Critical Notice: Cycles of Contingency – Developmental Systems and Evolution

The themes, problems and challenges of developmental systems theory as described in Cycles of Contingency are discussed. We argue in favor of a robust approach to philosophical and scientific problems of extended heredity and the integration of behavior, development, inheritance, and evolution. Problems with Sterelny's proposal to evaluate inheritance systems using his `Hoyle criteria' are discussed and critically evaluated. Additional support for a developmental systems perspective is sought in evolutionary studies of performance and behavior modulation of fitness.     

Stepwise Evolution of Nonliving to Living Chemical Systems

Steps by which a nonliving chemical system could have transformed into a living system are described and discussed, assuming general features of Wächtershäuser's chemo-autotrophic surface theory of the origin of life. Environmental species such as CO₂ and H₂S are proposed to have reacted to form a quasi-steady state metal-bound intermediate (CH₃-M) that slowly decayed into waste (CH₄). Unpredictable dispersive reactions expanded the system to include surface-bound forms of the citric acid cycle intermediates (oxaloacetate → citrate). Further reaction yielded an autocatalytic system in which raw materials are converted into the system at exponential rates. Combinatorial dispersive reactions that improved the performance of this system were automatically selected and incorporated into it. Systems evolved critical features of living systems (proteins, membranes, proteins, nucleic acids, etc.) using two related mechanisms called grafting and waste-conversion. Such living systems were transformed from less recognizable types (characterized by autocatalytic spreading, decentralization, poorly defined boundaries, etc.) into more recognizable ones (encapsulated by membranes, controlled by single-molecule genomes, etc.) that self-replicated by a cell division cycle and could evolve by the standard gene-based Darwinian mechanism. The resulting systems are viewed as having an autocatalytic network composed of three linked autocatalytic subreactions.     

Selection and the Evolution of Genetic Life Cycles

The evolution of haploid and diploid phases of the life cycle is investigated theoretically, using a model where the relative length of haploid and diploid phases is under genetic control. The model assumes that selection occurs in both phases and that fitness in each phase is a function of the time spent in that phase. The equilibrium and stability conditions that allow for all-haploid, all-diploid, or polyphasic life cycles are considered for general survivorship functions. Types of stable life cycles possible depend on the form of the viability selection. If mortality rates are constant, either haploidy or diploidy is the only stable life cycle possible. Departures from constant mortality can give qualitatively different results. For example, when survivorship in each phase is a linear, decreasing function of the time spent in the phase, stable haploid, diploid or polyphasic life cycles are possible. The addition of genetic variation at a coevolving viability locus does not qualitatively affect the outcome with respect to the maintenance of polyphasic cycles but can lead to situations where more than one life cycle is concurrently stable. These results show that trade-offs between the advantages of being diploid and of being haploid may help explain the patterns of life cycles found in nature and that the type of selection may be critical to determining the results.     

Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles

Most bacteria live in colonies, where they often express different cell types. The ecological significance of these cell types and their evolutionary origin are often unknown. Here, we study the evolution of cell differentiation in the context of surface colonization. We particularly focus on the evolution of a ‘sticky’ cell type that is required for surface attachment, but is costly to express. The sticky cells not only facilitate their own attachment, but also that of non-sticky cells. Using individual-based simulations, we show that surface colonization rapidly evolves and in most cases leads to phenotypic heterogeneity, in which sticky and non-sticky cells occur side by side on the surface. In the presence of regulation, cell differentiation leads to a remarkable set of bacterial life cycles, in which cells alternate between living in the liquid and living on the surface. The dominant life stage is formed by the surface-attached colony that shows many complex features: colonies reproduce via fission and by producing migratory propagules; cells inside the colony divide labour; and colonies can produce filaments to facilitate expansion. Overall, our model illustrates how the evolution of an adhesive cell type goes hand in hand with the evolution of complex bacterial life cycles.     

Studies on Order in Prebiological Systems at the Laboratory of Chemical Evolution

The basic tenet of investigations in the Laboratory of Chemical Evolution (LCE) under Cyril Ponnamperuma was that biology is a recapitulation of prebiology, and that protobiology is an outcome of simple molecular interactions, engendered by the physics and chemistry of the molecules themselves. Studies were undertaken to continue research into understanding the determining physical and chemical parameters of molecular interactions leading to increasing complexity in pre- and proto-biological systems. Among other, related work, research was performed on the origin of the genetic code, the origin of order in prebiotic polymers, and related studies on the origins of optical activity in biological macromolecules. Highlights of some these studies are presented here.     

