Protein Folding and Evolution are Driven by the Maxwell Demon Activity of Proteins

In this paper we propose a theoretical model of protein folding and protein evolution in which a polypeptide (sequence/structure) is assumed to behave as a Maxwell Demon or Information Gathering and Using System (IGUS) that performs measurements aiming at the construction of the native structure. Our model proposes that a physical meaning to Shannon information (H) and Chaitin's algorithmic information (K) parameters can be both defined and referred from the IGUS standpoint. Our hypothesis accounts for the interdependence of protein folding and protein evolution through mutual influencing relationships mediated by the IGUS. In brief, IGUS activity in protein folding determines long term tendencies that emerge at the evolutionary time-scale.Thus, protein evolution is a consequence of measurements executed by proteins at the cellular level, where the IGUS imposes a tendency to attain a highly unique stable native form that promotes the updating of the information content. The folding kinetics observed is, thus, the outcome of an evolutionary process where the polypeptide-IGUS drives the evolution of its linear sequence. Finally, we describe protein evolution as an entropic process that tends to increase the content of mutual algorithmic information between the sequence and the structure. This model enables one: 1. To comprehend that full determination of the three-dimensional structure by the linear sequence is a tendency where satisfaction is only possible at thermodynamic equilibrium.2. To account for the observed randomness of the amino acid sequences. 3. To predict an alternation of periods of selection and neutral diffusion during protein evolutionary time.     

Role of Utility and Inference in the Evolution of Functional Information

Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism’s behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality, and they evolve towards higher adaptability on a long time scale.     

Evolutionary History of Cathepsin L (L-like) Family Genes in Vertebrates

Cathepsin L family, an important cysteine protease found in lysosomes, is categorized into cathepsins B, F, H, K, L, S, and W in vertebrates. This categorization is based on their sequence alignment and traditional functional classification, but the evolutionary relationship of family members is unclear. This study determined the evolutionary relationship of cathepsin L family genes in vertebrates through phylogenetic construction. Results showed that cathepsins F, H, S and K, and L and V were chronologically diverged. Tandem-repeat duplication was found to occur in the evolutionary history of cathepsin L family. Cathepsin L in zebrafish, cathepsins S and K in xenopus, and cathepsin L in mice and rats underwent evident tandem-repeat events. Positive selection was detected in cathepsin L-like members in mice and rats, and amino acid sites under positive selection pressure were calculated. Most of these sites appeared at the connection of secondary structures, suggesting that the sites may slightly change spatial structure. Severe positive selection was also observed in cathepsin V (L2) of primates, indicating that this enzyme had some special functions. Our work provided a brief evolutionary history of cathepsin L family and differentiated cathepsins S and K from cathepsin L based on vertebrate appearance. Positive selection was the specific cause of differentiation of cathepsin L family genes, confirming that gene function variation after expansion events was related to interactions with the environment and adaptability.     

Simulation of the evolution of genomic complexity.

A general evolutionary trend is the generation of organisms of increasing complexity, notwithstanding that reduction and simplification phenomena do occur in the evolutionary process. This paper proposes an evolutionary model incorporating the mechanisms of gene amplification and deletion. The evolutionary process leading to genomic complexity and the coexistence of simpler organisms with complicated ones were both simulated using the proposed model. The model was also used to investigate the influence of various factors on the evolution of complexity. The simulations indicated that the evolution of complexity is largely influenced by adaptation to complicated environments. Nevertheless, complex organisms require relatively more resources for survival and replication, which limits the on going tendency towards complexity. Moreover, the analysis showed that if the environment varies rapidly and the profit obtained from complexity is greater than the resources consumed, selection will tend to favor complexity. However, high living cost will tend to limit the trend of complexity and if the environment is relatively stable, reduction and simplification will become the dominant trends.     

