code seems
model that is free of these particular difficulties. The to be more attractive than the RR Y code, on the
suggestion of using the general codon pattern RNY, basis of three arguments.
where N stands for any of the four nucleotides A, 1. Selective enhancement of RNA molecules must
U, G, C, is also to be credited to Crick et al. [1].
be effective for the plus as well as the minus strand.
However, it was disfavored by its authors on the Symmetric RNY patterns can fulfil this requirement
grounds of a disadvantage: If N represents a pyrimi-
more easily than RR Y sequences, which differ from
dine, then the anticodon loop, having the general
their minus strands (R YY) and hence cannot both
sequence 3'@GYNRU@, can in some cases use
become equivalent targets for specific recognition by
only its five central nucleotides to form stable base
enzymes.
pairs with the messenger. This argument may,
however, be counteracted by the observation that 2. In view of the high complexity, there is little chance
an RNY code can assign eight amino acids, so that finding the very few sequences that offer useful prop-
one may exclude certain combinations that do not erties for replication and translation. If these se-
fulfil the stability requirements for the messenger- quences, being symmetric structures, fulfil the require-
peptidyl-tRNA complex (cf. below). ments listed under (1), both the plus and the minus
What are the advantages of a general code pattern strands may be candidates for representing such func-
RNY? First of all, the RNY code, like its RR Y tions.
analog, is comma-free. Moreover, it is symmetric with 3. Evolution of the translation apparatus with its
respect to plus and minus strands. If read from 5' various tRNAs and messengers requires a mutual sta-
to 3', the general frame structure of both the plus bilization of all replicative molecules. As will be
and the minus strand is R~Y where Nand N' are shown below, hypercycles may emerge more easily
complementary, situated at mirror-image positions in from a quasi-species if this, on account of its symme-
the sequences of both strands. Similar symmetries try, offers two complementary functions.

64
be important if absolute rates of the historical
processes are to be estimated.
Here we simply start from the assumption that when
self-organization began all kinds of energy-rich mate-
rial were ubiquitous, including in particular:
amino acids in varying degrees of abundance,
nucleotides involving the four bases A, U, G, C,
polymers of both preceding classes, i.e., proteinoids as
well as tRNA-like substances, having more or less ran-
dom sequences.
'Less random' in this context means the existence of
nearest-neighbor and more complex folding interac-
tions, leading to a preference of certain structures,
while 'more random' refers to their primary unre-
latedness to any functional destination, which - if ini-
a b c tially present - could only be coincidental.
Fig. 50. Symmetric secondary structures of RNA require a corres- On the other hand, we definitely do not suppose the
ponding internal complementarity (cf. Fig. 14 in Part A). Plus presence of any adapted protein machinery, such as
and minus strands will then exhibit similar foldings. RNY-codon specific polymerases,
patterns are able to produce such structures. A game has been
adapted synthetases, or any of the ribosomal functions.
devised, the rules of which take into account the physical interac-
tions observed with oligonucleotides and tRNAs [17, 18]. It shows This does not exclude an involvement of non-
which of the structures is most likely to occur. Hairpins require
two complementary halves of the molecule, e.g., a 5'-RR Y sequence instructed, poorly adapted protein catalysts, in facili-
linked up to its minus strand involving a 5'RYY pattern tating the start of replication and translation. How-
ever, not being able to reproduce and improve selec-
tively, those proteins must be subsumed together with
other catalytic surfaces under 'constant environmen-
A system can accumulate information and eventually tal factors'.
evolve to higher complexity only if it adopts the' Darwi-
nian logic' of selective self-organization. However, this
logic must find its basis and its expression in material XIII. 2. Abundance of Nucleotides
properties. All that the constituents can recognize at
the beginning is natural abundance and strength of in- Since nucleic-acid-like structures are the only ones
teraction. These are the properties with which we shall that offer inherent self-reproductive properties, it is
have to deal in order to understand the start of transla- important to analyze first their abundances as well
tion. as their mutual interactions in more detail.
The monomeric nucleotides, especially their energy-
rich oligophosphate forms, are more difficult to ob-
XIII. Physics of Primordial Coding tain (using possible pre biotic mechanisms) than are
amino acids. Quantitative statements of relative abun-
XIII. 1. The Starting Conditions dance are therefore scarce. S. Miller and 1. Orgel
([63], p. 104) emphasize the central role of adenine
Self-organization as a multimolecular process requires nucleotides both in genetic processes as well as in
monomers as well as polymers to be present in suffi- energy transfer and correlate it with the relative ease
ciently high concentrations. Its onset therefore must with which this substance is formed. J. Or6 and his
have been preceded by an extended phase of pre biotic co-workers [64] found that adenine can be obtained
synthesis, during which all the material necessary for in yields of 0.5% in concentrated aqueous solutions
yielding a 'highly enriched soup' was accumulated. of ammonium cyanide, while Miller and Orgel ([63],
We do not intend to dwell on these processes of pri- p. 105) showed that even hydrogen cyanide alone, in
mordial chemistry, nor do we quarrel about details a reaction catalyzed by sunlight, yields the important
of historical boundary conditions. Questions as to intermediate
whether the 'soup' originated in the oceans, in a
pond, or even in small puddles, or whether interfaces,
coarse-grained, or porous surfaces were involved, may
4 HeN -+ tetramer ~
N=C

H2N
X)---
N

NH
adenine

65
The same intermediate can also react with cyanate, of 10- 3 *, while s is the stability constant of a single
urea, or cyanogen to give guanine. Less well under- pair within the cooperative stack. For homogeneous
stood are the mechanisms of pyrimidine synthesis. sequences of AU pairs this parameter s is about one
A pathway could be demonstrated for the synthesis order of magnitude smaller than for homogeneous
of cytosine, using cyanoacetylene - an electric-dis- sequences of GC pairs, or in a rough quantitative
charge product of mixtures of methane and nitro- representation:
gen-in combination with cyanate. Uracil, on the SAU>::::: 10 while SGC>::::: 100.
other hand, appears to be a hydrolysis product of
Higher absolute stabilities than predicted by relation
cytosine and may possible owe its primordial exis-
(91) are found if one of the complementary strands
tence to this source.
can assume the particular stacking configuration pre-
Only little can be said about the primordial natural
sent in the anticodon loop of tRNA. Presumably the
abundance of the purines and pyrimidines. The rate
cooperativity parameter {3 is changed in this case.
of template-instructed polymerization is proportional
Yet O.C. Uhlenbeck, J. Batter and P. Doty [65, 66]
to the concentration of the monomer to be included.
found that tri- and tetranucleotides, complementary
For complementary instruction, at least two nucleo-
to the anticodon region of a tRNA and differing
tides are required and they will have to be equivalently
in one AU pair, exhibit a difference of one order
represented in informational sequences. Therefore the
inclusion of the less abundant nucleotide will always of magnitude in their stability constants, quite in
be the rate-limiting step, at least for chain elongation. agreement with the figure quoted above. It is also
reasonable that the largest absolute values of stability
A possible large excess of A over U in the primordial
monomer distribution would then have been of little constants found are those for the interaction of two
tRNAs that are complementary in their anticodons
help in favoring AU over GC copolymers, except
in cases where the nucleation of oligo-A primers is [67].
the rate-limiting step. The capacity for replicative The data obtained with defined short sequences may
serve at least for a comparison between various repli-
growth is limited to the template function of the less
abundant member of the complementary nucleotide cation and translation models and for conclusions
pair. If under primordial conditions the abundance about their relative significance. It is obvious that
single isolated AU or GC pairs are unstable under
of G and C was intermediate to that of A and U
then GC- and AU-rich copolymers may well hav~ any realistic conditions of concentration. The start
formed with comparable rates. of replication, therefore, requires special help in the
form of primer formation, and it is particularly this
We therefore cannot maintain the earlier, speculative step that calls first for enzymic support. Present-day
view that the first codons were recruited exclusively phage RNA replicases are also specifically adapted
from a binary alphabet, made up of A U copolymers to a primary sequence pattern of the phage genome.
alone. For chain elongation, the incoming nucleotide is
bound cooperatively on top of a stack of base pairs
of the growing chain. Here the data suggest that the
XII!. 3. Stability of Complementary Structures GC pair is about ten times more stable than the AU
The stability of base pairing may provide clues that pair, resulting in a relatively higher fidelity q for G
are more illuminating with respect to the question and C than for A and U. If the rate of replication
of the first codons. Stabilities and rates of base pairing is limited by the formation of the covalent link in
have been studied using various nucleotide combina- the polynucleotide backbone (rather than by base-pair
tions. These results have been discussed in detail in formation) the fidelity can be correlated with the
earlier reviews [44, 4]. They reveal quantitatively the monomer concentrations mR and my and the pair-
generally accepted view that GC pairs within a co- stability constants K Ry , K RR , and K yy . The reproduc-
tion fidelity for any given nucleotide then may be
operative stack provide considerably more stability
obtained from the geometric mean of the fidelities
than AU pairs.
for both complementary processes,
The stability constant of a continuous and homoge-
neous oligomeric sequence of n nucleotide pairs can R-*Y; Y-*R:
be represented by the relation
(92)
Kn={3sn (91)
which refers to a linear Ising model. The factor {3 * Such a relation is formally valid for both the internal base
is a cooperativity parameter, which for both the AU pairing within a given sequence and the binary association of two
and GC pairs amounts to an order of magnitude complementary sequences, where fJ has the dimension M - '.

66
where KRy~KYR and summation is extended over all higher fidelity than A and U. Depending on the
N =A, U, G, C. Those q values are identical for superiority of the selected sequences (CT, cf. Eq.
A and U or G and C, respectively, since the error (28), Part A), the reproducible information content
can appear either in the plus or in the minus strand. of GC-rich sequences in early replicative processes
If the monomeric concentrations are of equal magni- is limited to about twenty to one hundred nucleotides,
tudes, the stability constants determine what fidelities i.e., to tRNA-like molecules, while that of AU-rich
are obtainable. Then it follows that G and C repro- sequences can hardly exceed ten to twenty nucleotide
duce considerably more accurately than A and U. residues per replicative unit. It should be emphasized
The ratio of the error rates for GC and AU reproduc- at this point, that longer sequences of any composi-
tion in mixed systems, however, does not exactly re- tion may well have been present. However, they were
semble the (inverse) ratio of the corresponding stabil- not reproducible and therefore could not evolve ac-
ity constants, owing mainly to the presence of GU cording to any functional requirement.
wobble interactions, which are the main source of From an analysis of experimental data for phage rep-
reproduction errors-even in present-day RNA phage lication we concluded in Part A that even well-
replication [34]. adapted RNA replicases would not allow the repro-
We have made a guess of q values based on various ducible accumulation of more than 1000 to 10000
sets of data for enzyme-free nucleotide interactions. nucleotides per strand. This is equivalent to the actual
They are summarized in Table 15. The first three gene content of the RNA phages.
sets refer to equal monomeric concentrations of A, We may now complete our statement regarding pri-
U, G, and C. This assumption may be unrealistic mordial replication mech<l;nisms: A size as large as
and is therefore modified in the last three examples. tRNA is reproducibly accessible only for GC-rich struc-
One may object to the application of stability data tures. Hence:
that were obtained from studies with oligonucleotides.
GC-rich sequences qualify as candidates for early tRNA
However, the inclusion of a single nucleotide in the
adapters and for reproducible messengers, at least as
replication process involves cooperative base-pair in-
long as replication is not aided by moderately adapted
teractions and hence should resemble the relative or-
enzymes.
ders found with oligonucleotides. All that is required
for calculating the q values are relative rather than A similar conclusion can be drawn with respect to
absolute stabilities. the start of translation. As was emphasized by Crick
The conclusion from the different estimates presented et al. [3], stability of the peptidyl-tRNA-messenger
in Table 15 is: G and C reproduce with an appreciably complex is critical for any primitive translation mo-

Table 15. Estimates of fidelities and error rates for G and C vs. A and U reproduction

