Emergence in complex systems based on synthetic replicators

Biopolymers with defined recognition pattern were used to generate the first artificial replicating systems. Stripping down these systems to their most fundamental properties allowed to move away from the biological origins to construct replicators consisting of simple organic molecules. These systems have proven highly instructive for the in-depth understanding of the main requirements for the targeted development of efficient replicators. With this knowledge at hand, it is now possible to combine several replicators for the formation of molecular networks, and to use the unique properties of replication to manipulate these networks by external stimuli. In the thesis presented, the investigation of a family of self-replicators culminated in the successful construction of several examples of a multicyclic system in which four building blocks are able to react via two autocatalytic and two reciprocal pathways. Owing to the connectivity in this reaction system, it was demonstrated that its outcome can be influenced in a programmable manner by the addition of informational template. Some of the responses can be deduced directly from the functioning of the individual systems, others however are to be classified as emergent properties of the network. Upon elucidation of the multicyclic systems, it became apparent that working in closed reaction systems puts intrinsic boundaries on the possibility to bias the outcome of the reaction network. This limitation prevented the extinction of the inferior type of replicators even under highly unfavourable conditions and instead always led to coexistence for all species

Institutional change, institutional isolation and biodiversity governance in South Africa: a case study of the trout industry in alien and invasive species regulatory reforms

The world, in recent decades, has witnessed an incalculable surge in global “wicked” policy problems that have long-term, and most often irreversible, impacts, not least terrorism, climate change, biodiversity losses and desertification. Wicked problems are wicked because there is no single epistemological system that can adequately coordinate policy action for addressing them. Literature abounds with international case studies of opposition to national institutions that are designed to put into effect global and regional policies for resolving wicked problems. This raises questions about what constitutes reasonable institutions, how such institutions can be designed and why societies sometimes fail to develop such institutions despite the obvious need for them. As a point of entry into these issues, the thesis adapted and extended the Northean (2007, 2012) macro meta-theoretic framework for studying the violence-development relationship, which focuses on the role of political and economic competition in the emergence of ‘right’ institutions that promote development, while containing violence. The Northean framework conceptualises two mutually exclusive social orders – the limited access order and the open access order – which provide the socio-cultural context for the evolution of specific institutions. The macro meta-theoretic framework was transformed into a micro metatheoretic framework in such a way that the limited access order and the open access order co-existed in the evolution of specific institutions. This reconceptualisation built on Bromley’s (2004, 2006) two realms of public policy: the realm of reasons (legislative-judicial system) and the realm of rules (administrative system) as well as the feminist concept of epistemic violence, which broadened the concept of violence from being exclusively physical to including the sociocognitive. The feminist concept of epistemic oppression logically fitted into, and became a new sub-category of, Commons’ (1899, 1924, 1934) theories of sovereignty and negotiational psychology. The innovations showed that either of these realms can be a limited access order, while the other can be an open access order or both can be open access orders or both can be limited access orders. The conceptual innovations were then used as an interpretive scheme in analysing the evolution of the South African invasive alien species regulatory reforms under the National Environmental Management: Biodiversity Act of 2004, using a case study of the trout sector, which was the most opposed to the reforms. There was a general perception among socioeconomic sectors that utilise invasive alien species that the regulatory reform processes for the governance of such species had institutionally isolated the sectors. Because of this perception, the regulatory reform process was contested, and implementation of the Fifth Chapter of the Act, which deals with the governance of invasive alien species, was delayed for nearly a decade. The thesis evaluated whether institutional isolation existed and how and why it came to be since it has implications for the reasonableness of emerging regulatory institutions, economic performance of sectors and efficient allocation of fiscal resources in institutional design processes. A mixed methods methodology was used, which included data analysis techniques such as semiosis, exploratory factor analysis, econometric estimation and document analysis. Policy documents, an online survey and key informant interviews comprised the data. The findings suggested six dimensions of institutional change that a theory of institutional change might have to address: the origin and continuity of pecuniary institutions; selfreinforcing mechanisms of the limited access policymaking order; succession and disbandment of the limited access policymaking order; exclusivity of negotiations in institutional design; tiers of institutional isolation; and the role of administrative discontinuities. Findings suggested that institutional isolation existed in the regulatory process, manifesting in three forms: administrative isolation, epistemological isolation and sectoral isolation. Administrative isolation was the most complex of the three in that it also involved a less obvious process of institutional isolation in the form of administrative redefinition of opportunity sets that were already legislatively redefined. The mechanisms of institutional isolation through which administrative isolation was sustained were administrative financing of research and careerism. The two mechanisms created a revolving door-type scenario through which invasion biologists supplied the administrative agency with candidates for senior (decision making) positions and the administrative agency, in turn, demanded specific types of knowledge over which the same epistemic community had a monopoly. The revolving door-type scenario was found to ideologically and physically entrench invasion biologists into the regulatory community. The consequence of the entrenchment was institutional hegemony, which manifested itself through the mechanism of epistemic violence insofar as the invasion biologists became the epistemic arbiters about what kinds of ideas and institutions really mattered in the governance of invasive alien species. Econometric estimates suggested that the extent to which an emerging institution is perceived to be reasonable by regulated sectors depends on the extent to which the institution is designed in a participatory and inclusive manner (that is, using integrative knowledge systems), the extent to which the designers used credible evidence and contextualised international evidence as well as the extent to which the emergent biodiversity governance institution was anthropocentric. However, findings suggested that the South African regulatory reform process fell short on all these four dimensions of reasonable institutions, which is characteristic of institutional design process shaped by hegemonic social imaginaries, resulting in institutional isolation. Emerging from the findings are several theoretical insights. Bush’s (1987) concept of institutional spaces under the Veblenian Dichotomy was extended, the result of which was identification of two stable institutional equilibria – one ceremonial and another instrumental. The ceremonial equilibrium was a typical limited access policymaking order and was responsible for the historical and present emergence of regressive institutions. Findings also suggested that the entrenched invasion biologists ceremonially encapsulated the knowledge fund that had been accumulated since the 1980s, which could have facilitated the consensual design of regulatory institutions for invasive alien species without protracted controversy. Findings suggested that a limited access policymaking order could only be disbanded by the intervention of an external sovereign agent (in this case the office of the state president) since the administrative agency, and the epistemic community that advised it, adopted the solutions that were empirically tested and proposed in the 1980s only after the intervention of the external sovereign agent. The instrumental equilibrium repealed the contested prisoner’s dilemma that was characteristic of the policy process and turned it into an assurance policy game by facilitating the identification of common interests. This finding logically links the study to a recent theoretical development in institutional theory – Ordonomics – which focuses on the causality between ideas and institutions. The findings imply that it is possible to design reasonable institutions as long as integrative (transdisciplinary) knowledge systems, including the non-scientific knowledge of the resource users, are incorporated. Integrative knowledge systems facilitate semantic innovations, which create social DNA, but epistemic violence destroys social DNA. They also imply that reliance on unidisciplinary knowledge systems in institutional design induces a large and inefficient transaction cost burden of public policy on the fiscus and private agents alike because of the inevitability of controversy, especially for wicked policy problems