COEVOLUTION AS AN EVOLUTIONARY GAME

Coevolution is modeled as a continuous game where the fitness-maximizing strategy of an individual is assumed to be a function of the strategy of other individuals who are also under selection to maximize fitness. An evolutionary stable strategy (ESS) is sought such that no rare alternative strategies can invade the community. The approach can be used to model coevolution because the ESS may be composed of a coalition of more than one strategy. This work, by modeling frequency-dependent selection, extends the approach of Roughgarden (1976) which only considered density-dependent selection. In particular, we show that the coevolutionary model of Rummel and Roughgarden (1985) does contain frequency-dependent selection, and thus, their application of Roughgarden's criterion for evolutionary stability to a model for which it is not applicable leads to the erroneous conclusion that the ecological and evolutionary processes are in conflict. The utility of the game theoretic approach is illustrated by two examples. The first considers an ESS composed of a single strategy, the second an ESS composed of a coalition of two strategies. Evolution occurs on a frequency-dependent adaptive landscape. For this reason, the approach is appropriate for modeling competitive speciation (Rosenzweig, 1978). Also, the game theoretic approach is designed to combine the interplay between the background environment (including the biotic components) and the evolutionary potential of the populations or organisms. The actual application of this theory will require knowledge of both.     

Ecological aspects of the evolutionary processes

Darwin in his On the Origin of species made it clear that evolutionary change depends on the combined action of two different causes, the first being the origin of genetically based phenotypic variation in the individual organisms comprising the population and the second being the action of selective agents of the external environment placing demands on the individual organisms. For over a century following Darwin, most evolutionists focused on the origin of inherited variation and its transmission; many workers continue to regard genetics to be the core of evolutionary theory. Far less attention has been given to the exact nature of the selective agents with most evolutionists still treating this cause imprecisely to the detriment of our understanding of both nomological and historical evolutionary theory. Darwin was vague in the meaning of his new concept of "Natural Selection," using it interchangeably as one of the causes for evolutionary change and as the final outcome (= evolutionary change). In 1930, natural selection was defined clearly as "non-random, differential reproduction of genes" by R. Fisher and J.B.S. Haldane which is a statement of the outcome of evolutionary process and which omits mention of the causes bringing about this change. Evolutionists quickly accepted this outcome definition of natural selection, and have used interchangeably selection both as a cause and as the result of evolutionary change, causing great confusion. Herein, the details will be discussed of how the external environment (i.e., the environment-phenotype interaction) serves as selective agents and exerts demands on the phenotypic organisms. Included are the concepts of fitness and of the components of fitness (= adaptations) which are respectively (a) survival, (b) direct reproductive and (c) indirect reproductive features. Finally, it will be argued that historical-narrative analyses of organisms, including classification and phylogenetic history, are possible only with a full understanding of nomological evolutionary theory and with functional/adaptive studies of the employed taxonomic features in addition to the standard comparative investigations.     

Eco-Evolutionary Feedback and the Tuning of Proto-Developmental Life Cycles

Multicellular organisms depend on developmental programs to coordinate growth and differentiation from single cells, but the origins of development are unclear. A possible starting point is stochastic phenotypic variation generated by molecular noise. Given appropriate environmental conditions, noise-driven differentiation could conceivably evolve so as to come under regulatory control; however, abiotic conditions are likely to be restrictive. Drawing from an experimental system, we present a model in which environmental fluctuations are coupled to population growth. We show that this coupling generates stable selection for a single optimal strategy that is largely insensitive to environmental conditions, including the number of competitors, carrying capacity of the environment, difference in growth rates among phenotypic variants, and population density. We argue that this optimal strategy establishes stabilizing conditions likely to improve the quality and reliability of information experienced by evolving organisms, thus increasing opportunity for the evolutionary emergence of developmental programs.     

Selektion und Evolutionstheorie: Müssen »altdarwinistische Dogmen« durch eine kritische Evolutionstheorie ersetzt werden?

Some authors (mainlyBonik, Gutmann, andPeters) have tried to revise current evolutionary concepts, fraught — in their opinion — with “1paleodarwinistic dogmas”. Some points of their theories are reviewed critically in the present paper: (1) Evolution is of course inimaginable without selection, but an “internal selection” eliminating misshaped embryos has nothing to do with evolution. This is stabilizing selection which reduces genetic variation and would even block evolutionary change completely if it was perfect. When this kind of internal selection was “neglected” by earlier authors, this cannot be qualified as paleodarwinistic dogmatism being in contradiction with the premises of evolutionary theory. — (2) Energetic rationalisation of organisms is certainly an important factor in selection but not an absolute law explaining everything about evolution. There are many adaptive processes resulting in less “economic” formations; e.g. heavy armors like those of tortoises, ankylosaurs, and stegosaurs. Among others, protective functions justify a certain waste of energy. — (3) Comparing organisms with technical machines provides an interesting analogy, but again this cannot be considered as the only possible approach for evolutionary models. »Maschinenanalogie« combined with a generalized »internal selection« (i.e. with the nature of adaptive changes determined by the internal construction of organisms) leads inevitably to an underestimation of selective pressures resulting from the ecologic and biocoenotic context. The simple fact of diverging evolutionary lineages shows that the same species (“machine”) can be improved in different ways under the influence of different external factors.     

