Here, I introduce a concept called autonomous selection to refer to a source of selection that is part of the individuals upon which it acts. The concept is motivated by a set of phenomena with the following characteristics: Natural selection shaped a variant (e.g., gene, epigenetic mark, or combination thereof) to act in a manner that reduces the frequency of one or more heritable traits of the individual in which it is located if those traits are detrimental to individual or group fitness. Phenomena with these characteristics are peculiar to traditional evolutionary theory but have been identified rather frequently in recent decades. They are also relevant to adaptive evolution: By reducing the frequency of a trait detrimental to fitness, the variant accelerates the evolution of adaptations, which allows its holders to adapt better to constantly changing environments. The variant is shaped by (natural) selection, but also does (autonomous) selection. Several phenomena with these characteristics have been invoked by proponents of the extended evolutionary synthesis (EES). The concept of autonomous selection helps resolve some of the controversy surrounding the EES: EES proponents call attention to the incompleteness of contemporary theory, emphasizing individuals’ processes that influence which adaptations those individuals evolve. I argue for the special importance of individuals’ processes that do not just influence those individuals’ adaptations, but also accelerate the adaptive evolution of those individuals. All known phenomena that fit this description are examples of autonomous selection. Other phenomena raised by EES proponents do not meet this threshold.

Animals, with their complex and obligate multicellularity, evolved from microbial eukaryotes that were likely obligately or facultatively unicellular. The nature of the unicellular progenitors of animals has intrigued biologists since the late 19^th century, coinciding with the parallel spread of the cell theory and the theory of evolution. However, views on the ancestry of animals have been extremely varied. The huge diversity of single-celled organisms, the tremendous plasticity of animal cellular phenotypes, and the difficulties of organizing both into clear phylogenies in the pre-molecular era allowed a wide range of hypotheses to flourish, with nearly every major single-celled lineage, at one time or another, having been proposed as the precursor of animals. Most of these hypotheses never gained followers beyond their originator (such as the ideas that animals evolved directly from either bacteria, Volvox or fungi) and will not be discussed here. Three concepts, however, have been enduring and influential: (1) the amoeboid theory; (2) the flagellate theory; and the (3) the ciliate theory – to which a fourth category can now be added: (4) a mixed model, in which the ancestor was phenotypically plastic. We will discuss their origin, history, and current relevance.

Deep learning has taken over - both in problems beyond the realm of traditional, hand-crafted machine learning paradigms as well as in capturing the imagination of the practitioner sitting on top of petabytes of data. While the public perception about the efficacy of deep neural architectures in complex pattern recognition tasks grows, sequentially up-to-date primers on the current state of affairs must follow. In this review, we seek to present a refresher of the many different stacked, connectionist networks that make up the deep learning architectures followed by automatic architecture optimization protocols using multi-agent approaches. Further, since guaranteeing system uptime is fast becoming an indispensable asset across multiple industrial modalities, we include an investigative section on testing neural networks for fault detection and subsequent mitigation. This is followed by an exploratory survey of several application areas where deep learning has emerged as a game-changing technology - be it anomalous behavior detection in financial applications or financial time-series forecasting, predictive and prescriptive analytics, medical imaging, natural language processing or power systems research. The thrust of this review is on outlining emerging areas of application-oriented research within the deep learning community as well as to provide a handy reference to researchers seeking to embrace deep learning in their work for what it is: statistical pattern recognizers with unparalleled hierarchical structure learning capacity with the ability to scale with information.

Genes and gene trees have been extensively used to study the evolutionary relationships among populations, species, families and higher systematic clades of organisms. This brought modern Biology into a sophisticated level of understanding about the evolutionary relationships and diversification patterns that happened along the entire history of organismal evolution in Earth. Genes however have not been placed in the center of questions when one aims to unravel the evolutionary history of genes themselves. Thus, we still ignore whether Insulin share a more recent common ancestor to Hexokinase or DNA polymerase. This brought modern Genetics into a very poor level of understanding about sister group relationships that happened along the entire evolutionary history of genes. Many conceptual challenges must be overcome to allow this broader comprehension about gene evolution. Here we aim to clear the intellectual path in order to provide a fertile research program that will help geneticists to understand the deep ancestry and sister group relationships among different gene families (or orthologs). We aim to propose methods to study gene formation starting from the establishment of the genetic code in pre-cellular organisms like the FUCA (First Universal Common Ancestor) until the formation of the highly complex genome of LUCA (Last UCA), that harbors hundreds of genes families working coordinated into a cellular organism. The deep understanding of ancestral relationships among orthologs will certainly inspire biotechnological and biomedical approaches and allow a deep understanding about how Darwinian molecular evolution operates inside cells and before the appearance of cellular organisms.

