Emergent diversity in an open-ended evolving virtual community

Understanding the dynamics of biodiversity has become an important line of research in theoretical ecology and, in particular, conservation biology. However, studying the evolution of ecological communities under traditional modeling approaches based on differential calculus requires speciesʼ characteristics to be predefined, which limits the generality of the results. An alternative but less standardized methodology relies on intensive computer simulation of evolving communities made of simple, explicitly described individuals. We study here the formation, evolution, and diversity dynamics of a community of virtual plants with a novel individual-centered model involving three different scales: the genetic, the developmental, and the physiological scales. It constitutes an original attempt at combining development, evolution, and population dynamics (based on multi-agent interactions) into one comprehensive, yet simple model. In this world, we observe that our simulated plants evolve increasingly elaborate canopies, which are capable of intercepting ever greater amounts of light. Generated morphologies vary from the simplest one-branch structure of promoter plants to a complex arborization of several hundred thousand branches in highly evolved variants. On the population scale, the heterogeneous spatial structuration of the plant community at each generation depends solely on the evolution of its component plants. Using this virtual data, the morphologies and the dynamics of diversity production were analyzed by various statistical methods, based on genotypic and phenotypic distance metrics. The results demonstrate that diversity can spontaneously emerge in a community of mutually interacting individuals under the influence of specific environmental conditions.This research was partially supported by a grant for the GENEX project (P09-TIC-5123) from the Consejería de Innovación y Ciencia de Andalucía. J.D.F. was supported by a FPU grant from the Spanish Ministerio de Educación. R.D. wishes to thank the Région Ile-de-France for supporting his research position at the Complex Systems Institute, Paris Ile-de-France

Faster than a speeding bullet, more powerful than a locomotive, able to rule by sense of smell! Superhuman Kingship in the Prophetic Books

An exploration of the Hebrew Bible's prophetic literature vis-à-vis Science Fiction and Science Fiction theor

Faster than a speeding bullet, more powerful than a locomotive, able to rule by sense of smell! Superhuman Kingship in the Prophetic Books

An exploration of the Hebrew Bible's prophetic literature vis-à-vis Science Fiction and Science Fiction theor

Non-random genome editing and natural cellular engineering in cognition-based evolution

Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alterna-tive approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a ‘harnessing of stochasticity’. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.publishersversionpublishe

Climates of Mutation: Posthuman Orientations in Twenty-First Century Ecological Science Fiction

Climates of Mutation contributes to the growing body of works focused on climate fiction by exploring the entangled aspects of biopolitics, posthumanism, and eco-assemblage in twenty-first-century science fiction. By tracing out each of those themes, I examine how my contemporary focal texts present a posthuman politics that offers to orient the reader away from a position of anthropocentric privilege and nature-culture divisions towards an ecologically situated understanding of the environment as an assemblage. The thematic chapters of my thesis perform an analysis of Peter Wattss Rifters Trilogy, Larissa Lais Salt Fish Girl, Paolo Bacigalupis The Windup Girl, and Margaret Atwoods MaddAddam Trilogy. Doing so, it investigates how the assemblage relations between people, genetic technologies, and the environment are intersecting in these posthuman works and what new ways of being in the world they challenge readers to imagine. This approach also seeks to highlight how these works reflect a genre response to the increasing anxieties around biogenetics and climate change through a critical posthuman approach that alienates readers from traditional anthropocentric narrative meanings, thus creating a space for an embedded form of ecological and technoscientific awareness. My project makes a case for the benefits of approaching climate fiction through a posthuman perspective to facilitate an environmentally situated understanding. By mapping the aspects of bare life, posthuman becomings, multispecies community, and environmental agency that situate these texts within their climate-focused twenty-first-century contexts, my dissertation models its own series of entanglements. It also reveals areas of concern that include infectious agencies, subversions of biopolitical containment, and the co-constitutive transformative powers of the environment and nonhuman life. Climates of Mutation addresses the ways that these contemporary science fiction narratives have responded to cultural and scientific developments to invite critical engagement from readersespecially in terms of embracing concepts of environmental assemblage and imagining potential multispecies futures. By taking an assemblage approach to these works of posthuman ecological science fiction, my project draws attention to how they critically subvert anthropocentrism by privileging nonhuman and environmental agencies in which humans are an entangled part of biopolitical forces, multispecies collectives, and ecological assemblages