A Virtue Made of Necessity: Is the Increasing Hierarchical Complexity of Sexual Clades an Inevitable Outcome of Their Declining (Macro)evolutionary Potential?

The increasing maximal hierarchical complexity of organisms is one of the best-supported macroevolutionary trends. The nature and causes of this trend, as well as several accompanying macroevolutionary phenomena are, however, still unclear. In this theoretical article, we propose that the cause of this trend could be the increasing pressure of species selection, which results from the gradual decrease of (macro)evolutionary potential (i.e. the probability of producing major evolutionary innovations). As follows from the Theory of Frozen Evolution, this process is an inevitable consequence of the sorting of genes, traits, and their integrated groups (modules) based on their contextually dependent stability. In turn, this causes effectively unchangeable elements of genetic architecture to accumulate during the existence of evolutionary lineages. Although (macro)evolutionary potential can be partially restored by several processes, a profound restoration of (macro)evolutionary potential is probably possible only by means of a transition to a higher level of hierarchical complexity. However, the accumulation of contextually more stable elements continues even on this higher level. This leads to the integration of the modular character of composite organisms and a repeated pressure to increase the level of hierarchical complexity. Our model explains all components of McShea’s “Evolutionary Syndrome,” i.e. the trend of increasing the hierarchical complexity of organisms, the growth of variability among elements on the immediately lower level, and their gradual machinification. This pattern should be characteristic of sexual eukaryotes and especially their complex representatives. Our model also sheds new light on several related macroevolutionary phenomena, such as the gradual acceleration of the trend or the striking difference between pre-Neoproterozoic and Phanerozoic evolution.     

Evolving views of viral evolution: towards an evolutionary biology of viruses.

Despite considerable interest in viral evolution, at least among virologists, viruses are rarely considered from the same evolutionary vantage point as other organisms. Early work of necessity emphasized phenotype and phenotypic variation (and therefore arguably was more oriented towards the broader biological and ecological perspectives). More recent work (essentially since the development of molecular evolution in the 1960's but beginning earlier) has concentrated on genotypic variation, with less clarity about the significance of such variations. Other aspects of evolutionary theory, especially considerations of natural selection and of evolutionary constraints, have not widely been applied to viruses, and an evolutionary framework for virology has long been lacking. This becomes apparent in considering 'emerging' viruses, which have often been treated on an ad hoc basis. It was often felt that, because previously unrecognized viruses are involved, mechanisms of viral emergence must mirror the unpredictability of mutations in the viral genome. However, most examples of viral emergence are independent of mutation, at least initially, and are often pre-existing viruses in changed circumstances ('viral traffic'). This conclusion also readily follows from ordinary Darwinian premises, which would require that, like other living species, 'new' organisms are descended only from existing species. In this respect, from a Darwinian perspective, viruses would appear to resemble other organisms.     

From asexual to eusocial reproduction by multilevel selection by density-dependent competitive interactions

A game theoretical model is developed to illustrate that multilevel selection by density-dependent competitive interactions in mobile organisms might have played a major role in the evolutionary transitions from asexual over sexual to eusocial reproduction. The model has four equilibria with selection occurring among interacting units of respectively one, two, three, and up to infinitely many individuals. The different equilibria are characterised by different levels of competitive interactions among interacting units, and these levels select for different levels of sexual and co-operative reproduction among the individuals of the units. The model predicts: (i) that low-energy organisms with negligible body masses have asexual reproduction; (ii) that high-energy organisms with non-negligible body masses in evolutionary equilibria have sexual reproduction between a female and a male; (iii) that high-energy organisms with non-negligible body masses that increase exponentially at an evolutionary steady state have co-operative reproduction between a sexual pair and a single sexually produced offspring; and (iv) that high-energy organisms with upward constrained body masses have eusocial reproduction between a sexual pair and up to an infinite number of sexually produced offspring workers.     