Music in Evolution and Evolution in Music

Music in Evolution and Evolution in Music by Steven Jan is a comprehensive account of the relationships between evolutionary theory and music. Examining the ‘evolutionary algorithm’ that drives biological and musical-cultural evolution, the book provides a distinctive commentary on how musicality and music can shed light on our understanding of Darwin’s famous theory, and vice-versa. Comprised of seven chapters, with several musical examples, figures and definitions of terms, this original and accessible book is a valuable resource for anyone interested in the relationships between music and evolutionary thought. Jan guides the reader through key evolutionary ideas and the development of human musicality, before exploring cultural evolution, evolutionary ideas in musical scholarship, animal vocalisations, music generated through technology, and the nature of consciousness as an evolutionary phenomenon. A unique examination of how evolutionary thought intersects with music, Music in Evolution and Evolution in Music is essential to our understanding of how and why music arose in our species and why it is such a significant presence in our lives

The Origin and Early Evolution of Life

What is life? How, where, and when did life arise? These questions have remained most fascinating over the last hundred years. Systems chemistry is the way to go to better understand this problem and to try and answer the unsolved question regarding the origin of Life. Self-organization, thanks to the role of lipid boundaries, made possible the rise of protocells. The role of these boundaries is to separate and co-locate micro-environments, and make them spatially distinct; to protect and keep them at defined concentrations; and to enable a multitude of often competing and interfering biochemical reactions to occur simultaneously. The aim of this Special Issue is to summarize the latest discoveries in the field of the prebiotic chemistry of biomolecules, self-organization, protocells and the origin of life. In recent years, thousands of excellent reviews and articles have appeared in the literature and some breakthroughs have already been achieved. However, a great deal of work remains to be carried out. Beyond the borders of the traditional domains of scientific activity, the multidisciplinary character of the present Special Issue leaves space for anyone to creatively contribute to any aspect of these and related relevant topics. We hope that the presented works will be stimulating for a new generation of scientists that are taking their first steps in this fascinating field

The developmental, physiological, neural, and genetical causes and consequences of frequency-dependent selection in the wild.