Monomer concentrations Stability constants Fidelity q Error rate I-q


of base pairs
GC AU GC AU

mA=mG=mC=mu KRR =Kyy = I 0.93 0.59 0.Q7 0.41


KAC = I; Kau= 10
KAU = 10; Kac= 100
mA=mG=mC=mu KRR::::;Kyy %, I 0.95 0.67 0.05 0.33
KAC = I; Kau= 10
KAu=lO; KGc=IOO
mA=mG=mC=mu KRR=Kyy%'1 0.97 0.78 0.03 0.22
KAc=l; Kau=5
KAU = 10; Kac= 100
mA=IOmG KRR::::;Kyy %, I 0.93 0.81 0.07 0.19
mG=mc KAc=l; KGu=5
mc= IOmu KAU = 10; Kac= 100
mA=IO mG KRR::::;Kyy %, I 0.95 0.69 0.05 0.31
mG=mc KAC = I; KGu=5
mc=lOmu K AU = 10; KGc= 100
mA= 10 ma KRR=Kyy = I 0.86 0.25 0.14 0.75
mG=mc KAC=2; Kau= 10
mc=IO mu K AU = 10; KGc= 100

67
del. Applying the data quoted above, the stability those in which G and C residues predominated. The
constant of a complex including five GC pairs first codons were then exclusively combinations of
amounts to these two residues. The requirement for a comma-free
read-off excludes the symmetric combinations GGG/
K5GC~I07 M- 1
CCC and GCG/CGc. This may be easily verified
while that for five AU pairs is five orders of magni- by writing down such sequences. Adaptors with the
tude lower: correCt anticodon combinations can bind in various
overlapping positions. This will have even more dele-
K5AU~I02 M- 1 terious consequences, if further codon combinations,
Again these values must be seen as relative; they derived from symmetric precursors, are introduced.
might actually be somewhat larger if the stacked-loop We are thus left with two. complementary pairs of
region or tRNA (as we know it today) were involved, combinations, namely, GGC/GCC and CCG/CGG
which, however, would not invalidate the argument (all patterns to be read from 5' to 3'). From the
based on relative magnitudes. point of view of symmetry both appear completely
We might also evaluate the models on the basis of equivalent. There is, however, a slight asymmetry
lifetime data. The recombination-rate constants, as based on wobble in the third position. Let us compare
measured for complementary chains of oligonucleo- messenger sequences consisting exclusively of either
tides, were found consistently to lie in the order of CNG or GNC codons. In the first case the wobble
magnitude of base G is always situated in the third codon position,
while in the second case it is restricted to the first
kR~106 M- 1 S-l.
position, in both the plus and the minus strands (if
Given the stability constants quoted above, the life- consistently read from 5' to 3'). For replication the
times of the respective complexes would amount to different codon positions are not distinguishable.
Hence, wherever a wobble base occurs, an ambiguity
T5GC~ 10 s and T5AU~ 10- 4 s. may be introduced in the complementary strand,
Again, these numbers might shift to larger values which, when it comes to translation, in one case af-
if stabilities turned out to be higher, and if two ad- fects the first, in the other case the third codon posi-
jacent tRNAs are able to stabilize each other when tion:
attached to the messenger chain. Then lifetimes might
just suffice for GC-rich sequences to start primitive 5'----CNG CNG CNG----3'
translation. The lifetimes are certainly much too short 1
if AU pairs are in excess. We see now that the slight 5' ----5N'G5N'G5N'G----3'
disadvantage of the RNY relative to the RR Y code and
resulting from stabilities can be balanced by utilizing
primarily G and C at least for part of the Rand 5'----GNC GNC GNC----3'
Y positions. A four-membered GC structure is defin- 1
itely more stable than any five-membered structure, 5' ----GN5GN5GN5 ----3'
including more than two AU pairs. Only in the second case are the reproduced sequences
The conclusion is:
correctly translated, i.e., if wobble interactions with
The start of translation is highly favored by GC-rich the adapter occur preferentially in the third rather
structures both of the tRNA precursors and of the mes- than in the first codon position.
sengers. In other words, an adapter with the anticodon 3'CNG
can read both 5'GN'C and 5'GN'U, whereas an adap-
ter with the anticodon 3'GNC will only read 5'CN'G,
but reject 5'UN'G. The argument might be weak if
XIV. The GC-Frame Code
five base pairs are required to keep the adapter bound
to the messenger, since then wobble positions may
XlV. I. The First Two Codons
not be as clearly distinct. Nevertheless, this asymmet-
ric relationship between the first and third codon posi-
If we combine the conclusions drawn from stability
tions does exist and is obvious in the present genetic
data with the arguments produced by Crick et a!.,
code. * Relatively small selective advantages are usually
we can predict which codon assignments were proba-
sufficient to bias the course of evolution. Crick et al.
bly the first ones.
The only sufficiently long sequences that are able * Our argument is aided by the fact that in the stationary distri-
to reproduce themselves faithfully must have been bution G is more persistent than C.

68
obviously preferred the RRY (or RNY) model on x/V. 2. The 'Aperiodic Linear GC Lattice'
the basis of such arguments, too.
We are now able to make a unique assignment for The tRNA-like molecule with its internal folded struc-
the first two codons, namely ture strengthened by hydrogen bonds may be consid-
ered a microcrystallite. If it involves longer stretches
5'GGC and 5'GCC of complementary GC pattern, the resulting internal
structure may be quite inert. From melting curves
which are complementary if aligned in an anti parallel of tRNA loops or corresponding oligonucleotides we
fashion. This choice was dictated by four arguments, know that an uninterrupted sequence of only four
viz., GC pairs is already quite stable. S. Coutts [68] studied
stability of adapter-messenger interaction and an oligonucleotide corresponding to the extra loop
fidelity of replication, both favoring GC combinations of tRNA~~~ from yeast, which contains 4 GC pairs
to start with, (and was obtained by partial digestion of the tRNA
comma-free read-off in translation requiring an un- molecule). He found a melting temperature of
symmetric GC pattern, and 84 ± 10 C and a A H of 44 ± 4 kcal/mol. This is equiva-
consistency of translation restricting wobble ambi- lent to a stability constant of about 2 x 10 5 at 25 0 C,
guities to the third codon position. in good agreement with the figures mentioned above.
What is rated in the selection of a quasi-species is
We should like to emphasize that these arguments not merely the structural stability of the strands, but
are based exclusively on the properties of nucleic rather a favorable combination of structural stability
acids. It is satisfying to notice that the two codons with reproductive efficiency. Efficient template func-
GGC and GCC in the present genetic code refer to tion requires a quick partial unwinding of a loop,
the two simplest amino acids, glycine and alanine, a procedure for which excessively long stretches of
which in experiments simulating primordial condi- GC pairs are prohibitive. However:
tions indeed appear with by far the greatest abun-
Natural sequences are not perfect anyway.
dance.
One may object that translation products consisting Given a high abundance of A-monomers and the
of these two residues only, will hardly represent cata- limited fidelity of base pairing, the GC microcrystal-
lysts of any sophistication. We shall return to this lites will always be highly doped with A-residues,
question in Section XVI. At the moment it suffices acting like imperfections in the linear GC lattice. A
to note that translation at this stage is not yet a priori, there may be any kind of sequence from high
property required for the conservation of the underly- to low A, U, G, or C content. What is to be selected
ing messengers. The first GC-rich strands are selected and then reproducibly mulitplied, will be a sequence
solely on the basis of structural stability and their rich in GC, but not perfect. If, for instance, every
ability to replicate faithfully. Many different GC se- fifth position in such a sequence is substituted by
quences would serve this purpose equally well and an A or U residue, then base-paired regions, depend-
hence may have become jointly selected as (more or ing on internal complementarity, will involve on the
less degenerate) partners of one quasi-species. Sym- average no more than four GC pairs (cf. present
metric structures are greatly favored here, because tRNA). Those structures can melt 10cal1Jy with ease,
they can fulfil the criteria of stability for the plus especially if the replication process is aided by a
and for the minus strand simultaneously. protein, which then represents the most primitive
Among stable members, perhaps induced by template form of a replicase.
function of anticodon loops and subsequent pattern
Note: A-U imperfections in the aperiodic GC lattice
duplications, comma-free code sequences may have
are selectively advantageous.
occurred and then started translation. If their transla-
tion products add any advantage to the stability or As Thomas Mann * said: 'Life shrinks back from
to the reproduction rates of their messengers, they absolute perfection. '
will evolve further by a Darwinian mechanism and
thereby change continuously the quasi-species distri-
bution. Before we come back to such a stabilization X/V.3. From GNC to RNY
by means of translation products, let us enlarge some-
what more on the question of stability of structure
Given a certain abundance of A (and complementary
versus efficiency of replication, because it seems that U) imperfections in the GC-rich strands of the
both required properties are based on conflicting pre-
requisites. * Th. Mann: Der Zauberberg (The Magic Mountain)

69
selected quasi-species, the next step in the evolution more general R Y frame code. All together this brings
of a code seems to be preprogrammed. Mutations four more amino acids onto the scene. The first substi-
might occur in any of the three codon positions, but tution still occurs under the stability constraint, which
their consequences are quite different. Substitution forces the AU content to be as low as possible. Hence
of the middle base of a codon would enforce a com- it introduces the two codons 5' AGC (= serine) and
plementary substitution of the middle base of the 5' ACC (=threonine). Their complementary se-
corresponding anticodon occurring in the minus quences affect the third codon position, yielding
strand and hence immediately introduce two new co- 5'GCU and 5'GGU, which reproduce the assignments
dons, GAC and GUc. Changes in the first or third for alanine (GCC) and glycine (GGC). The degener-
position, on the other hand, would be complemented acy, accounting for the wobble interactions in the
by changes in the third (or first) position, respectively, reproduction of these latter codons, may have been
of the minus strand and - by wobble arguments - fi- the primary cause of the· appearance of AGC and
nally lead to' only one further assignment. Moreover, ACC co dons and their assignments.
the GC frame for comma-free reading would be If with the evolution of an enzymic machinery more
perturbed. than one AU pair is allowed in the codon region
Stability requirements do not initially allow for a sub- we arrive at two more new assignments, namely,
stitution of more than one AU pair in the five-base- AAg(asparagine) and AUg (isoleucine). This
pair region of the messenger-tRNA complex. Hence completes all possible assignments for an RNY code.
the most likely codons to occur next are 5'GAC and The further evolution of the genetic code requires
5'GUC. Being mutants of the pre-existing pair a relaxation of the constraint of nonoverlapping
5'GGCj5'GCC, they may be abundantly present as frames. Adaptation of ribosomal precursors is there-
members of the selected GC-rich quasi-species. fore now imperative.
However, if these mutants are assigned a function
in translation, they have to become truly equivalent
to the dominant 5'GGCj5'GCC species. It is at this X/V.4. The Primary Alphabet of Amino Acids
stage that hypercyclic stabilization of the four codon
adapters (and the messengers which encode the coup- Quite reliable estimates can be made for the primor-
ling factors) becomes an absolute requirement. With- dial abundance of various amino acids. Structure and
out such a link the different partners of the primary composition already provide the main clues for a
translation system may coexist for some time, but guess about the likelihood of synthesis under primor-
they would never be able to evolve or to optimize dial conditions. In Figure 51 the family tree of the
their cooperation in any coherent fashion. first dozen nonpolar aliphatic amino acids as well
The four codons allow four different amino-acid as- as a few branches demonstrating the kinship relations
signments, which can now offer a rich palette of func- for the simpler polar side chains are shown. Interest-
tions. The resulting proteins therefore could become ing questions concerning Nature's choice of the
efficient coupling factors. Messengers and tRNAs, protein alphabet arise from this diagram.
as members of the same quasi-species, might have The two simplest amino acids, glycine and alanine,
emerged from complementary strands of the same are' natural' representatives. It was apparently easier
RNA species, thus sharing both functions. to fulfil requirements for hydrophobic interaction by
On the other hand, this may be too restrictive a con- adding some of the higher homolog, such as valine,
straint for their further evolution. We then have to leucine, and iso leucine. This specific choice may have
assume that they were derived from a common pre- been subject to chance; perhaps it was biased also
cursor, but later on diverged into different seqences by discriminative interactions with the adapters avail-
owing to their quite different structural and functional able. Among the polar side chains we find some ob-
requirements. vious aliphatic carboxylic acids (aspartic and glutamic
The assignments for GAC and GUC, according to acid) as well as alcohols (serine and threonine), but
the present table of the genetic code, are aspartic not the corresponding amines (a., fJ-diaminopropionic
acid and valine. Before we discuss the amino-acid acid and a.,y-diaminobutyric acid). Only the second
aspect in more detail we may look briefly at some next homolog (lysine) appears among the twenty 'nat-
further steps in the evolution toward a more general ural' amino acids, while the intermediate (ornithine)
code. still shows its traces. The reason may be that upon
High stability of codon-anticodon interaction is re- activation of the second amino group lactame forma-
quired less and less as the translation products be- tion or elimination occurs, which terminates the poly-
come better adapted. Wobble interactions are finally merization. Moreover, the second amino group may
admitted and the GC frame code can evolve to the lead to a branching of the polypeptide chain (although