Cinema and commercial space tourism:The politics of escapism

Space tourism has been one of the most enduring tropes in the cinema from the early 1900s until the present day, yet there exists no systematic, comprehensive investigation situating these widely diversified depictions of space tourism within a broader historical context of technological innovation and associated social transformation. The contemporary social climate, whereby commercial space tourism is an emergent possibility, calls for the decolonisation of the term ‘tourism’ and its categorical associations, in order to assess how visions of space tourism within cinematic, science-fiction futures project the history of tourism and its detrimental environmental, commercial, and colonial implications. The written portion of the dissertation uses close-textual-analysis and discursive transcoding as the primary methodologies to identify and investigate five unique trends in the thematic representation of cinematic space tourism, each linked to a distinct ‘moment’ of widespread crisis and transformation. Ultimately, this will contribute to a broader understanding concerning how science-fiction explores social constructions of race, class, and gender. As a practice-based accompaniment to these critical discussions, I relay my findings in a space film which compiles knowledge drawn from film and literature scholarship, as well as from the analysis of the selected case studie

RNA, the Epicenter of Genetic Information

The origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information. Key Features Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other. Integrates the influences of biochemistry and genetics on the landscape of molecular biology. Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress. Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA. Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology. Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers

De novo evolution of genetic function from random sequences

The study of de novo gene birth has opened the doors for evolutionary biologists to approach old questions about the origin of innovation from new perspectives. There are still many questions about what makes a functional gene, how likely it is for a non-coding sequence to become one, how common is this phenomenon in nature, and how do novel genes become essential for an organism. In this thesis, I present three projects that aim to explore some of these questions. In chapter 1, I revisit a study published in 2017 that used a library of random sequences in E. coli, in order to quantify the likelihood that a random sequence expressed in a cell provides a fitness advantage. I successfully replicated these results, and I improved the analysis pipeline to examine sequences in greater depth. I confirmed that expression of random DNA sequences is well tolerated by E. coli, and found that sequence length is a determinant factor of its effect on fitness. In chapter 2, I transferred the random sequence experiment to a eukaryotic model to determine what proportion of random sequences are well tolerated by eukaryotic cells despite the different complexity. The results indicate that eukaryotic cells are at least as tolerant to the expression of random sequences as bacteria. However, no specific feature of the sequences correlated with their tolerability. Finally, in chapter 3, I expressed three putative de novo genes identified in mouse in a human cell line. The selected genes are taxonomically restricted to species of mice, with transcription and proteomic evidence. Interestingly, expression of the novel genes had little effect on the transcriptome of the cells. The results presented in this thesis add to the mounting evidence that cells are much more tolerant to the expression of new sequences than previously thought. This insight generates new questions about the birth of genes that should be explored in the future

De novo evolution of genetic function from random sequences

The study of de novo gene birth has opened the doors for evolutionary biologists to approach old questions about the origin of innovation from new perspectives. There are still many questions about what makes a functional gene, how likely it is for a non-coding sequence to become one, how common is this phenomenon in nature, and how do novel genes become essential for an organism. In this thesis, I present three projects that aim to explore some of these questions. In chapter 1, I revisit a study published in 2017 that used a library of random sequences in E. coli, in order to quantify the likelihood that a random sequence expressed in a cell provides a fitness advantage. I successfully replicated these results, and I improved the analysis pipeline to examine sequences in greater depth. I confirmed that expression of random DNA sequences is well tolerated by E. coli, and found that sequence length is a determinant factor of its effect on fitness. In chapter 2, I transferred the random sequence experiment to a eukaryotic model to determine what proportion of random sequences are well tolerated by eukaryotic cells despite the different complexity. The results indicate that eukaryotic cells are at least as tolerant to the expression of random sequences as bacteria. However, no specific feature of the sequences correlated with their tolerability. Finally, in chapter 3, I expressed three putative de novo genes identified in mouse in a human cell line. The selected genes are taxonomically restricted to species of mice, with transcription and proteomic evidence. Interestingly, expression of the novel genes had little effect on the transcriptome of the cells. The results presented in this thesis add to the mounting evidence that cells are much more tolerant to the expression of new sequences than previously thought. This insight generates new questions about the birth of genes that should be explored in the future