Models of cultural niche construction with selection and assortative mating

Niche construction is a process through which organisms modify their environment and, as a result, alter the selection pressures on themselves and other species. In cultural niche construction, one or more cultural traits can influence the evolution of other cultural or biological traits by affecting the social environment in which the latter traits may evolve. Cultural niche construction may include either gene-culture or culture-culture interactions. Here we develop a model of this process and suggest some applications of this model. We examine the interactions between cultural transmission, selection, and assorting, paying particular attention to the complexities that arise when selection and assorting are both present, in which case stable polymorphisms of all cultural phenotypes are possible. We compare our model to a recent model for the joint evolution of religion and fertility and discuss other potential applications of cultural niche construction theory, including the evolution and maintenance of large-scale human conflict and the relationship between sex ratio bias and marriage customs. The evolutionary framework we introduce begins to address complexities that arise in the quantitative analysis of multiple interacting cultural traits.     

Environs: The Superniches of Ecosystems

Evolution proceeds by natural selection of heritable variationsof individual organisms based on direct influences of environment.However, indirect effects probably vastly outweigh direct onesin ecosystems. Therefore, why is evolution based on direct effectsonly? The ecological niche represents the point of direct contactbetween organisms and their environments. To encompass indirectinfluences, niches are extended to new structures, environs,which are units of organism-environment coevolution. The motiveforce for coevolution is closure of outputs back upon inputsof the organism members of ecosystems. Closure is achieved bybiogeochemical cycling and feedback interactions, direct andindirect, between organisms. To the extent that closure doesnot occur, there is no imperative for organism-environment coevolution.Coevolution at the system level based on indirect effects iscompatible with normal evolution at the individual organismlevel based on direct effects. The organism is the unit of thelatter, but environs are the unit of coevolution.     

Evolutionarily stable strategies in food selection models with fitness sets

Most current models for optimal food selection apply to ecological and behavioural optimization. In this paper optimal food selection theory is extended to apply to evolutionary optimization. A general evolutionary model for optimal food selection must incorporate the concept of fitness sets--or that variables, changing as a result of natural selection in evolutionary time, cannot, in general, vary independently of each other. A "Charnov type" optimal food selection model with a fitness set is investigated, and evolutionarily stable strategy (ESS) solutions of the evolutionary variables (i.e., the efficiencies of using available food types) are found. From this analysis it follows that the relative frequency of various food types in the environment may, under specified conditions, influence the evolutionarily optimal diet. Secondly, the analysis demonstrates that a food type not in the optimal diet may, in evolutionary time, be added to this by becoming more abundant. Thirdly, it follows from the analysis that the ecological result of MacArthur and Pianka, that food types are worth eating even if there is competition for them, is not generally applicable when referring to an evolutionary time scale. Finally, it is pointed out that for the diet to be an ESS, it is necessary that the consumer's density is stable and that the consumer's population dynamics are subjected to some density-dependent factor.     

The ancient lakes of Indonesia: towards integrated research on speciation

Ancient lakes have provided considerable insights into the drivers of speciation and adaptive radiation in aquatic organisms. Most studies of species-flocks, however, focus only on a single group of organisms, and few have attempted to integrate geological, limnological, ecological, and genetic drivers of speciation on multiple species-flocks at various trophic levels. As such, there is a need for a comprehensive model system for research on speciation in aquatic environments where multiple radiations are investigated at various levels of biological organization (e.g., individual, population, and ecosystem) and placed in light of geographical and geological setting. The ancient Malili Lakes of Sulawesi, Indonesia, are ideal candidates for such a model, and represent the only hydrologically connected ancient lakes in the world. These lakes are characterized by ultra-oligotrophy and unique physicochemical conditions that govern the composition and production of planktonic communities. At higher trophic levels, there are three recurring trends: (1) low taxonomic richness and simple community structures, (2) adaptive radiations with trophic specialization, and (3) remarkably high endemism with evolutionary innovations throughout the lakes and species-flocks. Furthermore, the restricted geographic distributions of species-flocks within the Malili Lakes indicate that each lake constitutes a unique environment, and dispersal among lakes is limited, despite close contemporary connectivity. These observations suggest that ecological and evolutionary processes are regulated from the bottom up, and speciation is primarily facilitated by interspecific and intraspecific competition for limited resources. The Malili Lakes represent an outstanding natural model for integrative research into speciation as they offer the opportunity to explore the roles of geography, dispersal, and selection in the radiation of aquatic organisms.     