70
• O"t. .... a similar argument may be raised for the carboxylic

.t
III... OJ ... ~"l '0'"
C"Z i", groups). Positively charged side chains may well have
~ ~"z ~I

....
~J
"JC-C-CIt)
"ZH. bt
....:&00, HIH'~H
C"z
H1 N.t.OI,
~

t_
been dispensible in the first functional polypeptides.
Even in present sea water the concentration of Mg2 +
~
COOl< COON
n..-·I......
t." 1ewclll'lt
is high enough (~50 mM) to cause an appreciable
... I 71•
I
G.l'I. complexation with carboxylic groups. Under reducing
~HI
conditions even more divalent ions (such as Fe 2 +)
-
-
~H2 ~"J

~ - may have been dissolved in the oceans. Those metal


'--- C"z 01,
HIN.eH H,N.C.OII
&nt &nt ions, attached to carboxylic groups and still having
•• 0 .. " 0).,..
fMH· woh n4'
free coordination sites, are especially important for
I
"'I. IS'I. close interactions between early proteins and (nega-
~H:)
tively charged) polynucleotides. From this point of
~"z ~H,
H1 N. ~H I-- M1 N -~-CHl view, side chains containing negatively charged li-
CCOt< COCH
Q- ........ ,... Q -~·I.
gands seem to be less dispensible than those contain-
~t'rlC

I
KI(I ""'1'"
""" ing positive charges.
The' natural' amino acids not appearing in Figure
'""
....t 51 bear considerably more complex sidechains and

--
were therefore present in the primordial soup at com·
paratively low concentrations.
I These guesses from structure and composition are
excellently confirmed by experiments simulating the
..
.....1:0,.
prebiotic synthesis of amino acids, carried out by
S. Miller and others (reviewed in [63]). The yields
- incl. allol$o\eucine
obtained for the natural amino acids (but also for
JI,...
other branches of the family tree) correspond grossly
o to the chemist's expectations (cr. numbers in Fig. 51),
although many interesting items of detailed informa·

-y-a
tion are added by these experiments. The results are,
HO-CH I OJ'4 ~"J -ax:-~H1 furthermore, in good agreement with data obtained
{><; CH, CH,
from meteorite analysis [69, 70] reflecting the occur-
h

.-'
~ ~,
I-- c"J rence of amino acids in interstellar space. Table 16
~
"t'.~
COOH
H,N-~H
CDOH
"zN-CH
~
tOOK
y.~ contains a compilation of data (taken from [63]),
Mf·I.-..cj""
which are relevant for our discussion.
I . There is no doubt that the primordial soup was very
HO-~HI
011
1'1.
~
c"z
ocx'~l
."'''1: 1
rich in glycine and alanine. In Miller's experiments
CHI
tNtZ

--
~ - h ~
"t'+COOt!
HlN ... ~tt
COOH
"2 "-01
aJCtI
Mr"'~
COOII
these amino acids appear to be about twenty times
more frequent than any of the other 'natural' repre-
ftOI'_"IO.11M
sentatives. The next two positions in the abundance
I .J
scale of natural amino acids are held by aspartic acid
DO'" "." " ...
rI.
and valine with a clear gap between these and leucine,
;:g:
" Hl" "'~
~ IO-~
~I
~"J
~HZ
---~
~ ~ glutamic acid, serine, isoleucine, threonine, and pro-
"z"'CH H2 N -~~ y.Cti HIH-~
bJoH COON &10M COOl< line.
~.
Q.- dI'I'IIM-f'I-
!:J;K","= There is every reason to assume that assignments of

-
IIIIIIW'C aeJCf
1. . . . . -
I

_
codons to amino acids actually followed the abun-
OJ... "... .
~ V'" dance scale. If glycine and alanine are by far the
IO-tz f'J ODe· 'jI'z most abundant amino acids, why should they not

--
HI N -~HI

- -
....... ~ "1"-01 "zOI-QI K1 N -~M
~ have been assigned first, as soon as chemical mecha-
....
CDOH
<>,p.-.
.1 .....

I Fig. 51. The family tree of the first aliphatic amino acids and

-
some branches for the simplest polar side chains. The number
~ in the left upper corner of each plate refers to Miller's data of
,
Mr-

-
relative yields under primordial conditions [63] (i.e., molar yield
Inc\. allo\h,eonine ..,... of the particular amino acid divided by the sum of yields of all
amino acids listed in their Table 7-2 on p. 87). The plates for the
b natural amino acids are shaded

71
Table 16. Abundance of natural amino acids in simulated prebiotic results from the protein-sequence analysis of nucleo-
synthesis and in the Murchison meteorite. The first column refers tide-binding enzymes, which are believed to have
to those amino acids which appear in the proteins. The data in existed more than 3· 10 9 years ago under precellular
the second column are typical results from S. Miller's experiments
(as reviewed in [63]). They were obtained by sparking 336 mMol conditions [71, 72]. The data suggest the existence
of methane in the presence of nitrogen and water. The total yield of a precursor sequence of the nucleotide-binding sur-
of amino acids (including those which do not appear in the face, which include the amino acids valine, aspartic
proteins) based on carbon was 1.9%, the corresponding yields (and glutamic) acid, alanine and glycine besides iso-
of glycine and alanine 0.26% and 0.71 %, resp. The yields in the
table refer to molar abundance. Similar data are obtained under
leucine, lysine and threonine (although these data ac-
different conditions, gly, ala, asp, val usually occurring as the tually refer to a later stage of precellular evolution
most abundant natural amino acids. The meterorite data were than is discussed in this paper).
reported by J. Oro et al. [69] and by K.A. Kvenvolden et al. [70],
D-isomers appeared in all cases to be close to 50%. Further litera-
ture can be found in [63]
XV. Hypercyclic Organization
Compound Yield [11M] I1g/g meteorite of the Early Translation Apparatus

Glycine 440 6 Any model for the evolution of an early code and
Alanine 790 3
translation apparatus will have to provide conditions
Aspartic acid 34 2
Valine 19.5 2 that allow tRNA-like adapters as well as gene precur-
Leucine 11.3 sors (or messengers) for various enzymic factors not
Glutamic acid 7.7 3 only to coexist, but also to grow coherently and to
Serine 5.0 evolve to optimal function. In Parts A and B it was
Isoleucine 4.8
Threonine" 1.6
shown that such a self-organization requires cyclically
Proline 1.5 closed reactive links among all individual partners,
unless they all can be integrated structurally into one
" Including allothreonine replicative unit. In this section we have to show how
realistic code models are correlated with an hypercy-
clic organization, and how such systems can evolve.
An apparent difficulty of the hypercycle is how it
nisms of activation became available? The first pri- is to originate. In plain language, the abundant pres-
mordial polypeptides - the instructed as well as the ence of all members of the hypercycle seems to be
noninstructed - must then have been largely gly-ala a prerequisite for its origin. In more scientific terms,
copolymers with only occasional substitutions by the hypercycle, being a higher-order-reaction net-
other amino acids, probably including also those work, has to 'nucleate' by some higher-order mecha-
which finally did not become assigned. nism in order to come into existence.
The agreement between the abundances of natural Consider, for comparison, a simple replicative unit
amino acids and the order of the first four codon that grows according to a first-order autocatalytic
assignments is striking. It should be emphasized that rate law. In a solution buffered with energy-rich build-
our choice of codons is based exclusively on argu- ing material one copy is sufficient to start the multipli-
ments that are related to the structure of nucleic acids. cation process. Those experiments have been carried
Not only do the first four GC frame codons coincide out with phage RNA or its noninfectious variants
exactly with the order of abundance, but furthermore [7, 8, 32, 34, 73]. One template strand is sufficient
the four additional RNY codons are assigned to to produce - within a few minutes - a large popula-
amino acids which - with the exception of aspara- tion of identical copies (cf. Part A).
gine - are well represented with appreciable yields in A hypercycle never could start in this way. A single
Miller's table. One may well ask whether the assign- template copy would not multiply unless a sufficiently
ment of AAg to asparagine is a primary one or-as large number of its specific catalytic correspondents
suggested by the intimate neighborhood to the lysine were present. These in turn are encoded by templates
codon - was originally related to any of the lower which themselves could not have multiplied without
diamino acid homologs, which appear in Miller's table the help of their translation products. The growth
with a reversed order of yields as compared with of all templates in the system is dependent upon cata-
aspartic acid (O(,y-diaminobutyric acid) and glutamic lytic support, but the catalysts cannot grow unless
acid (O(,j3-diaminopropionic acid). Without further ev- the templates multiply. How large is the probability
idence, however, this might be a too far-reaching spec- that nucleation will occur through some accidental
ulation. fluctuation? Let us assume a test tube with 1 ml of
Also of importance in this respect are some recent sample solution. Diffusion-controlled reactions of

72
macromolecules may have rate constants of the order concomitantly and thereby become two adapters for
of magnitude of 10 8 M- 1 s- 1. Hence at least 10 8 complementary codons, or whether the plus strand
identical copies of a given catalytic reaction partner as messenger encodes for the coupling factor, while
have to be present in order to start template multipli- only the minus strand acts as an adapter - to Section
cation with a half-time of about one day. There is XVI. Here we study the problem of how hypercyclic
no chance that correlated functions among several organization can gradually evolve out of a quasi-
such partners could result from coincidences of such species distribution.
giant fluctuations. It may, of course, be possible that Figure 52 shows how such a process can be envisaged.
the various templates multiply according to mixed- Assume two abundant mutants of the quasi-species,
order terms; in other words: that first-order (enzyme- whose plus and minus strands are able to act as adap-
free) autocatalytic terms (representing template multi- ters of (at most) two amino acid pairs (e.g., gly/ala
plication without catalytic help by other members) and asp/val), and which at the same time may be
are superimposed upon the second-order catalytic translated into a protein made up of (at most) four
replication terms. The hypercyclic link would then classes of amino acids. If the translation products
become effective only after concentrations have risen offer any catalytic function in favor of the reproduc-
to a sufficiently high level. However, the system can- tion of their messengers, one would probably encoun-
not know in advance which of the many alternative ter one of the situations represented in Figures 52
sequences multiplying according to a first-order auto- or 53.
catalysis are the ones which provide the useful infor- Both messengers, being closely related mutants, en-
mation for the catalysts required at the later stages code for two proteins with closely related functions.
of organization. If one is a specific replicase, the other will be too,
There is only one solution to this problem: both functions being self- as well as mutually enhanc-
The hypercycle must have a precursor, present in high
natural abundance, from which it originates gradually
by a mechanism of mutation and selection.
Such a precursor, indeed, can be the quasi-species
consisting of a distribution of GC-rich sequences. All
members of a stable quasi-species will grow until they
are present in high concentrations. As was shown
in Section XIV, some GC-rich sequences may be able
to start a translation by assigning amino acids to
defined anticodons. At this stage the translation pro-
ducts are really not yet necessary for conserving the
system, so translation can still be considered a game Fig. 52. Two mutant genes II and 12 , encoding for their own repli-
of trial and error. If, however, it happens that one cases EI and E 2 , may show equivalent couplings for self- [II,
of the translation products offers advantages for the 22] and mutual [21, 12] enhancement due to their close kinship
reproduction of its own messenger, this messenger relation. Analogous behavior can be found in present RNA-phage
replicases
may become the dominant representative of the quasi-
species distribution.
A single RNA species could at best assign a two-
amino-acid alphabet, if both the plus and the minus
strands act as adapters for two complementary co-
dons (e.g., GGC and GCC). If adapter sequences
are sufficiently abundant, there is also a finite chance
that coexisting mutants assign the two or even four
codons (including GAC and GUC for aspartic acid
and valine), again possibly utilizing both plus and
minus strands. All this may still happen during the
quasi-species phase. a b c d
Such a system, however, can evolve only if the differ- Fig. 53. The evolution principle of hypercyc/es is illustrated by the
ent RNA species stabilize each other with the help four possible situations arising from the couplings between two
mutants shown in Figure 52. The thick lines indicate a preference
of their translation products. We defer a discussion in coupling (however small it may be). A stable two-membered
of the details of assignments - e.g., as to whether plus hypercycle requires a preference for mutual enhancements as
and minus strands of a given RNA species can evolve depicted in d)