Abstract We outline roles of frequency-dependent selection (FDS) in coadaptation and coevolutionary change. Coadaptation and coevolution occur because correlational selection (CS) and correlated evolution couple many traits. CS arises from causal interactions between traits expressed in two or more interactors, which invariably involve different traits (signalers-receivers). Thus, the causes of CS are due to FDS acting on trait interactions. Negative FDS, a rare advantage, is often coupled to positive FDS generating complex dynamics and FD cycles. Neural mechanisms of learning and perception create analogous routes by which traits are reinforced in cognitive and perceptual systems of interactors, substituting for positive FDS. FDS across all levels of biological organization is thus best understood as proximate causes that link interactors and shape genetic correlations within and among interactors on long timescales, or cognitive trait correlations within interactors on short timescales. We find rock-paper-scissors dynamics are common in nature

Can culture be considered in continuity with natural evolution? : susan blackmore’s memtic approach and its critiques

This work is about cultural evolution. Memetics and particularly Susan Blackmore’s memetic approach is examined as an example of a Darwinian Theory of cultural evolution. It is questioned whether Susan Blackmore’s account of cultural evolution has original insights and whether this account is sufficient for explaining the phenomenon of culture. Her account is examined theoretically and conceptually. This dissertation consists of four main parts. In the first part, the forerunners and the background of Susan Blackmore are outlined. In the second part, key points of Susan Blackmore’s memetic approach are summarized. The third part is devoted to criticisms of Susan Blackmore’s memetic approach from within the memetics and some of the shortcomings of it are reviewed. Finally, coherency of this memetic approach is evaluated in the perspective of social sciences and its implications for cultural studies are discussed. It is concluded that Blackmore’s theory of cultural evolution that takes gene-based evolution as a model has a number of shortcomings to shed a proper light on the matter of culture. Key words: Evolution, cultural evolution, memetics, Susan Blackmore, culture, imitation, genes, memes.ABSTRACT!...............................................................................................................................!iii! ÖZ!...............................................................................................................................................!iv! ACKNOWLEDGEMENTS!.........................................................................................................!v! TABLE!OF!CONTENTS!...........................................................................................................!vi! INTRODUCTION!......................................................................................................................!8! CHAPTER!1!.............................................................................................................................!14! THE!FORERUNNERS!OF!SUSAN!BLACKMORE’S!MEMETIC!APPROACH!...............!14! 1.1.!Memetics:!A!Darwinian!Theory!on!Culture!..................................................................!14! 1.2.!The!Father!of!Memetics:!Richard!Dawkins!..................................................................!20! 1.3.!Philosopher!of!Memetics:!Daniel!Dennett!....................................................................!29! CHAPTER!2!.............................................................................................................................!38! THE!PRESENTER!OF!MEMETICS:!SUSAN!BLACKMORE!............................................!38! 2.1.!Universal!Darwinism:!The!Theory!of!Everything!......................................................!38! 2.2.!Actors!of!Darwinian!Scenario:!Replicators!..................................................................!40! 2.3.!Genes!or!Memes?!The!Relationship!of!the!Two!Replicators!..................................!42! 2.4.!Imitation:!Crucial!Point!for!Defining!Memes!...............................................................!45! 2.5.!What!is!Copying!in!Imitation?:!Copy\the\product!or!copy\the!instruction!.......!47! 2.6.!Technical!Problems!with!Memes!....................................................................................!49! 2.7.!The!Problems!To!Which!Memetics!Offers!Solutions!.................................................!52! 2.7.1.!Why!we!have!big!brains!...............................................................................................................!52! 2.7.2.!The!Problem!of!the!Origin!of!Language!.................................................................................!55! 2.7.3.The!Problem!of!Diversity!of!Sexual!Behavior!In!Modern!Times!.................................!57! 2.7.4.!The!Problem!of!Darwinian!Explanation!of!Altruism!.......................................................!59! 2.8.!Memeplexes:!Religion!and!the!Problem!of!Self!is!Explained!.................................!61! CHAPTER!3:!............................................................................................................................!67! THE!CRITICISMS!OF!SUSAN!BLACKMORE’S!MEMETIC!APPROACH!FROM! WITHIN!MEMETICS!.............................................................................................................!67! 3.!1.!Behaviorist!Criticisms!........................................................................................................!73! 3.2.!Mentalist!Criticisms!.............................................................................................................!79! 3.3.!Critiques!on!the!Way!of!Transmission,!or!Doubts!About!Imitation!.....................!88! 3.!4.!Anthropocentric!Bias!.........................................................................................................!94! 3.5.!Methodological!Problems!..................................................................................................!97! CHAPTER!4:!.........................................................................................................................!104! CRITIQUES!OF!SUSAN!BLACKMORE’S!MEMETIC!APPROACH!FROM!OUTSIDE!OF! MEMETICS:!Four!Possible!Critiques!...........................................................................!104! 4.1.!Anthropological!Criticism:!The!matter!of!culture!..................................................!105! 4.2.!Metaphysical!criticism:!The!Problem!of!Analogy!...................................................!115! 4.3.!Discursive!criticism:!The!Ideology!of!Third!Culture!..............................................!123! 4.4.!Philosophical!Criticism:!The!Specter!of!Plato!..........................................................!133! CONCLUSION!.......................................................................................................................!144! REFERENCES:!......................................................................................................................!153

Systems protobiology:Origin of life in lipid catalytic networks

Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systemstextemdashhallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin