A New Replicator: A theoretical framework for analysing replication

<p>Abstract</p> <p>Background</p> <p>Replicators are the crucial entities in evolution. The notion of a replicator, however, is far less exact than the weight of its importance. Without identifying and classifying multiplying entities exactly, their dynamics cannot be determined appropriately. Therefore, it is importance to decide the nature and characteristics of any multiplying entity, in a detailed and formal way.</p> <p>Results</p> <p>Replication is basically an autocatalytic process which enables us to rest on the notions of formal chemistry. This statement has major implications. Simple autocatalytic cycle intermediates are considered as non-informational replicators. A consequence of which is that any autocatalytically multiplying entity is a replicator, be it simple or overly complex (even nests). A stricter definition refers to entities which can inherit acquired changes (informational replicators). Simple autocatalytic molecules (and nests) are excluded from this group. However, in turn, any entity possessing copiable information is to be named a replicator, even multicellular organisms. In order to deal with the situation, an abstract, formal framework is presented, which allows the proper identification of various types of replicators. This sheds light on the old problem of the units and levels of selection and evolution. A hierarchical classification for the partition of the replicator-continuum is provided where specific replicators are nested within more general ones. The classification should be able to be successfully applied to known replicators and also to future candidates.</p> <p>Conclusion</p> <p>This paper redefines the concept of the replicator from a bottom-up theoretical approach. The formal definition and the abstract models presented can distinguish between among all possible replicator types, based on their quantity of variable and heritable information. This allows for the exact identification of various replicator types and their underlying dynamics. The most important claim is that replication, in general, is basically autocatalysis, with a specific defined environment and selective force. A replicator is not valid unless its working environment, and the selective force to which it is subject, is specified.</p

Memetic Science: I-General Introduction

Memetic Science is the name of a new field that deals with the quantitativeanalysis of cultural transfer.The units of cultural transfer are entities called "memes". In a nutshell, memes are to cultural and mental constructs as genesare to biological organisms. Examplesof memesare ideas,tunes, fashions, and virtuallyany culturaland behavioral unit that gets copiedwitha certaindegree of fidelity. It is arguedthat the under standing of memes is of similar importance and consequence as the understanding of processes involving DNA and RNA in molecular biology.Thispaperpresentsa rigorousfoundation fordiscussion ofmemes and approaches to quantifying relevantaspects of memegenesis, inter action, mutation, growth,deathand spreadingprocesses. It is also argued inthispaper that recombinant memetics is possible incomplete analogy to recombinant DNA/ genetic engineering. Special attention is paid to memes in written modern English

Graphagos: evolutionary algorithm as a model for the creative process and as a tool to create graphic design products

Evolution is a substrate-neutral algorithm that creates design, working with three conditions: replication, variation, and selection. The memetic theory posits that elements of human culture are subject to the algorithm of evolution as the memes that code for them are replicated, varied and selected. Within this paradigm, human creativity can be explained as an evolutionary process within the brain where random variations are unconsciously selected in milliseconds. Digital evolutionary algorithms are being used today to create design and to solve optimization problems. Graphic design, due to its functional nature, has the potential to be a very fruitful area of research and application for evolutionary algorithms. Gráphagos uses genetic algorithms to randomly mutate and replicate the designs according to a human user's evaluation. The program is primarily designed as a model for the creative process occurring in the system that consists of the graphic designer and the sketching medium. Gráphagos demonstrates how graphic design can emerge when random mutations are selected and accumulated. The program additionally offers a new tool for making graphic design. It may also be used as a tool for gathering data about our visual preferences

Design and Characterisation of a Novel Artificial Life System Incorporating Hierarchical Selection

In this thesis, a minimal artificial chemistry system is presented, which is inspired by the RNA World hypothesis and is loosely based on Holland's Learning Classier Systems. The Molecular Classier System (MCS) takes a bottom-up, individual-based approach to building artificial bio-chemical networks. The MCS has been developed to demonstrate the effects of hierarchical selection. Hierarchical selection appears to have been critical for the evolution of complexity in life as we know it yet, to date, no computational artificial life system has investigated the viability of using hierarchical selection as a mechanism for achieving qualitatively similar results. Hierarchy in MCS is enforced by constraining artificial molecules, which are modeled as individuals, to exist within externally provided containers - protocells. This research is focused on the period of time surrounding the conjectured first Major Transition - from individual replicating molecules to populations of molecules existing within cells. Protocells can be thought of as simplified versions of contemporary biological cells. Molecular replication within these protocells causes them to grow until they undergo a process of binary fission. Darwinian selection is continuously and independently applied at both the molecular level and the protocell level. Experimental results are presented which display the phenomenon of selectional stalemate where the selectional pressures are applied in opposite directions such that they meet in the middle. The work culminates with the presentation of a stable artificial protocell system which is capable of demonstrating ongoing evolution at the protocell level via hierarchical selection of molecular species. Supplementary results are presented in the Appendix material as a set of experiments where selectional pressure is applied at the protocell level in a manner that indirectly favours particular artificial bio-chemical networks at the molecular level. It is shown that a molecular trait which serves no useful purpose to the molecules when they are not contained within protocells is exploited for the benefit of the collective once the molecules are constrained to live together. It is further shown that through the mechanism of hierarchical selection, the second-order effects of this molecular trait can be used by evolution to distinguish between protocells which contain desirable networks, and those that do not. A treatment of the computational potential of such a mechanism is presented with special attention given to the idea that such computation may indeed form the basis for the later evolution of the complicated Cell Signaling Pathways that are exhibited by modern cells

‘The uses of ethnography in the science of cultural evolution’. Commentary on Mesoudi, A., Whiten, A. and K. Laland ‘Toward a unified science of cultural evolution’

There is considerable scope for developing a more explicit role for ethnography within the research program proposed in the article. Ethnographic studies of cultural micro-evolution would complement experimental approaches by providing insights into the “natural” settings in which cultural behaviours occur. Ethnography can also contribute to the study of cultural macro-evolution by shedding light on the conditions that generate and maintain cultural lineages

Artificial and Natural Genetic Information Processing

Conventional methods of genetic engineering and more recent genome editing techniques focus on identifying genetic target sequences for manipulation. This is a result of historical concept of the gene which was also the main assumption of the ENCODE project designed to identify all functional elements in the human genome sequence. However, the theoretical core concept changed dramatically. The old concept of genetic sequences which can be assembled and manipulated like molecular bricks has problems in explaining the natural genome-editing competences of viruses and RNA consortia that are able to insert or delete, combine and recombine genetic sequences more precisely than random-like into cellular host organisms according to adaptational needs or even generate sequences de novo. Increasing knowledge about natural genome editing questions the traditional narrative of mutations (error replications) as essential for generating genetic diversity and genetic content arrangements in biological systems. This may have far-reaching consequences for our understanding of artificial genome editing

Language Evolution as a Darwinian Process: Computational Studies

This paper presents computational experiments that illustrate how one can precisely conceptualize language evolution as a Darwinian process. We show that there is potentially a wide diversity of replicating units and replication mechanisms involved in language evolution. Computational experiments allow us to study systemic properties coming out of populations of linguistic replicators: linguistic replicators can adapt to specific external environments; they evolve under the pressure of the cognitive constraints of their hosts, as well as under the functional pressure of communication for which they are used; one can observe neutral drift; coalitions of replicators may appear, forming higher level groups which can themselves become subject to competion and selection