73
Table 17. Fixed-point analysis of the two-member hypercycle a
represented in Figure 52 has been carried out using the simplified
rate equations

x(= L klkXtXk-2 I I k1mxtx m


k=1,2 C /"",1,2 m _ l,2

i=I,2; XI +X 2 =C

yielding the three fixed points and their eigenvalues:

X2 =(0, c); co(2)=(k I2 -k22)C

c
x3=(k22-kI2,kll-k21)k -k +k -k ;
11 21 22 12

(3) (k ll -k21)(k22 -k12)


co C.
kll-k21 +k22-kI2 If in addition to the second-order term of the rate equations a
linear autocatalytic term is introduced (yielding a growth function
Four cases may be distinguished
of the form I;=k,x,+ I k'jx,x), the region of stable hypercyclic
a) k l1 >k 21 ; k22>k12 yielding competition between II and 12 j _ 1,2
b) k ll >k 21 ; k22<k12 yielding selection of II coexistence of both species I I and 12 is the space above the folded
c) kll <k 21 ; k22>k12 yielding selection of 12 sheet in the three-dimensional parameter space with the coor-
d) kll < k 21 ; k22 < k12 yielding hypercyclic stabilization of II dinates:
and 12
a = k'l+ kl, - k,, - ku
The fixed-point diagrams of these four cases are (cf. Part B) (J - k 12 - kl' +k" - kll
2
y= - (k, - kl)
c a
1 2 3
a e--------o----4
( C.O) (O.C)

3

1 2
(>0-,-

.
b
(C.O) (O.C)

3 2
c --~
(C.O) (O.C)

3 2
d 0
(C.O)
• -0
( O.C)

y
A unified representation can be achieved if the two coordinates: rt
=k 12 +k21 -kll -k22 and fJ=k12 -k21 +kll -k22 are introduced.

ing. There may, however, be specificity, too, because (1) El favors II over 12, and E2 favors 12 over II
both proteins do not necessarily recognize both se- (Fig. 53a).
quences equally well, nor do they recognize unrelated Consequence: II and 12 both are hypercyclically en-
sequences at all. The sequences provide a specific forced by their respective enzymes, leading to strong
binding site for initiating replication. The differences competition. Only one of the competitors can survive,
in binding strength for the four possible interactions even if they are selectively equivalent.
of El and E2 with II and 12 may be slight. These (2) El favors II over 12, and E2 also favors II over
differences, indicated by the line strengths, however 12 (Fig. 53b).
small they are, will have drastic consequences, as fol- Consequence: II will win the competition and 12 will
lows from an inspection of the corresponding fixed- die out.
point diagrams (Table 17). We may distinguish four (3) E2 favors 12 over 110 and so does El (Fig. 53c).
cases: Consequence: 12 is now the winner, while II dies out.

74
(4) El favors 12 over Ij, and E2 favors 11 over 12
(Fig. 53 d).
Consequence: Here we obtain a mutual, hypercyclic
stabilization of 11 and 12 ,
It is important to note that small differences suffice
to produce the behavior outlined above. In this re-
Ei---
spect it is of interest to see what happens if both
El and E2 are exactly equivalent in their treatment
of 11 and 12 , Here we have complete impartiality,
regardless of how much the population numbers Xi
or Yi differ. 11 or 12 can die out in consequence of
a fluctuation catastrophe, since there is no mutual a
stabilization present as in case 4. On the other hand,
the fluctuations do not amplify themselves, and if E,
the population numbers are large enough, a fluctua-
tion catastrophe will practically never occur. Quite
different in this respect is case (I), mentioned above.
Only for exactly equal population numbers of Ij, 12 ,
Ej, and E z is here the system in a dynamically bal-
anced state. A small fluctuation may disturb the bal-
ance and then, through self-amplification, inevitably
will lead to selection of one of the two species. The
same is true for any ensemble in which each messenger
provides help for its own replicase only (cf. Fig. 47).
The coupling resulting from a common translation b
function - all replicases (utilizing their RNA-recogni-
Fig. 54. The generalization of the evolution principle of hypercycles
tion sites) may function simultaneously as activating
is illustrated in this diagram. The couplings have to fulfil the criteria
enzymes-is not sufficient to enforce a coexistence. derived in Tables 17 and 18, i.e., mutual enhancement has to
As in the system shown in Figure 45, there will be prevail over self-enhancement (cf. thick lines). (a) A mutant of
only one survivor, and translation function will subse- 12 appears (12)' (b) The mutant (now 13 ) is incorporated in the
quently break down. hypercycle
The exact criteria for hypercycle formation are deri-
ved in Table 17. The figures give a clear representation
of the stability ranges in terms of generalized coordi-
nates referring to the rate parameters.
We have thus obtained an evolution principle for
hypercyc1es. This kind of organization can emerge
from a single quasi-species distribution, as soon as
means of reaction coupling develop. The prerequisites
for coexistence of precursors can be met generally
only by closely related mutants. Thus the emergence
of hypercyc1es requires the pre-existence of a molecu-
lar Darwinian system, but it will then lead to quite
new consequences. The evolution principle is effective
even with very small differences in rate parameters Fig. 55. The' realistic' four-membered hypercycle assigns four mes-
and hence responds sensitively to small changes sengers I I to I, (being mutants of a common precursor) to encode
brought about by mutations. Given a quasi-species for four replicases EI to E, with common function, but slight
preferences in specificity. The minus strands of II to I, may con-
distribution with developing interactions among the comitantly act as amino acid adapters
constituents, regardless, of how weak these interac-
tions are, a hypercyc1ic organization will inevitably
emerge whenever such interactions arise.
The hypercycle will also grow inevitably by way of tant I' then may either replace I, die out, or enlarge
mutations toward larger complexity (Fig. 54, 55). The the hypercycle to a size comprising n + I members
evolution principle can be generalized by induction (cf. XVI. 10.). More general evolution criteria can
so as to apply to any n-membered hypercycle. A mu- be derived as indicated in Table 18.

75
Table 18. Generalization of the evolution principle of hypercycles a) kD>k+, k_
b) k+ >k_ >ko
is explained by (he transition of a two-membered to a three- c) k_ >k+ >ko
membered system as depicted in Figure 54. d) k+ =k_ >ko
The general rate equations are of the same form as in Table 17. yielding the following fixed-point diagrams:
Starting from a stable two-membered hypercyc1e, introduction of a
third member 13 (e.g., being a mutant of 12 ) will frequently change
the previously stable fixed point to a saddle point. This is most Q C
clearly seen if cyclic symmetry is assumed. Under these conditions,
the notation can be simplified to:

yielding the following matrix of rate coefficients.


5
ko k k+
2O-~~---------O3
K= k+ ko k
k k+ ko

The fixed points and eigenvalues then are:

Corners: XI =(c,O,O); W\I)= (L -ko)c, w~')=(k+ -ko)c


X2 , X3 analogous
6
c O---_-E!)--___-C! 3
Edges: x4 =(0,kD-k_,kD-k+)2k -k -k o-------__~~.u3
D + - 4

wW
k_(kD'-k_)+k+(ko -k+)+k k_ -kf,
T
c
b d
I 2ko-k+ -k_ Large diagonal terms (k o }> k+, k_) lead to competition (diagram a).
(ko-k+)(ko-k J c In the opposite situation, i.e., with large off-diagonal elements of K,
wi4 ) 2ko-k+ -k_ the three species show cooperative behavior. The sense of rotation
around the spiral sink in the center of the simplex is determined by
x" X6 analogous the larger of the two constants k+ and k_. No rotational com-
ponent is observed for equal constants k + = k _. The central fixed
Interior: x7 = (3' Y3 '
c c C) point is then a focus.
The example treated in this table provides a good illustration of
the evolution to more complex hypercycles. In the absence of
W(7)
1,2 - V.J + -k .- )}~.
={2k D -k + -k - +i'l3(k 6 simplifying assumptions concerning the rate constants the analysis
becomes quite involved. We refer to a more detailed representation
Again four cases are of special interest: [98J, which includes a generalization to arbitrary dimensions.

XVI. Ten Questions to Darwinian behavior, with selection of one defined


quasi-species. The selected products are determined
concerning our earliest molecular ancestors and the plainly by an optimal selective efficiency, but their
traces which they have left in the biosynthetic appa- structure depends on their historical route, which is
ratus of present cells. strongly biased by self-copying of smaller oligonu-
cleodtide patterns.

xv!.]. One RNA precursor?


XVI. 2. What Does Selective Advantage Mean
This question is concerned with the complexity of to a Molecule?
the first molecules starting any reproducible function.
A nucleotide chain of 100 residues corresponds to Selective value is defined as an optimal combination
a complexity of about 10 60 alternative sequences. If of structural stability and efficiency of faithful replica-
on grounds of stability we restrict ourselves to (A U- tion. It can be expressed in quantitative terms related
doped) GC copolymers only, we are still left with to the physical properties of a molecule in a given
about 10 30 possible arrangements. In order to achieve environment. Structural stability, resistance toward
one or a few defined sequences, faithful self-reproduc- hydrolysis, and the development of cooperative prop-
tion is a necessary prerequisite. It will inevitably lead erties call for elongation. Small oligonucleotides can-

76
not fold in any stable manner and may therefore mutant combinations in one strand is very low. Se-
easily be hydrolyzed. Furthermore, they do not offer quences consisting of 100 G and C residues have
sufficient adhesive strength for faithful copying or
100 one-error mutants,
for translation. Length, on the other hand, is limited
4950 two-error mutants
by replication rates and by copying fidelity. The prop-
161700 three-error mutants, etc., or
erties of GC-rich sequences have been shown to be
advantageous for forming stable copies with extended Nk = e~O) k-error mutants
length. Whether these lengths resemble the sizes of
present-day tRNA is uncertain. Sequence homologies The number of strands containing n mutant genes,
have been found in tRNA [74], which indicate some each differing from the other in k specified positions
self-copying of internal regions. This, however, may (which may be necessary in order to qualify for a
well have happened before codons became assigned. function) amounts to
The onset of translation requires strong interactions
between adapters and messengers, and these cannot ( Nk+n-l) ~ N: (for n~Nk)'
be provided by molecules which are too small.
n n!
As soon as translation yields reproducible functions, e.g., for n=4 and k=3 to 3 x \019 alternative se-
selective value achieves a new dimension. It must, quences. Given even these small deviations in the
nevertheless, be expressed, for any given messenger, multiplied genes, the chance of finding a copy with
in terms of structural stability and efficiency of faith- a favorable combination within one giant strand is al-
ful reproduction. These properties now, however, also most nil for any reasonably sized population. Each of
depend on the qualities (and concentrations) of the the isolatedmutan t genes containing three substitutions,
translation products. Specific coupling - as required however, would be abundantly present in any macro-
for hypercyclic organization - is hence necessary for scopic population.
any system in which translation products are to be Last but not least, the tRNAs being the adapters
rated for selection and thereby become eligible for for translation must have been present anyway as
evolution. Such coupling is of a catalytic or protective separate strands. Evolution of a unified genome
nature. would have required complicated transcription con-
trol right at the start.
The isolated RNA strands, on the other hand, have
a natural origin in the quasi-species distribution. All
XV!.3. Why Hypercyclic Organization sequences were similar and so must have been their
of Single Mutant Genes Rather translation products. Whenever one translation pro-
than One Steadily Growing Genome? duct provides coupling functions, all of them will
do so, owing to their similarities. Cyclic coupling - as
The answer to this question has been largely given required for hypercyC\ic organization - may then oc-
in Part A. For a very primitive translation apparatus cur as well. We might even say that hypercyclic organ-
an amount of information would be required that ization is most naturally associated with any realistic
corresponds to (or even exceeds) that of present RNA primitive translation model.
phages. The information of the phage genome can Does the present genome organization, established
be preserved only with the help of a phage-specific in prokaryotic cells, offer any clue as to its early
enzyme complex, the availability of which is based structure? Present genes are certainly much larger
on the efficiency of a complete translation machinery, than the early messengers. Gene elongation, as well
provided by the host cell. If we accept the answers as duplication, provided an advantage whenever the
given to the first and second questions, the informa- steadily increasing fidelity of the enzymic machinery
tion needed to start translation must arise from coo- allowed for it. The translation products could gain
peration among several mutants coexisting in the in sophistication, and more complex multienzyme me-
quasi-species distribution, rather than from a mere chanism could evolve, utilizing differentiated enzymes
elongation of one sequence for which primarily no which had descended from a common precursor. Re-
selection pressure would exist. combinant mechanisms as utilized by present-day
The hypercyC\ic stabilization of several coexisting mu- cells will not have been available in primitive systems.
tants is equivalent to evolution by gene duplication. The present structure of the prokaryotic genome
Originally, mutants appeared as single strands rather therefore may have been achieved through elongation
than as covalently linked duplicates. Fidelity restric- of isolated genes, their duplication and triplication
tions would not allow for such an extension of length. to operons and their final mapping onto DNA, which
Moreover, the probability of obtaining the required can utilize more advanced means of reproduction so

