Temperature as a determinative factor in the evolution of genetic systems

Summary Heat induces a number of premutational lesions (for example, the deamination of cytosine to uracil) in DNA and RNA. These kinds of errors occur in resting as well as replicating polynucleotides. However, an increase in temperature also raises the probability of copying error occurring in nucleic acids because of increased thermal noise in the replicative machinery. In most modern genetic systems, the majority of heat-induced lesions are efficiently repaired. It follows that the importance of heat-induced error increases as the effectiveness of repair declines. We show in this paper that the error rate of enzymatic polynucleotide copying is expected to increase monotonically with temperature. We also explore the effects of temperature variations on the early evolution of biological information transmission mechanisms.     

Autonomy: an information theoretic perspective

We present a tentative proposal for a quantitative measure of autonomy. This is something that, surprisingly, is rarely found in the literature, even though autonomy is considered to be a basic concept in many disciplines, including artificial life. We work in an information theoretic setting for which the distinction between system and environment is the starting point. As a first measure for autonomy, we propose the conditional mutual information between consecutive states of the system conditioned on the history of the environment. This works well when the system cannot influence the environment at all and the environment does not interact synergetically with the system. When, in contrast, the system has full control over its environment, we should instead neglect the environment history and simply take the mutual information between consecutive system states as a measure of autonomy. In the case of mutual interaction between system and environment there remains an ambiguity regarding whether system or environment has caused observed correlations. If the interaction structure of the system is known, we define a "causal" autonomy measure which allows this ambiguity to be resolved. Synergetic interactions still pose a problem since in this case causation cannot be attributed to the system or the environment alone. Moreover, our analysis reveals some subtle facets of the concept of autonomy, in particular with respect to the seemingly innocent system-environment distinction we took for granted, and raises the issue of the attribution of control, i.e. the responsibility for observed effects. To further explore these issues, we evaluate our autonomy measure for simple automata, an agent moving in space, gliders in the game of life, and the tessellation automaton for autopoiesis of Varela et al. [Varela, F.J., Maturana, H.R., Uribe, R., 1974. Autopoiesis: the organization of living systems, its characterization and a model. BioSystems 5, 187-196].     

Thermodynamics and the conceptual structure of evolutionary theory

Thermodynamics and evolutionary theory have spent most of their shared history in adversarial relationship to one another. The point of this paper is to consider some qualitative ways in which thermodynamics can enrich both the theory and epistemology of evolution. The "autonomy of biology" posture in evolutionary theory hangs on the supposed uniqueness of why-questions in biology. With this posture, and with the general obstruction of constructive dialogue between evolution and the physical sciences it fosters, come the perennial accusations that Darwinism deals in adaptational teleology but not mechanisms. Thermodynamics provides for a two-tiered hierarchy of causation in nature in which the why-question is rendered not only legitimate materialistically, but essential to understanding the evolutionary process in its totality--from the emergence of life to the branching of lineages in speciation.     

A Universal Definition of Life: Autonomy and Open-Ended Evolution

Life is a complex phenomenon that not only requires individual self-producing and self-sustaining systems but also a historical-collective organization of those individual systems, which brings about characteristic evolutionary dynamics. On these lines, we propose to define universally living beings as autonomous systems with open-ended evolution capacities, and we claim that all such systems must have a semi-permeable active boundary (membrane), an energy transduction apparatus (set of energy currencies) and, at least, two types of functionally interdependent macromolecular components (catalysts and records). The latter is required to articulate a 'phenotype-genotype' decoupling that leads to a scenario where the global network of autonomous systems allows for an open-ended increase in the complexity of the individual agents. Thus, the basic-individual organization of biological systems depends critically on being instructed by patterns (informational records) whose generation and reliable transmission cannot be explained but take into account the complete historical network of relationships among those systems. We conclude that a proper definition of life should consider both levels, individual and collective: living systems cannot be fully constituted without being part of the evolutionary process of a whole ecosystem. Finally, we also discuss a few practical implications of the definition for different programs of research.     