Evolution of Metazoan Life Cycles and the Origin of Pelagic Larvae

Russian Journal of Developmental Biology - The problem of the origin of the metazoan life cycle is analyzed on the base of various hypotheses on the origin of multicellular animals. According to...     

有性生殖与食者—被食者体系中的极限环

1　引　言种群生物学的原始假设认为,在一定条件下,任一种群,不管是有性生殖种群还是无性生殖种群,其自然增长都遵守ＶｅｒｈｕｌｓｔＰｅａｒｌＬｏｇｉｓｔｉｃ方程。按照这一方程,种群有一个平衡点Ｓ,Ｓ=Ｋ,Ｋ是环境负荷容量;并且随着种群大小(或密度)Ｎ的增加,种群的个体(或相对)自然增长率ｄＮ/Ｎｄｔ单调下降。这是由于存在拥挤效应。Ｌｏｇｉｓｔｉｃ方程不含Ａｌｌｅｅ效应或过疏效应[1,2]。实际情况与Ｌｏｇｉｓｔｉｃ方程有所不同,由于存在“拥挤效应”和“过疏效应”,第一,有一个最适种群大小Ｎｍ:随着Ｎ增加,ｄＮ/Ｎｄｔ在Ｎ<Ｎ…     

Biochemical Systems as Generators of Local and Global Limit Cycles

It has recently been noted (8) that the global limit cycle (hard self-excitation) is apparently not uncommon in nature, especially in biochemical systems. This idea is confirmed by a more detailed study of many biochemical systems with quite different topological structures.

The present paper describes some of the cases considered; they were deliberately chosen to be simple, but they almost all have the following properties: for one set of parameters, the linearization method shows that there is a local limit cycle (soft self-excitation); for other parameters, the systems may have global limit cycles.     

Biochemical Systems as Generators of Local and Global Limit Cycles

It has recently been noted (8) that the global limit cycle (hard self-excitation) is apparently not uncommon in nature, especially in biochemical systems. This idea is confirmed by a more detailed study of many biochemical systems with quite different topological structures.

The present paper describes some of the cases considered; they were deliberately chosen to be simple, but they almost all have the following properties: for one set of parameters, the linearization method shows that there is a local limit cycle (soft self-excitation); for other parameters, the systems may have global limit cycles.     

Complex Adaptive Systems and the Evolution of Reciprocation

Complex adaptive systems play a major role in the theory of reciprocal altruism. Starting with Axelrod's celebrated computer tournaments, a wide variety of computer simulations show that cooperation can evolve in populations of selfish agents, both with direct and indirect reciprocation. Received 14 April 1998; accepted 16 June 1998.     

Chemical Ecology and Biomolecular Evolution

The belief in the Darwinian theory of evolution appeared to be shaken when one tried to interpret statements of molecular biology in it. As a consequence there arose a theory of non-Darwinian neutral evolution. The supporters of this theory believe that under natural conditions no factors exist which can distinguish and select organisms on their internal (molecular) structure. In the opinion of these neutralists natural selection cannot in principle control the molecular constitution of organisms. Contrary to the viewpoint of the critics of neutralism it is impossible to admit that nucleic acids, proteins and other biomolecules can evolve without the participation of natural selection. This controversy in contemporary theoretical biology can be solved by integrating the conceptions of molecular ecology with Darwinian theory. Molecular ecology acknowledges the interactions of organisms by means of chemical substances synthesized by them. Such chemical ecological factors play a leading part in the selective stages of biomolecular evolution. These diverse chemical ecological interrelations take place intensively when living beings interact with parasitic microbes.     