77
as to allow for the formation of a unified genome. structures. Are we able to infer a common ancestor
The present operon sizes correspond well to those from these analogies? According to an analysis
which can be handled by a sophisticated RNA repli- carried out by T.H. Jukes [76], this question may
case (e.g., 1000 to 10000 nucleotides). be answered with a cautious 'yes'. Why one
must be cautious may be illustrated with an example.
One of the common features exhibited by all proka-
XV/.4. Are tRNAs Necessary to Start With? ryotic and eukaryotic tRNAs studied so far is the
sequence TlJ'CG in the so-called T-loop, a common
This question may be alternatively posed as: Why recognition site for ribosomal control. Recent studies
not small oligonucleotide adapters? of methanogenic bacteria [77] revealed that these mi-
Adapters without messengers do not make much croorganisms, which are thought to be the' most an-
sense. Short nucleotide sequences do not qualify as cient divergences yet encountered in the bacterial
messengers. Decapeptides are already equivalent to line " lack this common feature of tRNA, but rather
almost half a tRNA molecule. Furthermore, short contain a sequence lJ'lJ'CG in one and U lJ'CG in
oligonucleotides may be unstable since they lack any another group. Although this finding does not call
tertiary structure. The simplest symmetric structure, in question but rather underlines the close evolution-
i.e., a single loop stabilized by four or five base pairs, ary relations of this class of microorganisms with
requires as many as fifteen nucleotides. Enzyme-free other prokaryotes, it shows definitely that whole
specific recognition of an amino acid involving simul- classes may concordantly adopt commont features.
taneously the anticodon loop and the 3' -end of the This is especially true for those molecules that are
adapter is possible only with more extended struc- produced by a common machinery, such as the ribo-
tures. The same is true for interactions between two some, which is the site of synthesis of all protein
adjacent adapters, necessary for the stabilization of molecules.
the messenger-peptidyl-tRNA complex, or for the Figure 56 shows an alignment of the sequences of
conformational change (e.g., from HF to fh) which four tRNAs from E. coli, which we think are the
may facilitate the transport of the growing peptide present representatives of early codon adpaters. Un-
chain along the messenger. G. Maass et al. [99] re- fortunately, the sequence of the alanine-specific
cently reported such a conformational change in the tRNA adapted to the codon GCC was not available.
anticodon loop of tRNA, which they recorded by If we compare this species, which has the anticodon
observing a fluorescence change of the Y base. The SAUGC, with its correspondent for valine, which has
effect appeared to be absent in the anticodon-loop the anticodon SAUAC, we observe a better agreement
fragment (i.e., a decanucleotide having the sequence
of the anticodon loop). All of this suggests that insuf-
ficiently long RNA sequences do not qualify for adap-
ter function.
We may then ask: What distinguishes an adapter
from a messenger? They both require comparable
minimum lengths. They both have to be specifically
folded structures, through which they may become UC G G
..
Oq GCGA GIQ ~GA GU UCGUUUCCCG p U C
..
reproducibly recognizable by coupling factors. A GG,AO"bUC UGCO GTQCGA UC CGCGCOCUCC C A CC
AGGGGbuC GCGG GTQCGA OU C C 0 occou L'c d GCCA
Since each tRNA and each messenger require a coup- UO OG"buC OOUO GTQCGA GU C A CUCGG A CG C CA
ling factor, e.g., a replicase, favoring their selective
stabilization, dual functions of the RNA sequences Fig. 56. Alignment of the sequences of tRNAs for the amino acids
gly, ala, asp, and val. Unfortunately, the sequence referring to
are indispensable. Plus and minus strands of a given the codon GCC (for ala) is not yet available. Correspondences
RNA sequence may thus be utilized jointly as messen- between gly- and ala-tRNAs are supposed to be closer for the
ger and adapter. correct sequence referring to the anticodon GCC (as suggested
by the similarities between the two sequences for ala and val,
referring to the anticodons ·UGC and *UAC, resp.). The sequences
show that base-paired regions consist predominantly of GC, and
XV/.5. Do Present-day tRNAs Provide Clues that close correspondences indicate the kinship between gly/ala
about their Origin? and asp/val (cf. S in position 8 for asp and val instead of U
for gly and ala, or the insertion of D between position 20 and
Similarities in structure might either be the conse- 21 for asp and val). A = adenosine, *A=2MA= N(2)-methyladeno-
sine, C = cytidine, D = 5,6-dihydrouridine, G = guanosine, *G =
quence of adaptation to a common goal or, alterna- 7MG = N(7)-methylguanosine, Q = 'f' = pseudouridine, S ='thiouri-
tively, indicate a common ancestor. Present tRNAs dine, T = ribosylthymine, U = uridine, *U = 5A U = 5-oxyacetyluri-
show many points of correspondence [75] in their dine

78
with the latter than with the one listed in the align- GGC (gly), GCC (ala), GAC (asp), and GUC (val)
ment (57 vis-a-vis 54 identical positions). Hence the derived from one quasi-species as single error mutants
correct alanine-tRNA with the anticodon GGC may of a common ancestor. However, the original sym-
have more coincidences with the gly-tRNA listed than metry was not sufficient (why should it have been?) to
for the 44 positions shown. Apart from this 'corporal allow adapter functions to derive from both the plus
defect' the data reveal and the minus strand of a given RNA.
1. That all representatives agree in more than half
of the positions (33 including the 'wrong' ala or 41
for gly, asp, and val), XVJ.6. How Could Comma-free Messenger Patterns
2. That the subgroup gly /ala is distinguished from Arise?
the subgroup asp/val by several features (thio-uridine
's' instead of U in position 8, insertion of a 5,6- The first messengers must have been identical with
dihydro-U between position 20 and 21), the first adapters (or their complementary strands).
3. That all representatives have a pronounced excess There is, indeed, a structural congruence behind adap-
of G and C over the A and U residues (or their ter and messenger function. Whatever codon pattern
derivatives), especially in the base-paired regions. occurs in the messenger sequence, it must have its
A comparison with other tRNA sequences, further- complementary representation at the adapter. In
more, indicates that these features - although cer- primitive systems such a requirement could be most
tainly not uncommon among most tRNAs - are espe- easily met by utilization of a common structural pat-
cially pronounced for this group. In particular, corre- tern for both types of molecules, such that the first
spondences are as close as for different adapters of adapters are the minus strands of the first messengers
the same amino acid in the same organism. (if we define the plus strand as always being associated
One finding is particularly illuminating. If we com- with a message) and that certain symmetries of struc-
pare the sequences of two adapters with complemen- ture allow both the plus and the minus strand to
tary anticodons (e.g., asp and val) the coincidences be recognized by the same replicase.
between both plus strands of the tRNAs are much The first extended RNA molecules were rich in G
more pronounced than those between one plus strand and C, a consequence of selection based on criteria
(read from 3' to 5') and the other minus strand (read of structural stability and fidelity of copying. Mole-
from 5' to 3'). Actually, if we compare in this way cules with a common codon pattern, such as GGCj
the plus and minus strands of the same tRNA, the GCC, require primer instruction (e.g., via catalysts
agreement is better. These coincidences are only the or via exposed loops of RNAs present) with subse-
expression of the remarkable internal symmetry of quent internal duplication. This will inevitably lead
tRNA, which places the anticodon almost exactly in to structures that contain at least two codon patterns
the middle of the sequence and thereby allows for with internal complementarity, e.g., 5'GGC3' and
the formation of a symmetric two-dimensional pat- 3'CCG5'.
tern. We may rate this property as an indication of There is a good example for the efficiency of internal
the early appearance of tRNA as an independent rep- pattern duplication in the de-novo synthesis and am-
licative unit. The requirement for the plus and minus plification of RNA sequences by phage replicases.
strands to assume a similar pattern is important only If QP replicase is severely deprived from any template,
if these represent independent replicative units rather it starts to 'knit' its own primers, which it then dupli-
than being structurally integrated into a large se- cates and amplifies (selectively) until finally a uniform
quence of a genome, as they appear to be nowadays. macroscopic population of RNA sequences-a few
We find a similar effect for phage RNAs or their hundred nucleotides in length - appears. Under dif-
variants, which have to multiply as single replicative ferent environmental conditions, different (but uni-
units [78]. form) sequence distributions are obtained [8]. S.
On the other hand, adaptation of tRNA to a common Spiegelman, D. Mills and their co-workers have se-
machinery must have brought about common devia- quenced some of these 'midivariants,' all of which
tions from symmetries originally required. The fact contain the specific recognition site for QP replicase
that the mirror images for plus and minus strands [78]. Further experiments [73] have thrown light on
of the same tRNA show still more symmetric resem- the mechanism of this de-novo synthesis, showing
blance than those for plus and minus strands of that small pieces corresponding to sequences that are
tRNAs with complementary anticodons suggests that recognized by the enzyme are made as primers and
both tRNAs evolved as mutants of the same rather then internally duplicated and selectively amplified.
than of two complementary strands. We may then Earlier studies [22] have shown that, in particular,
conclude that the present adapters for the co dons the sequences CCCCc) and UUCG can be recognized

79
e -c - N o- H 0- 0 0 - Rlstde chain)

Fig. 58. A simple enzyme precursor is represented by a {3-folded


structure of some 15 to 25 amino acids (requiring messengers of
45 t9 75 nuc1eotides). The active site includes a terminal amino
cc group that is a very efficient proton donor (pK - 8), a terminal
cc carboxylic group that acts as proton acceptor, and a catalytically
active side chain (e.g. , asp or serlo Many alternatives could be
Fig. 57. Alignment of the sequence of Q{3-midivariant (determined designed, only some of which have the correct pitch of the twisted
by S. Spiegelman et al. [78]) with an artificial sequence composed chains to yield an efficient active site
of CCC(C)- and UUCG-blocks, as well as their complements
[GGG(G) and CGAA]. Agreement at 169 of 218 positions suggests
that midivariant is a de-novo product made by the enzyme Q{3-
replicase, which possesses recognition sites for CCC(C) and UUCG
(EF Tu). The kinetics of de-novo synthesis indicates a tetramer should be answered with experiments. With mixed
formation at the enzymic recognition sites, followed by some inter- sequences, including a sufficiently large number of
nal self-copying with occasional substitutions. The specific midiva-
riant usually wins the competition among all appearing sequences
residues, say about fifteen to thirty, f3-sheet structures
and hence seems to be the most efficient template. The process may form with an active center, in which the terminal
demonstrates how uniform patterns can arise in primitive copying carboxylic group is placed in a defined position near
mechanisms the terminal amino group (Fig. 58). The proximal dis-
tance varies with the chain length, since the f3-struc-
ture involves a twist among both anti parallel chains
[79]. The pK of the terminal amino group is around
by the enzyme. UUCG corresponds to the sequence
eight, hence the catalytic site contains at least an
T'PCG common to all tRNAs and known to interact
efficient proton donor-acceptor system. Alternating
specifically with the ribosomal elongation factor
gly-ala residues are very favorable for the formation
EF Tu, which acts as a subunit in the Qf3-replicase
of f3-structures. However, there are serious solubility
complex. An alignment of the midi variant with a se-
problems for chains consisting exclusively of gly and
quence made up solely of the two oligonucleotides
ala, which would restrict them to interfaces only.
mentioned and their complementary segments-
The folding of f3-sheets has been studied by P.Y. Chou
GGG(G) and CGAA-shows agreement in more
and G.D. Fasman [80], who analyzed X-ray data for
than three-quarters of the positions, indicating the
29 proteins in order to elucidate 459 f3-turns in regions
efficiency of internal copying of primer sequences
of chain reversal. The three residues with the highest
(Fig. 57).
f3-turn potential in all four positions of the bend in-
In a similar way we may think of the existence of
clude gly and asp, while in regions following the p-
primordial mechanisms of uniform pattern produc-
turn, hydrophobic residues are predominant.
tion. If among the many possible patterns S'GGCf
An important prerequisite of catalytic efficiency is
5'GCC and possibly also 5'GACj5'GUC appeared,
the defined spatial arrangement of the terminal
those messenger patterns could have started a repro-
ducible translation according to the mechanism of groups. The utilization of two or more classes of
Crick et al. [3] and have · been capable of selective amino acids may be necessary for stabilizing a repro-
amplification with the help of their reproducible ducible folding . f3-Sheets have long been known to
translation products. be important building elements of protein structure.
According to M. Levitt [81], they may be utilized
in a very general manner to stabilize active conforma-
tions of proteins.
XV!. 7. What Did the First Functionally Active The large· abundance of glycine and alanine might
Proteins Look Like? have determined in essence the appearance of the
first proteins, but polar side chains are indispensible
The simplest protein could be a homogeneous poly- for the solubility of longer sequences. Four amino
peptide, e.g., polyglycine. Does it offer any possible acid classes would of course offer much more flexibil-
catalytic activity? This is a question that can and ity. If aspartic acid and valine were the next two