A rule-based approach to the modelling of bacterial ecosystems

This paper presents an approach to ecological/evolutionary modelling that is inspired by natural bacterial ecosystems and bacterial evolution. An individual-based artificial ecosystem model is proposed, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by rule-based learning classifier systems. The proposed ecosystem model consists of a n-dimensional environmental grid, which can contain different types of artificial resources in arbitrary arrangements. The resources provide the energy that is necessary for the organisms to sustain life, and can trigger different types of behaviour in the organisms, such as movement towards nutrients and away from toxic substances, growth, and the controlled release of signalling resources. The balance between energy and material is modelled carefully to ensure that the ecosystem is dissipative. Those organisms that are able to efficiently exploit the available resources gradually accumulate enough energy to reproduce (by binary fission) and generate copies of themselves in the environment. Organisms are also able to produce their own resources, which can potentially be used as markers to send signals to other organisms (a behaviour known as quorum sensing). The complex relationships between stimuli and actions in the organisms are stochastically altered by means of mutations, thus enabling the organisms to adapt to their environment and maximise their lifespan and reproductive success. In this paper, the proposed bacterial ecosystem model is defined formally and its structure is discussed in detail. This is followed by results from simulation experiments that illustrate the model's operation and how it can be used in evolutionary modelling/computing scenarios.     

Strong artificial selection in the wild results in predicted small evolutionary change

Estimates of genetic variation and selection allow for quantitative predictions of evolutionary change, at least in controlled laboratory experiments. Natural populations are, however, different in many ways, and natural selection on heritable traits does not always result in phenotypic change. To test whether we were able to predict the evolutionary dynamics of a complex trait measured in a natural, heterogeneous environment, we performed, over an 8-year period, a two-way selection experiment on clutch size in a subdivided island population of great tits (Parus major). Despite strong artificial selection, there was no clear evidence for evolutionary change at the phenotypic level. Environmentally induced differences in clutch size among years are, however, large and can mask evolutionary changes. Indeed, genetic changes in clutch size, inferred from a statistical model, did not deviate systematically from those predicted. Although this shows that estimates of genetic variation and selection can indeed provide quantitative predictions of evolutionary change, also in the wild, it also emphasizes that demonstrating evolution in wild populations is difficult, and that the interpretation of phenotypic trends requires great care.     

The evolutionary consequences of niche construction: a theoretical investigation using two-locus theory

This paper addresses the joint evolution of environment-altering (niche constructing) traits, and traits whose fitness depends on alterable sources of natural selection in environments. We explore the evolutionary consequences of this niche construction using a two-locus population genetic model. The novel conclusions are that niche construction can (1) cause evolutionary inertia and momentum, (2) lead to the fixation of otherwise deleterious alleles, (3) support stable polymorphisms where none are expected, (4) eliminate what would otherwise be stable polymorphisms, and (5) influence disequilibrium. The results suggest that the changes that organisms bring about in their niche can themselves be an important source of natural selection pressures, and imply that evolution may proceed in cycles of selection and niche construction.     

The artificial worlds approach to emergent evolution

Artificial worlds models of evolutionary systems are computer models that map the essential logical structure of ecological systems, defined as self-sustaining biological organizations. The artificial world comprises an artificial environment, with mass components, energy input, and physical states. It also comprises artificial organisms, including a genome, a phenome, and a (developmental) map that connects the genome to the phenome. Mass components are cycled and space is limited. The evolution process results, as in nature, from genetic variation combined with natural selection imposed by the finiteness of the environment. The selection criteria (fitness values) are not imposed, but rather emerge from the interactions of the organisms with each other and with the environment. The dynamics at the population level also emerges from these basic interactions. In this paper we describe the comparative properties of the EVOLVE family of artificial worlds models.