On the Spectrum of Prebiotic Chemical Systems

We reexamine Eigen’s paradox using the asymptotic limit theorems of information theory. Applying the homology between information source uncertainty and free energy density, under rate distortion constraints, the error catastrophe emerges as the lowest energy state for simple prebiotic systems without error correction. Invoking the usual compartmentalization – i.e., ‘vesicles’ – and using a Red Queen argument, suggests that information crosstalk between two or more properly interacting structures can initiate a coevolutionary dynamic having at least two quasi-stable states. The first is a low energy realm near the error threshold, and, depending on available energy, the second can approach zero error as a limit. A large deviations argument produces jet-like global transitions which, over sufficient time, may enable shifts between the many quasi-stable modes available to more complicated structures, ‘locking in’ to some subset of the various possible low error rate chemical systems, which become subject to development by selection and chance extinction. Energy availability, according to the model, is thus a powerful necessary condition for low error rate replication, suggesting that some fundamental prebiotic ecosystem transformation entrained reproductive fidelity. This work, then, supports speculation that our RNA/DNA world may indeed be only the chance result of a very broad prebiotic evolutionary phenomenon. Processes in vitro, or ex planeta, might have other outcomes.     

Evolution of Primate Social Systems

We review evolutionary processes and mechanisms that gave rise to the diversity of primate social systems. We define social organization, social structure and mating system as distinct components of a social system. For each component, we summarize levels and patterns of variation among primates and discuss evolutionary determinants of this variation. We conclude that conclusive explanations for a solitary life and pair-living are still lacking. We then focus on interactions among the 3 components in order to identify main targets of selection and potential constraints for social evolution. Social organization and mating system are more closely linked to each other than either one is to social structure. Further, we conclude that it is important to seek a priori measures for the effects of presumed selective factors and that the genetic contribution to social systems is still poorly examined. Finally, we examine the role of primate socio-ecology in current evolutionary biology and conclude that primates are not prominently represented because the main questions asked in behavioral ecology are often irrelevant for primate behavior. For the future, we see a rapprochement of these areas as the role of disease and life-history theory are integrated more fully into primate socio-ecology.     

The Evolution of One- and Two-Locus Systems

Assuming age-independent fertilities and mortalities and random mating, continuous-time models for a monoecious population are investigated for weak selection. A single locus with multiple alleles and two alleles at each of two loci are considered. A slow-selection analysis of diallelic and multiallelic two-locus models with discrete nonoverlapping generations is also presented. The selective differences may be functions of genotypic frequencies, but their rate of change due to their explicit dependence on time (if any) must be at most of the second order in s, (i.e., O( s²)), where s is the intensity of natural selection. Then, after several generations have elapsed, in the continuous time models the time-derivative of the deviations from Hardy-Weinberg proportions is of O(s²), and in the two-locus models the rate of change of the linkage disequilibrium is of O(s²). It follows that, if the rate of change of the genotypic fitnesses is smaller than second order in s (i.e., o(s²)), then to O(s²) the rate of change of the mean fitness of the population is equal to the genic variance. For a fixed value of s, however, no matter how small, the genic variance may occasionally be smaller in absolute value than the (possibly negative) lower order terms in the change in fitness, and hence the mean fitness may decrease. This happens if the allelic frequencies are changing extremely slowly, and hence occurs often very close to equilibrium. Some new expressions are derived for the change in mean fitness. It is shown that, with an error of O( s), the genotypic frequencies evolve as if the population were in Hardy-Weinberg proportions and linkage equilibrium. Thus, at least for the deterministic behavior of one and two loci, deviations from random combination appear to have very little evolutionary significance.     

Investigating the Evolution and Development of Biological Systems from the Perspective of Thermo-Kinetics and Systems Theory

Origins of Life and Evolution of Biospheres - Life itself is grander than the sum of its constituent molecules. Any living organism may be regarded as a part of a dissipative process that connects...     

Chemical Evolution and Meteorites: An Update

Carbonaceous chondrites are a primitive group of meteorites, which contain abundant organic material and provide a unique natural record of prebiotic chemical evolution. This material comprises a varied suite of soluble organic compounds that are similar, sometimes identical, to those found in the biosphere, such as amino acids, carboxylic acids, and sugar derivatives. Some amino acids of this suite also show L-enantiomeric excesses, and suggest the possibility they may have contributed to terrestrial homochirality by direct input of meteoritic material to the early Earth. This optical activity appears to be limited to the subgroup of alpha-methyl amino acids which, although not common in the extant biosphere, would have been well suited to provide the early earth with both enantiomeric excesses and means for their amplification by subsequent chemical evolution. We can also envision this exogenous delivery of carbonaceous material by meteorites and comets as having coincided with the endogenous formation of prebiotic precursors and influenced their evolution by complementary reactions or catalysis.