80
candidates, globular structures might have formed, hand, the conformational transition is still required
stabilized by hydrophobic interactions of the side since the mechanism of peptide-bond formation (cf.
chains of valine and alanine and solubilized by the Fig. 48) calls for a well-defined separation of the mes-
carboxylic side chains of aspartic acid. This residue senger and the growing peptide chain. The data
further offers many possibilities for forming specific quoted invite reflection about such possibilities. If,
catalytic sites with the participation of divalent metal on the other hand, a structure similar to the pattern
ions. c) shown in Figure 49 is likely to arise, the first amino-
Our imagination is taxed to estimate the vast number. acid assignments might even have been made without
of possibilities. Experiments that are supposed to test enzymic help. The tRNA structure as such certainly
various structures with respect to their efficiency in offers sufficient subtlety for specific recognition. It
discriminating between RNA sequences and their has been noted [85] that the fourth base from the
structural features are under way. Results obtained 3' -end (i.e., the one following 3' ACC) is somehow
with ribonucleases [82] encourage one to seek a 'mini- related to the ant·icodon. The primary expectations
mum structure', able to recognize RNA sequences regarding a unique correlation for all tRNAs finally
specifically. did not materialize. However, such a correlation may
have played a key role in the early specific recognition
of amino acids by tRNAs. Referring to data from
XV/.8. Are Synthetases Necessary to Start With? E. coli and T 4 phage, the nucleotides in the position
following 3' ACC are: U for gly, A for ala, G for
In the three-dimensional structure of present-day asp, and A for val. It was certainly important for
tRNAs (cf. Part A, Fig. 14) the anticodon loop is early adapters to ensure unique assignment by suffi-
fixed at a considerable distance from the amino acyl ciently discriminative sites. This property might have
site. Such a structure is adapted to the functional been partially lost during later phases of evolution.
needs of present tRNA molecules, imposed by the This is admittedly a speculation and calls for experi-
ribosomal mechanism and by the structure of synthe- mental confirmation.
tases. On the other hand, it is known that tRNA To conclude: Synthetases may have been dispensible
can undergo conformational changes that drastically at the very early stages, but tRNAs finally turned
alter its shape and dimensions. R. Rigler and his co- out to be an unsatisfactory attempt by Nature to
workers [83] studied conformational lifetimes as well make enzymes from nucleic acids. More efficient re-
as rotational relaxation times by fluorescence cognition may have evolved from the coupling factors,
methods and concluded the existence of at least three which were predestined to recognize tRNA-like struc-
different rapidly interconverting conformational tures specifically.
states. Analogous results were obtained by T. Olson
et al. [84], who used laser light-scattering techniques.
The population of the different conformational states
depends strongly on magnesium-ion concentration. XVJ.9. Which Were the First Enzymes?
It is important, again, to note that under conditions
that correspond to those present in sea water (Mg2 + ; If synthetases are not really necessary for a start of
'" 50 mM), a conformer is present that differs in shape translation (and this is a big' if!'), we are left with
from the L-form found by crystallographic studies, the coupling factors, probably replicases, as the only
being considerably more cylindric. absolute primary requirements for a coherent evolu-
This point is stressed because it is most relevant to tion of translation. Via such a function, a selective
the question raised. Early enzymes were made of only advantage occurring in a translation product can be
a very limited number of amino acid residues and most efficiently fed back onto the messenger. Hence
therefore cannot have been very bulky globular struc- specific replicases (all belonging to one class of similar
tures. In order to guarantee a unique assignment of protein molecules) not only provide the prerequisites
an amino acid to an anticodon, either enzymes as for hypercyclic coupling, but also turn out to be most
sophisticated as present-day aminoacyl synthetases important for the further evolution of proteins, since
had to be available, or else the tRNA structure had only they can tell the messenger what is phenotypi-
to allow a much closer contact between the aminoacyl cally advantageous and how to select for it at the
and anticodon sites than the L-form does, in order genotypic level, i.e., by enhanced synthesis of the par-
to admit a simultaneous checking of both sites. The ticular messenger. As will be seen in the next para-
high mutation rate at early stages would otherwise graph, such a selective coupling between geno- and
very soon have destroyed any unique coincidental phenotypic levels works best in combination with spa-
correspondence between these two sites. On the other tial separation or compartmentation.

81
Next, of course, we have to look for catalytic support XVI.JO. Why Finally Cells with Unified Genomes?
for the various translation functions. If replicases
have established a defined relationship with tRNA- Hypercycles offer advantages for enlarging the infor-
like messengers (including both the plus and the minus mation content by functional integration of a messen-
strands), their recognition properties may well be util- ger system, in which the single replicative unit is lim-
ized for synthetase and translatase (i.e., preribosomal) ited in length due to a finite fidelity of copying. The
functions. In other words, a gene duplicate of a repli- increase in information content allows the build-up
case may well be the precursor of a synthetase messen- of a reproducible replication and translation appa-
ger as well as of a translation factor such as EF Tu, ratus, by which the translation products can evolve
the more so since the chemistry of replicase and trans- to higher efficiency. This will allow better fidelities,
fer function is very similar and in present systems which in turn will increase the information content
appears to be effected by similar residues. of each single replicative unit and thereby, again, en-
Dual functions with gradual divergence may have hance the quality of the enzymes. Simultaneously,
been a very early requisite of replication and transla- as shown in Section XV, the hypercycle itself will
tion mechanisms, just as gene duplication was one evolve to higher complexity by integrating more dif-
of the main vehicles of evolution at later stages. ferentiated mutant genes.
Increase of information content will not only produce
Those dual functions have clearly left their traces
better enzymes; it may also allow each replicative
in present cell organelles, and viruses have utilized unit to inherit information for more than one enzyme.
them as well for their post biotic evolution in the host
Dual functions can thereby be removed from the list
cell. The genome of the phage Q/3 encodes for only of earlier evolutionary constraints, i.e., duplicated
one subunit of its replicase, but utilizes three more
messengers may develop independently, according to
factors of the host cell, which have been identified the particular functional needs of their translation
as the ribosomal protein Sl and the elongation factors
products. This may have been the origin of operon
EF Tu and EF Ts [87, 88].
structures with control mechanisms for simultaneous
Ch. Biebricher [89] has studied the properties of these replication of several structural genes. Replicases may
factors and found that they are involved simul- thus have evolved to common polymerases associated
taneously in several functions of ribosomal control, with specific control factors for induction or re-
utilizing their acquired property, namely, to recognize pression.
tRNA molecules. He argues that also the /3-factor After having realized the advantages of functional
of Q/3 replicase, which is encoded by the phage ge- coupling, which seems to be a requirement for any
nome, has its precursor in the E. coli cell, and this start of translation, we should ask why functional
seems, indeed, to be the case. Using immunologic coupling has finally been replaced by complete struc-
techniques, he was able to identify a protein contain- tural integration of all genes, the genomes of even
ing EF Tu and EF Ts that behaves like a precursor the most primitive known cells being structural units.
of the Q/3 replicase in uinfected E. coli and that ap- So where are the limitations of hypercyclic organiza-
pears to be involved in an -as yet unspecified- RNA- tion and what improv.ements can be made in it?
synthesis function of E. coli [87]. Further, similar cor- In a system controlled by functional links we have
respondences may yet be found with synthetases. It to distinguish two kinds of mutations. One class will
seems that once a certain function has been devel- primarily change the phenotypic properties of the
oped - such as the ability to recognize certain types messenger itself and thereby alter its target function
of RNA-then Nature utilizes this function wherever with respect to a specific replicase or control factor.
else it is needed (e.g., specific replication, ribosomal These mutations are especially important in the early
transport and control, amino acid activation). phases of evolution owing to the important role of
In some respects the formation of RNA phages may phenotypic properties of RNA structures. Those target
well have mimicked the evolution of early RNA mes- mutations will immediately become selectively effec-
sengers. Phages utilize as many host cell functions tive, advantageous mutations will be fixed, and disad-
as possible except one, namely, specific recognition vantageous ones will be dismissed.
of their own genome (i.e., coupling via specific repli- The second kind of mutation - which mayor may
cation). Different phages (e.g., Q/3, Ms2, R17) inherit not be neutral with respect to the target function-
different recognition factors [9], although they all de- refers to phenotypic changes in the translation pro-
rive from a common ancestor in the host cell. In ducts. The more precisely specified the messengers
Part A it was also shown that the primary phase are, the more specifically a mutation may alter the
of RNA-phage infection is equvalent to a simple hy- function of the translation product.
percyclic amplification process. Whether or not a mutant is specifically favored by

82
selection depends only on the target function, regard- be superior to the more conservative form of hyper-
less of whether the translation product is altered in cyclic organization.
a favorable or an unfavorable sense or whether it re- On the other hand, the subsequent evolution of mul-
mains neutral. For the later stages of precellular evo- ticellular [90] organisms may again have utilized anal-
lution the most common consequence of a mutation ogous or alternative forms of hypercyclic organization
will be a phenotypic change in the translation product (nonlinear networks) applied to cells as the new subu-
coupled with an unaffected target function. The mu- nits, and thereby have resembled in some respect the
tant may then proliferate further, but it is not specif- process of molecular self-organization.
ically selected against its former wild type, nor would
the system select against the mutant, if its translation
product proves to be unfavorable. What should really XVII. Realistic Boundary Conditions
be achieved is a rating of the system as a whole.
This may be accomplished by spatial separation of A discussion of the 'realistic hypercycle' would be
the messenger systems, by niches or - even more effi- incomplete without a digression on realistic boundary
ciently - by compartmentation. A messenger in a conditions. We shall be brief, not because we disre-
given compartment can enrich its environment with gard their importance in the historical process of evo-
its own translation products and compete with other lution - the occurrence of life on our planet is after
compartments using its efficiency of proliferation. To all a historical event - but because we are aware of
a limited extent this is also possible simply by spatial how little we really can say. While the early stages
separation. However, a compartment without hyper- of life, owing to evolutionary coherence, have left
cyclic organization does not work at all. The en- at least some traces in present organisms, there are
hanced competition among all messengers in the lim- no corresponding remnants of the early environment.
ited living space of the compartment would destroy In our discussion so far we have done perhaps some
any cooperative function. injustice to experiments simulating primordial, tem-
A compartment could proliferate more efficiently by plate-free protein synthesis, which were carried out
correlating its own reproduction with the re-duplica- by S.W. Fox r91] and others (cf. the review by K.
tion of its total gene content. This, of course, requires Dose and H. Rauchfuss [92]). It was the goal of our
a fairly involved control mechanism, which could be studies to understand the early forms of organization
facilitated by the integration of all genes into one that allowed self-reproduction, selection, and evolu-
giant replicative unit. Such an individualization of tionary adaptation of the biosynthetic machinery,
the total compartment requires high fidelity in the such as we encounter today in living cells. Proteins
replication machinery. In Part A we compared the do not inherit the basic physical prerequisites for such
information content of various stages of life with their an adaptive self-organization, at least not in any ob-
corresponding (and observed) replication fidelities (cf. vious manner as nucleic acids do. On the other hand,
Table 4). they do inherit a tremendous functional capacity, in
The individualization of compartments is probably which they are by far superior to the nucleic acids.
connected with the transition from RNA genes or Since proteins can form much more easily under pri-
operons to DNA genomes, since only the mechanism mordial conditions, the presence of a large amount
of DNA replication could guarantee sufficiently high of various catalytic materials must have been an es-
fidelity. The new individualized unit was the inte- sential environmental quality. Research in this field
grated Proto-cell. The previous functional organiza- has clearly demonstrated that quite efficient protein
tion of genes and gene products has been superseded catalysis can be present under primordial conditions.
and amended by a coupled structural and functional Interfaces deserve special recognition in this respect.
organization. A closer study of the cyclic arrangement If covered with catalytically active material they may
of genetic maps may still reveal some remnants of have served as the most favorable sites of primordial
the origins of structural organization, although re- synthesis. The restriction of molecular motion to the
combinative epigenetic effects may have covered dimensions of a plane increases enormously the effi-
many of the traces. ciency of encounters, especially if sequences of high-
As a consequence of unification and individualiza- order reactions are involved.
tion, the net growth of (asexual) multiplication of cells L. Onsager [93] has emphasized that under primordial
obeys a first-order autocatalytic law (in the absence conditions the oceans must have been extensively
of inhibitory effects). The Darwinian properties of covered with layers of deposited hydrophobic and
such systems allow for selective evolution as well as hydrophilic material cf. also [94]). Those multilayers
for coexistence of a large variety of differentiated must have offered favorable conditions for a primor-
species. The integrated unit of the cell turns out to dial preparative chemistry. In view of the obvious