Replicate after reading: on the extraction and evocation of cultural information

Does cultural evolution happen by a process of copying or replication? And how exactly does cultural transmission compare with that paradigmatic case of replication, the copying of DNA in living cells? Theorists of cultural evolution are divided on these issues. The most important objection to the replication model has been leveled by Dan Sperber and his colleagues. Cultural transmission, they argue, is almost always reconstructive and transformative, while strict ‘replication’ can be seen as a rare limiting case at most. By means of some thought experiments and intuition pumps, I clear up some confusion about what qualifies as ‘replication’. I propose a distinction between evocation and extraction of cultural information, applying these concepts at different levels of resolution. I defend a purely abstract and information-theoretical definition of replication, while rejecting more material conceptions. In the end, even after taking Sperber’s valuable and important points on board, the notion of cultural replication remains a valid and useful one. This is fortunate, because we need it for certain explanatory projects (e.g., understanding cumulative cultural adaptations).     

Life, Autonomy and Cognition: An Organizational Approach to the Definition of the Universal Properties of Life

This article addresses the issue of defining the universal properties of living systems through an organizational approach, according to which the distinctive properties of life lie in the functional organization which correlates its physicochemical components in living systems, and not in these components taken separately. Drawing on arguments grounded in this approach, this article identifies autonomy, with a set of related organizational properties, as universal properties of life, and includes cognition within this set.     

The Method of Local Restriction: in search of potential great ape culture-dependent forms

Humans possess a perhaps unique type of culture among primates called cumulative culture. In this type of culture, behavioural forms cumulate changes over time, which increases their complexity and/or efficiency, eventually making these forms culture-dependent. As changes cumulate, culture-dependent forms become causally opaque, preventing the overall behavioural form from being acquired by individuals on their own; in other words, culture-dependent forms must be copied between individuals and across generations. Despite the importance of cumulative culture for understanding the evolutionary history of our species, how and when cumulative culture evolved is still debated. One of the challenges faced when addressing these questions is how to identify culture-dependent forms that result from cumulative cultural evolution. Here we propose a novel method to identify the most likely cases of culture-dependent forms. The ‘Method of Local Restriction’ is based on the premise that as culture-dependent forms are repeatedly transmitted via copying, these forms will unavoidably cumulate population-specific changes (due to copying error) and therefore must be expected to become locally restricted over time. When we applied this method to our closest living relatives, the great apes, we found that most known ape behavioural forms are not locally restricted (across domains and species) and thus are unlikely to be acquired via copying. Nevertheless, we found 25 locally restricted forms across species and domains, three of which appear to be locally unique (having been observed in a single population of a single species). Locally unique forms represent the best current candidates for culture-dependent forms in non-human great apes. Besides these rare exceptions, our results show that overall, ape cultures do not rely heavily on copying, as most ape behaviours appear across sites and/or species, rendering them unlikely to be culture-dependent forms resulting from cumulative cultural evolution. Yet, the locally restricted forms (and especially the three locally unique forms) identified by our method should be tested further for their potential reliance on copying social learning mechanisms (and in turn, for their potential culture-dependence). Future studies could use the Method of Local Restriction to investigate the existence of culture-dependent forms in other animal species and in the hominin archaeological record to estimate how widespread copying is in the animal kingdom and to postulate a timeline for the emergence of copying in our lineage.     

Group selection of early replicators and the origin of life

A major problem of the origin of life has been that of information integration. As Eigen (1971) has shown, a mutant distribution of RNAs replicating without the aid of a replicase cannot integrate sufficient information for the functioning of a higher-level unit utilizing several types of encoded enzymes. He proposed the hypercycle model to bridge this gap in prebiology. It can be shown by a nonlinear game model, incorporating mutation of a hypercycle, that the selection properties of hypercycles make them inefficient information integrators as they cannot compete favourably with all kinds of less efficient information carriers or mutationally coupled hypercycles. The stochastic corrector model is presented as an alternative resolution of Eigen's paradox. It assumes that replicative templates are competing within replicative compartments, whose selective values depend on the internal template composition via a catalytic acid in replication and "metabolism". The dynamics of template replication are analyzed by numerical simulation of master equations. Due to the stochasticity in replication and compartment fission the best compartment types recur. An Eigen equation at the compartment level is set up and calculated. Even selfish template mutants cannot destroy the system though they make it less efficient. The genetic information of templates is evaluated at both levels, and the higher (compartment) level successfully constrains the lower (template) one. Compartmentation together with stochastic effects is sufficient to integrate information dispersed in competitive replicators. Compartment selection is considered to be group selection of replicators. Implications for the origin of life are discussed.     