83
~a
mers do not approach a steady-state value but de-
......
;:::~
crease either monotonically or in damped oscillations.
~~ Consequently, the macromolecules die out after some
~I!! DIFFUSION
DEGRADATION
time (Fig. 60).
' \ 01 d l
°l,h l
(B) Above a certain threshold value of total concen-
tration, we find limit cycle behavior in systems with

o n < 4. The situation is analogous to the low-concentra-


tion limit in a homogeneous solution (Fig. 61).

o
(C) At sufficiently high concentrations we finally ob-
tain a stationary state:
· -
I1m 1hi= 0 I'1 m -= 0
°Yi
d"tone. «rl
t~oo at ' 1-00 at
Fig. 59. Schematic representation of a heterogeneous reaction mo- and Xi> 0, Yi > 0, i = 1,2 ... n (Fig. 62), Xi and Yi being
del including hypercyclic coupling. Three spatial regions are dis- the concentrations of enzymes and messengers, re-
tinguished: r = 0 bound to interface, r = 1 transition layer at inter- spectively, Xi and Yi their final stationary values, and
face , r> 1 bulk of solution phase. Diffusion to and from interface
t the time.
is superimposed on chemical reactions proceeding according to
a hypercyclic scheme In systems of lower dimensions (n ~ 4) behavior of
types (A) and (C) only was observed.
These model calculations were supplemented by se-
veral studies of closely related problems using sto-
advantages offered by interfaces we have examined chastic computer-simulation techniques. The results
the properties of hypercycles under corresponding en- again showed the close analogy of behavior of hyper-
vironmental boundary conditions. cycles at interfaces and in homogeneous solution (as
As a simple model we consider a system such as described in detail in Part B).
that depicted schematically in Figure 59. Polymer syn- Consideration of realistic boundary conditions is a
thesis is restricted to a surface layer only (r = 0), which point particularly stressed in papers by H. Kuhn [96].
has a finite binding capacity for templates and en- We do not disagree with the assumption of a 'struc-
zymes. The kinetic equations are similar to those ap- tured environment', nor do we know whether we can
plying to homogeneous solutions except that we have agree with the postulation of a very particular envi-
to account explicitly for diffusion. We distinguish a ronment, unless experimental evidence can be
growth function that refers to the surface concentra- presented that shows at least the usefulness of such
tions of replicative molecules and enzymes. Diffusion postulates.
within the surface is assumed to be fast and not rate- Our models are by no means confined to spatial uni-
determining. Adsorption and desorption of macro- formity (cf. the above calculations). In fact, the logical
molecules is treated as an exchange reaction between inferences behind the various models-namely, the
the surface layer (r = 0) and a solution layer next to existence of a vast number of structural alternatives
the surface (0 < r ~ 1). Decomposition may occur at requiring natural selection, the limitation of the infor-
the interface and/or (only) in the bulk of the solution. mation content of single replicative units due to
Finally, transport to and from the interface is re- restricted fidelities, or the need for functional coup-
presented by a diffusion term. ling in order to allow the coherent evolution of a
Depending on the mechanism of synthesis assumed, complete ensemble - apply to any realistic environ-
it may be necessary to consider independent binding ment. Kuhn's conclusion that the kind of organiza-
sites for both templates and enzymes. We used this tion proposed is 'restricted to the particular case of
model to obtain some clues about the behavior of spatial uniformity' is beside the point. Who would
hypercycles with translation (cf. Sect. IX in Part B). claim today, that life could only originate in porous
Numerical integration for several sets of rate parame- material, or at interfaces, or within multilayers at
ters was performed according to a method described the surface of oceans, or in the bulk of sea water?
in the literature [95]. Three characteristic results - two The models show that it may originate - with greater
of which are in complete analogy to the behavior or lesser likelihood - under any of those boundary
of hypercycles in homogeneous solutions - can be dis- conditions, if-and only if-certain criteria are
tinguished: fulfilled. These criteria refer to the problem of gener-
(A) At very low concentrations of polynucleotides ation and accumulation of information and do not
and polypeptides or large values of Ki [see Eqs. (73), differ qualitatively when different boundary condi-
(75), and (79) in Part B], the surface densities of poly- tions are applied.

84
Much the same can be said with respect to temporal In order to decide whether fluctuations of tempera-
uniformity or nonuniformity. It has been shown in ture improve the selection of strands with higher in-
Part B that selection criteria may assume an especially formation content, one must analyze carefully the
simple form if they apply to steady-state conditions. relative temperature coefficients of all processes
Since they refer to relative rather than to absolute involved. The tempererature coefficient of hydrolysis
reaction rates, they are qualitatively the same, regard- is likely to be the largest of all. Instructed replication
less of whether the system is growing, oscillating, or is by no means generally enhanced at high tempera-
in a stationary state. tures. The incoming nucleotide has to bind coopera-
It is true that annealing is a useful procedure for tively to its complementary base at the template, at
many problems related to phase separations. the same time utilizing the stacking interaction with
Whether, however, thermal fluctuations serve equally the top bases in the growing chain. This is not possible
well for selection of longer polynucleotides, remains above the melting point of the templates. These con-
to be shown by experiments. siderations apply to any kind of environment, be it
an aqueous bulk phase, a surface layer, or a compart-
ment in a coarse-grained or porous material.
The important point for raising the information con-
tent is the relative strength of complementary vis-a-vis
noncomplementary interactions. Discrimination gen-
erally works better at lower than at higher tempera-
tures. S. Miller and L. Orgel ([63], p. 126) conclude
from their experimental data:
"We do not know what the temperature was in the
primitive ocean, but we can say that the instability
of various organic compounds and polymers makes
a compelling argument that life could not have arisen
in the ocean unless the temperature was below 25° C.
A temperature of 0° C would have helped greatly,
and - 21 ° C would have been even better. At such
low temperatures, most of the water on the primitive
earth would have been in the form of ice, with liquid
sea water confined to the equatorial oceans.
There is another reason for believing that life evolved

Figs. 60 to 62. Solution curves, obtained by numerical integration.


for a system of partial differential equations corresponding to the
model depicted in Figure 59. The rate equations account for a
growth function A; as introduced in Part B, which refers to a
four-membered hypercycle with translation (B. IX) and which has
nonzero catalytic-rate terms only at the interface (r=O). The equa-
tions furthermore take care of adsorption and desorption (ab d;
describing the transition of particles between r=O and r= I), hydro-
lysis (effective at r~ I), and diffusion in the bulk of solution (r> 1,
i.e., to and from the transition layer at r= I). Each set of three
curves refers to the three spatial positions r= 0 (upper), r= I (me-
dium) and r= 2 (lower). Figures 60 to 62 differ only in the assump-
tion of different values for the stability constants of the catalytically
active complexes Ii x Ei." which are highest (0.16) in Figure 60,
intermediate (0.06) in Figure 61, and lowest (0.04) in Figure 62.
The balance between production and removal is sufficient to make
the assumption of a dilution flux dispensable. As a consequence
-~- of the values chosen (relative to the uniform parameters j" ki -ac-
['--~------ cording to B,IX - ai, di and D) autocatalytic production cannot
compete with removal by transport and decomposition in Figure
60, where all partners Ii and Ei die out. In both other cases a
stable hypercyclic organization is established at the interface, where
population numbers are either oscillatory (Fig. 61) or stationary
- 11- ig. 62 (Fig. 62)

85
at low temperatures, whether in the oceans or lakes.
All of the template-directed reactions that must have FIRST POLYNUCLEOTIDES
led to the emergence of biological organization take
~
ee--.
place only below the melting temperature of the ap-
propriate organized polynucleotide structure. These
temperatures range from 0° C, or lower, to perhaps GC-RICH QUASI SPECIES
35° C, in the case of polynucleotide-mononucleotide
helices.
The environment in which life arose is frequently re- CODON ASSIGNMENTS;
TRANSLATION PRODUCTS,
ferred to as a warm, dilute soup of organic com- RICH IN GLY AND ALA,
pounds. We believe that a cold, concentrated soup E
would have provided a better environment for the
HYPERCYCLIC FIXATION
origins of life."

~"
OF GC-FRAME CODE,
ASSIGNMENTS OF GLY,
ALA, ASP AND VAL
PRIMITIVE REPLICASES
XVIII. Continuity of Evolution

It has been the object of this final part of the trilogy


EVOLUTION OF HYPERCYCLIC
to demonstrate that hypercycles may indeed represent ORGANISATION, RNY CODE,
realistic systems of matter rather than merely imagi- REPLICASES, SYNTHETASES,
RIBOSOMAL PRECURSORS,
nary products of our mind. EVOLUTION OF CODE,
Evolution is conservative and therefore appears to SPATIAL COMPARTMENTATION,
be an almost continuous process - apart from occa-
sional drastic changes. Selection is in fact based on
instabilities brought about by the appearance of advan- FULLY COMPARTMENTALIZED
tageous mutants that cause formerly stable distribu- HYPERCYCLES, ADAPTED RE-
PLICATION AND TRANSLATION
tions to break down. The descendents, however, are ENZYMES, EVOLUTION OF
usually so closely related to their immediate ancestors METABOLIC AND CONTROL
FUNCTIONS, OPERON STRUCTURE,
that changes emerge very gradually. Prebiotic evolu- RNA CORRESPONDS IN LENGTH
TO PRESENT RNA-VIRUSES,
tion presents no exception to the rule.
Let us summarize briefly what we think are the essen-
tial stages in the transition from the nonliving to
the living (cf. Fig. 63). PROTOCELL
1. The first appearance of macromolecules is dictated INTEGRATED GENOME: DNA
SOPHISTICATED ENZYMES
by their structural stability as well as by the chemical CONTROL MECHANISMS FOR
abundances of their constituents. In the early phase, READ OFF, FURTHER DAR-
WINIAN EVOLUTION ALLOWS
there must have been many undetermined protein-like FOR DIVERSIFICATION
substances and much fewer RNA-like polymers. The E
RNA-like polymers, however, inherit physically the
Fig. 63. Hypothetical scheme of evolution from single macromole-
property of reproducing themselves, and this is a nec- cules to integrated cell structures
essary prerequisite for systematic evolution.
2. The composition of the first polynucleotides is also
dictated by chemical abundance. Early nucleic acids
are anything but a homogeneous class of macromole-
cules, including L- and D-compounds as well as complementary patterns (possibly being the minus
various ester linkages, predominantly 2'-5' besides strands of messengers) represent suitable adapters.
3'-5'. Reproducibility of sequences depends on faith- The first amino acids are assigned to adapters accord-
fulness of copying. GC-rich compounds can form the ing to their availabilities. Translation products look
longest reproducible sequences. On the other hand, monotonous, since they consist mainly of glycine and
AU substitutions are also necessary. They cause a alanine residues. The same must be true for the bulk
certain structural flexibility that favors fast reproduc- of noninstructed proteins.
tion. Reproducible sequences form a quasi-species 4. If any of the possible translation products offers
distribution, which exhibits Darwinian behavior. catalytic support for the replication of its own messen-
3. Comma-free patterns in the quasi-species distribu- ger, then this very messenger may become dominant
tion qualify as messengers, while strands with exposed in the quasi-species distribution and, together with

86
its closely related mutants, will be present in great C. The early phase of self-organization left traces,
abundance. The process may be triggered by some but no witnesses, so that many important steps still
of the noninstructed environmental proteins, which remain in the dark.
in their composition reflect the relative abundance It was not even our intention to uncover historical
of amino acids and hence may mimic primitive truth. For a process so largely dependent upon
instructed proteins in their properties. chance - where indeterminate microscopic events,
5. The mutants of the dominant messenger - accord- such as mutations, amplify and finally determine the
ing to the criteria for hypercyclic evolution - may be- course of macroscopic development - a complete re-
come integrate.d into the reproduction cycle, whenever construction of history is not possible at all. Even
they offer further advantages. Thus hypercyclic or- in biology there is a 'poverty of historicism'. On
ganization with several codon assignments can build the other hand, the principles governing the historical
up. Such a hypercyclic organization is a prerequisite process of evolution - even in their finer details - may
for the coherent evolution of a translation apparatus. well be susceptible to our understanding. The traces
More and more mutants become integrated, and the of history in present systems may provide enough
steadily increasing fidelities will allow a prolongation clues to allow one day the construction of 'those
of the sequences. Different enzymic functions (repli- n equations for the n unknowns'.
cases, synthetases, ribosomal factors) may emerge All we wanted to show in this part is that the unique
from joint precursors by way of gene duplication and class of reaction networks, which we have termed
subsequently diverge. Units, including several struc- hypercycles, is indeed the simplest realistic molecular
tural genes, i.e., which are jointly controlled by one organization that ensures the coexistence of function-
coupling factor. ally related self-replicative units. Self-replication is
6. The complex hypercyclic organization can only required for the conservation of information. Hence
evolve further if it efficiently utilizes favorable pheno- the hypercycle is the simplest system that can allow
typic changes. In order to favor selectively the corre- the evolution of reproducible functional links. It can
sponding genotypes, spatial separation (either by originate from one self-replicating unit and its mu-
compartmentation or by complex formation) becomes tants, i.e., from a single (molecular) quasi-species.
necessary and allows selection among alternative mu- Its emergence was inevitable, whenever the conditions
tant combinations. Remnants of complex formation laid down by Nature allowed it. And yet:
may be seen in the ribosomes. "If anyone can name a more beautiful triangle under-
We do not know at which stage such a system was lying the composition of bodies, we will greet him
able to integrate its information content completely not as an opponent but as a friend in the right."
into one giant genome molecule. For this a highly (Plato, Timaios) [97]
sophisticated enzymic machinery was required, and
the role of information storage had to be gradually
transferred to DNA (which might have happened at This work was greatly stimulated by discussions with Francis Crick,
Stanley Miller, and Leslie Orgel; which for us meant some 'selec-
quite early stages).
tion pressure' to look for more continuity in molecular evolution.
These glimpses into the historical process of precellu- Especially helpful were suggestions and comments by Ch. Biebri-
lar evolution may suffice to show in which direction cher, I. Epstein, B. Gutte, D. Piirschke, K., Sigmund, P. Woolley,
a development, triggered by hypercyclic integration and R. Wolff.
of self-replicative molecular units, may lead, and how The work at Vienna was supported by the Austrian' Fonds zur
Fiirderung der wissenschaftlichen Forschung' (Project Nr. 3502).
the developing system may finally converge to give R uthild Winkler-Oswatitsch designed most of the illustrations and
an organization as complex as the prokaryotic cell. was always a patient and critical discussant.
We want to stress the speculative character of part Thanks to all for their help.

87
L
91
gly
9u
~u ~a
•• I vd
va 6

Ie
gly asp ala va l
gly asp ala val

·'9
.'g Iysy. I I ...
Ih ' "'.
,I. 6
ser asn thr ile
ser asn thr ile

·'9 gin
I pro ... 6
·'9
Qrg
gin
his
pro
pro leu
It u

arg his lpro leu


-
Fig. 64. The genetic code is the universal key for translation of
trp lor'" ", lou 6 genetic information from the legislative language of nucleic acids
term St, lou
cys tyr ser phe into the executive language of proteins. In this representation the
cys tyr ser phe three coordinates of geometric space are assigned to the positions
of letters in the triplet codewords. The four letters of the nucleic
acid alphabet are arranged in such a way that the codewords for
the most abundant amino acids appear in the top layer of the cube

88
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90
Subject Index

adapter, see RNA, transfer Darwin's principle, see Darwinian evolu- - - edge 45-47
Ai' definition of 8, 12, 29 tion - - map 32-43, 74
amino acids, prebiotic abundance 2, 71, 72 decision" once for ever" 2, 31, 54, 59 flow, individual 8
anticodon 60,61,63,64,66,68-70,78-81 decomposition rate 8, 13 -, total 9
attractor, definition of 33, 34 degree of growth functions 30, 31, 36, 37, - reactor 9, 50
-, strange 33, 34 41 flowing edge 45, 47
autocatalysis 5, 7, 13, 24, 37, 51, 61, 72, differential equations, autonomous 28 fluctuation 13, 33, 42, 45, 85
73, 83, 85 - -, non-autonomous 29 fluxes, constant 9, 12, 13, 30
- -, for selection 8, 28, 30, 35 forces, constant 30
diffusion 72, 84, 85 formation, spontaneous, definition of 8,
p-structure of polypeptides 80
basin of an attractor 33, 45, 49 DNA polymerase, phage specific 20, 22, 29
boundary of the concentration simplex 45, 81 functional linkage 26
49 - replication 4, 19-22, 24, 83
dynamic systems, definition of 28 f" definition and properties of 29, 30, 35
- - for hypercycles 45-47 game models 13, 16, 17, 26, 28, 65
center 33, 45-47 genetic code I, 2, 50, 61-72
chains, catalytic 38-40, 43, 46, 57, 58 - recombination 21,22
E" definition of 9, 12, 29
chirality I, 86 genotype 10,17,23,26,38,59,60,61,81,
E. coli, see escherichia coli
closed orbit, stable 33, 34, 42, 48, 49, 52, 87
ecologic niches 30, 83
53 growth, constrained 30
eigenvalues 10-12, 33, 35, 36, 42, 43, 45,
codon 61-66, 68-70, 72, 73, 78, 79, 87 -, exponential 5, 12, 29
74,76
codons, the first 68-70, 72 - functions 29-31, 36,41,43, 44
eigenvectors 10, 35
coexistence 6, 26, 31, 36, 59, 74, 83, - -, homogeneous 31,36,41
environmental factors 84
87 -, hyperbolic 5, 6, 29-31, 54
equilibrium, internal 31, 32, 36, 39, 43, 54,
compartmentation 26, 58, 81, 83, 85, 87 -, linear 5, 12,29,31,36
55,57
competition between hypercycles 54, 58 -, unlimited 29,31,54,55
error catastrophe 15, 16, 25
competitors, independent 36, 38-40, 51,
copy 8, 10, 11, 15
55, 58, 61, 74 Hopf bifurcation 36, 41, 52, 53
-, multiple 10, II, 77
concentration simplex 34, 35 ff. hypercYcle, broken 45, 46
-, single 10, II, 17,77,79
- space 29, 34, 48 -, catalytic, definition of 2, 5, 6
rate 18, 20-22, 24, 67
- vector 29 -, classification of 40
threshold 15-18, 22, 24, 26
concentrations, time averaged 49, 54 -, compound 41,43,44, 59
Escherichia coli 18, 22, 24, 78, 81, 82
constraint 2, 13, 29, 30, 36 -, coupling between 58
- -, phage infection of 18, 81
cooperative behaviour 26,31,38,39,49, - with diffusion 84, 85
eukaryotic cell 22, 24, 78
53, 57-59, 76, 83 -, elementary 41, 44, 45, 47-49, 51
evolution experiments 9, 18, 72
- stack 66 -, extinction 45
-, historical route of 1,2,7,76,86,87
- properties 76 -, formation 45, 57, 72, 75
- principle of hypercycles 73, 75, 76
crossing over 21 -, need for 23
excess productivity, definition of 9, 12; 29
cycle, catalytic 4, 5 of second degree 5, 6, 40
extracistronic regions 18, 19
-, citric acid 3 - with translation 50-53, 73, 75, 84, 85
extremum principle 10, 13
-, carbon 3
information 14, 19,22-24,27,28,38,40,
D" definition of 8, 12 4>" definition and properties of 8, 29, 30 44, 59, 60, 65, 73, 77, 84
Ll i , definition of 29 4>" definition and properties of 9, 30, 31, - content 14, 18, 22, 24, 25, 67, 82, 83
Darwinian evolution 2,6, 10, 12, 13, 15, 35 interior of the concentration simplex 45,
19, 24-26, 29-32, 59, 60, 65, 69, 75, 76, fixed point analysis 27, 32-43, 45, 49, 47,49
83,86 55-58, 74, 76 Ising model 66
91
Jacobian matrix 35,45 polymerization, template directed 50, 51 -, flower model of 23
population genetics 2, 6, 7 -, sequences of 78, 79
limit cycle 33, 34, 42, 48, 49, 52, 53 - -, Mendelian 6,7, 14
Lyapunov function 45, 46, 48 - variables, normalized 31, 34 am' superiority parameter II, 12, 15,
prokaryotic cell 4, 22, 60, 62, 77, 78, 87 17-19,22,24,25
messenger, see RNA, messenger saddle, definition and properties of 32, 33,
metabolism 7, 8, 26 Q.. definition and properties of 8, II, 12, 42,45
metal coordination 71,81 14, 15, 18, 27 selection constraint 2,6,9, 13,29-31,36,
meteorite analysis 71, 72 qm, average digit quality II, 14-18,22, 40,51
Michaelis-Menten mechanism 3, 12, 50 24-27, 66, 67 self-reproduction 4, 5, 7, 8, 22, 23, 28, 30,
mutation I, 7, 8, 13, 18,31,40,59, 70, Qp-RNA phage 10, II, 13, 17-19,23,24, 50, 51, 55, 57, 76, 83
73, 75, 77, 79, 82, 83, 86 64, 79, 82 separatrix 32, 33
-, neutral II, 14 -, midivariant of 18, 19,23,64,79,80 serial transfer 9
quality factor 8, II, 12, 15, 18,26,27 singularity of solution curves 29, 30
Vmax>maximum degree of polymerization quasi-species 9-15,22,24,26,36-38,60, sink, definition and properties of 32, 33
II, 15, 16,24-26 64, 69, 70, 73, 75-77, 79, 86, 87 source, definition and properties of 32, 33
non-Darwinian evolution 12, 54 stability, asymptotic 42
normal mode analysis, definition of 35, 36 reaction networks, cyclic, catalytic 3, 6, stochastic approach II, 13
nucleoside triphosphates 4, 50 25, 32, 40, 55, 57, 72, 83, 87 synthesis, pre biotic 70-72, 83
repair mechanism 19-22 synthetase function 61,62,65,81,82
optimization principle 2, 10 replication fork 19, 20 trajectories 33, 35, 42, 45-49, 51-53
organization, constant overall 9, 30, 31, ribonuclease 81 translation 5, 6, 22, 24-26, 38,44, 50, 51,
40, 42-44, 51, 55 ribosome 60, 61, 63, 65, 78, 82, 87
59-62, 64, 65, 67-70, 72, 73, 77, 80-83,
oscillation 28, 43, 48, 49, 51-54, 84, 85 RNA, de novo synthesis of 79, 80
86,87
-, messenger 6,44,61-65,67-70,72,73,
transport term 8
Pi> definition of 30, 36 75, 77-79, 81-84, 86
parameter space 29 phage infection 5, 17-19,22,24,25 value selective 9, 10, 12, 18, 25-28, 76
parasitic coupling 55, 56, 59 replicase, phagespecific 5,11,17-19,23 vector field 35, 57, 58
perturbation theory 12 replication 4, 5, 11, 13, 17-20, 22,
phenomenological equations 28 23-25, 44, 50, 51, 60-62, 64, 65, 69, 78 Wii , definition and properties of 9, 12, \8,
phenotype 10, 17, 18, 23, 25, 26, 38, 59, - selfcopying of internal regions 77, 80 29
60, 81-83, 87 -, transfer 17,22-24,26,60-70,72,73, wild-type distribution 10-12, 18
polymerase 5, 50, 64, 65, 82 75, 77-82, 86 wobble 18,67-70

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