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.     

Pseudocyclical similarities and structural evolution of modular organisms

It was found that pseudocyclical similarities are common in modular organisms due to the peculiarities of their morphogenesis and ontogenesis and the system specifics of the modular organization. An analysis of the structural evolution in the different groups of modular living beings according to the concept of pseudocycles is topical, as it will contribute to the further development of evolutionary morphology and theoretical biology.     

Generation of valuable information and the problem of goal self-setting in living systems

The problem of origination of capacity for goal self-setting is discussed. It was shown that the definition "goal" in living systems differs from the definition "target function" in physical problems concerned with nonliving systems. It was also shown that the main goal of the elements of a system is the storage of information. In biology, this goal is the extension of the principle of struggle for existence. Conditions were determined that the dynamic system describing the goal self-setting process must satisfy. It was shown that living systems meet these conditions. In inorganic nature, such systems may also arise but only as a result of long-term evolution, after which they become living.     

Development of asymmetry in the caenogastropods Amphissa columbiana and Euspira lewisii

Abstract. The asymmetry displayed by the body plan of gastropods has been directly or indirectly attributed to an evolutionary process called torsion. Torsion is defined as a rotation of 180° between the cephalopodium (head and foot) and visceropallium (visceral organs, mantle, mantle cavity, and shell). During development, the displacement of anatomical components occurs during a process called "ontogenetic torsion." Although ontogenetic torsion is central to theories of gastropod evolution, surprisingly few studies have documented actual tissue movements during the development of asymmetry in gastropods. We investigated the development of the mantle cavity and pleurovisceral nerve connective (visceral nerve loop) in the caenogastropods Amphissa columbiana and Euspira lewisii , because displacements of both of these structures are interpreted as major consequences of torsion. Scanning electron micrographs, histological sections, and immunofluorescence images showed that the developing vis-ceropallium twists by 90° relative to the cephalopodium, the mantle cavity initially forms on the right side, and displacements of the visceral nerve loop become evident on the left side before the right side. A developmental stage in which the mantle cavity is confined to the right side has also been reported in members of the Vetigastropoda and Heterobranchia. We suggest that further comparative studies should test the hypothesis that early development throughout the Gastropoda converges on an embryonic organization in which the mantle cavity and anus are located laterally, despite clade-specific differences in developmental patterns both before and after this stage.     

The relationship between the error catastrophe, survival of the flattest, and natural selection

Background  

The quasispecies model is a general model of evolution that is generally applicable to replication up to high mutation rates. It predicts that at a sufficiently high mutation rate, quasispecies with higher mutational robustness can displace quasispecies with higher replicative capacity, a phenomenon called "survival of the flattest". In some fitness landscapes it also predicts the existence of a maximum mutation rate, called the error threshold, beyond which the quasispecies enters into error catastrophe, losing its genetic information. The aim of this paper is to study the relationship between survival of the flattest and the transition to error catastrophe, as well as the connection between these concepts and natural selection.     

A systems-analytical approach to macro-evolutionary phenomena.

Two sets of evolutionary phenomena find no explanation through current theory. For the static phenomena (such as homology, homonomy, systematic weight, and "Type") there is no causal base, although these principles are responsible for all phenomena of predictable order in the living world. The dynamic phenomena (such as homodynamy, coadaptation, parallel evolution, orthogenesis, Cartesian transformation, typostrophy, hetermorphosis, systemic mutation, and spontaneous atavism) have no causal explanation, although they are responsible for all directed phenomena in macroevolution. These phenomena share one unifying principle which can be explained by a system theory of evolution based on, but extending, the current synthetic theory. This system theory envisages feedback conditions between genotype and phenotype by which the chances of successful adaptation increase if the genetic units, by insertion of superimposed genes, copy the functional dependencies of those phene structures for which they code. This positive feedback of the adaptive speed (or probability) within a single adaptive direction is compensated by negative feedback in most of the alternative directions. The negative feedback operates as selection not be environmental but by systemic conditions developed by the organization of the organism. The consequences are an imitatively organized system of gene interractions, the rehabilitation of classical systematics, the reality of the "natural system," and, in general, the resolution of the contradiction between neodarwinists and their critics, between reductionists and holists, between "a priori" and "a posteriori" views, between idealism and materialism, and between the notions of freedom and of purpose in evolution.     

The transition to civilization and symbolically stored genomes

The study of culture and cultural selection from a biological perspective has been hampered by the lack of any firm theoretical basis for how the information for cultural traits is stored and transmitted. In addition, the study of any living system with a decentralized or multi-level information structure has been somewhat restricted due to the focus in genetics on the gene and the particular hereditary structure of multicellular organisms. Here a different perspective is used, one which regards living systems as self-constructing energy users that utilize their genome as a library of information, making the genetic system just another component that adds fitness to the overall integrated unit. In this framework, basic fitness is measured as the ability to gather energy for growth and reproduction, and the fitness of the genetic system is broken down into two aspects: first, the effectiveness in searching for new somatic functional information, and second, the effectiveness in searching for better structures to store and process information. With this more generalized perspective, major evolutionary transitions to higher levels of organization become competitions between different information structures; furthermore the functioning and fitness of cultural systems can be more easily described and compared with other modes of information storage within biological systems. Modern technological societies are self-constructing systems that rely on written (symbolic) information storage and very complex algorithms that effectively search for variation with a high probability of successful selection. These systems are currently competing with traditional organic systems, and this competition constitutes the latest major evolutionary transition. Upon comparison of the energy-gathering potential of symbolic-based systems with DNA-based life, it appears that symbolic systems have a tremendous fitness potential and the current shift to a higher level of selection may be as significant and far-reaching as any of the previous major evolutionary transitions.     

Cultural evolution and the variable phenotype

It is common in attempts to extend the theory of evolution to culture to generalize from the causal basis of biological evolution, so that evolutionary theory becomes the theory of copying processes. Generalizing from the formal dynamics of evolution allows greater leeway in what kinds of things cultural entities can be, if they are to evolve. By understanding the phenomenon of cultural transmission in terms of coordinated phenotypic variability, we can have a theory of cultural evolution which allows us to avoid the various difficulties with the elaboration of informational entities such as the cultural replicator, or meme. Such an account is a boon to the project of evolutionary epistemology since it confirms the presumption in favor of the general adaptiveness of culture, illuminating rather than obscuring the inherent intimacy of our relationship to (e.g.) our ideas.     

Is matter inanimate?: Protobiological information from within

Biological information refers to the process of how matter informs matter through endogenous boundary conditions, exhibiting a sharp contrast to Shannon's information referring to the process of how coded messages inform a human receiver or observer. The origin and evolution of protobiological and biological information occur because prior polymeric products successively provide new boundary conditions to the subsequent production process. The transition from what looks like inanimate matter to living beings is a continuous process. The underlying mechanism is the physical process that prior products provide new boundary conditions to the subsequent production process in a successive manner. Biological information resides in perpetuating cellular production process which eventually leads to an enhancement of evolutionary specificity. Cellular units are prerequisite to biological evolution, not vice versa.     

Is matter inanimate? Protobiological information from within

Biological information refers to the process of how matter informs matter through endogenous boundary conditions, exhibiting a sharp contrast to Shannon's information referring to the process of how coded messages inform a human receiver or observer. The origin and evolution of protobiological and biological information occur because prior polymeric products successively provide new boundary conditions to the subsequent production process. The transition from what looks like inanimate matter to living beings is a continuous process. The underlying mechanism is the physical process that prior products provide new boundary conditions to the subsequent production process in a successive manner. Biological information resides in perpetuating cellular production process which eventually leads to an enhancement of evolutionary specificity. Cellular units are prerequisite to biological evolution, not vice versa.