Three different fields intersect in search of an understanding of the point-of-origin of modern-age diseases: 1) D-amino acids and their role under stress conditions; 2) evolutionary origin of the mitochondrion organelle in the eukaryotic cell; and 3) gut microbiota and human healthHere it is first suggested that D-amino acids function as universal signaling agents, after having evolved as prokaryotic communication, part of an organic communication process that governs the basic activities of all the cells and coordinates cell action.Mitochondria (symbiotic prokaryotic organelles), are creative source of D-amino acids as signaling agents in the central nervous system and in the neuroendocrine systems.Amino acids racemases catalyzes the conversion between the L-enantiomers ( protein building blocks) into D-enantiomers (signaling agents).It is suggested that hectic modern life may affect human health by causing stress to the gut microbiota. These affected, gut microbiota then secrete D-amino acids that enter the blood stream, as signaling agents, causing communication errors in the central nervous system, and in the neuroendocrine systems due to excessive quantity of D-amino acids.Treating gut microbiota with inhibitors of amino acids racemases or finding D-amino acid scavengers may be used in developing novel therapeutic strategies for diseases related to the central nervous system and neuroendocrine systems caused by stressed gut microbiota.

In this paper, we look at how Artificial Swarm Intelligence can evolve using evolutionary algorithms that try to minimize the sensory surprise of the system. We will show how to apply the free-energy principle, borrowed from statistical physics, to quantitatively describe the optimization method (sensory surprise minimization), which can be used to support lifelong learning. We provide our ideas about how to combine this optimization method with evolutionary algorithms in order to boost the development of specialized Artificial Neural Networks, which define the proprioceptive configuration of particular robotic units that are part of a swarm. We consider how optimization of the free-energy can promote the homeostasis of the swarm system, i.e. ensures that the system remains within its sensory boundaries throughout its active lifetime. We will show how complex distributed cognitive systems can be build in the form of hierarchical modular system, which consists of specialized micro-intelligent agents connected through information channels. We will also consider the co-evolution of various robotic swarm units, which can result in development of proprioception and a comprehensive awareness of the properties of the environment. And finally, we will give a brief outline of how this system can be implemented in practice and of our progress in this area.

To cope with a projected global population increase from 7.2 bn to 9.6 bn by 2050, many more cities must be built. Although there are great benefits to modern urban living, there also great costs, such as the seemingly unstoppable rise in Type 2 diabetes, obesity, coronary issues and various cancers. The new towns should be designed to contain or constrain the epidemic of those ‘Western Lifestyle Diseases’ that currently plagues today’s cities. But how might this be achieved? It is suggested here that a greater understanding of human evolution combined with the potency of the ‘Palaeolithic genome’ holds the key to our future urban wellbeing. Consequently, a new paradigm is suggested that underpins positive forward thinking on townplanning and city lifestyles to create healthier urban environments. This builds directly on the ‘Evolutionary Determinants of Health’ programme initiated at University College London (UCL). A four-stage model is proposed that integrates and develops both evolutionary-concordant personal and institutional health behaviours with appropriately reconfigured town-planning and building regulations. When integrated, these strands could deliver a healthier urban culture within greened, active townscapes by proactively constraining or eliminating some of the key underlying causes of the so-called ‘Western Lifestyle Diseases’.

Beer is a fermented beverage with a history as old as human civilization and its productive process has been spread all around the world becoming unique in every country and iconic of entire populations. Ales and lagers are by far the most common beers; however, the combination of raw materials, manufacture techniques and aroma profiles are almost infinite, so it is not surprising to notice that there is a large amount of different beer styles, each of them with unique characteristics. Nowadays, diversification is becoming increasingly important in the brewing market and the brewers are continuously interested in improving and extending the already wide range of products, especially in craft brewery. One of the major components that can have a deep impact on the final product is yeast, since it is able to convert carbohydrates in wort, especially maltose and maltotriose, into ethanol, carbon dioxide and other minor aroma-active compounds. Saccharomyces cerevisiae (top‐fermenting yeasts used to produce ales) and Saccharomyces pastorianus (cryotolerant bottom‐fermenting hybrids between S. cerevisiae and Saccharomyces eubayanus responsible for the fermentation of lagers) are most used in breweries. However, an increasing number of different yeast starter cultures are commercially available, to improve the production efficiency also at relative low temperatures and to obtain desirable and diversified aroma profiles avoiding undesired compounds. Four main genetic engineering-free trends are becoming popular in craft brewing yeast development: 1) the research for novel reservoirs as source of new performant S. cerevisiae yeasts; 2) the creation of synthetic hybrids between S. cerevisiae and Saccharomyces non-cerevisiae in order to mimic lager yeasts by expanding their genetic background; 3) the exploitation of evolutionary engineering approaches; 4) the usage of non-Saccharomyces yeasts either in co-coculture or in sequential fermentation with S. cerevisiae. In the present work we summarized pro and contra of these approaches and provided an overview on the most recent advances on how brewing yeast genome evolved and domestication took place. Finally, we delineated how the correlations maps between genotypes and relevant brewing phenotypes can assist and further improve the search for novel craft beer starter yeasts.

Cooperation is widely recognized to be challenging for the well-balanced development of human societies. The emergence of cooperation in populations has been largely studied in the context of the Prisoner's Dilemma game, where temptation to defect and fear to be betrayed by others often activate defective strategies. In this paper we analyze the decision making mechanisms fostering cooperation in the two-strategy Stag-Hunt and Chicken games, which include the mixed strategy Nash equilibrium, describing partially cooperative behavior. We find the conditions for which cooperation is asymptotically stable in both full and partial cases, and we show that the partially cooperative steady state is also globally stable in the simplex. Furthermore, we show that the last can be more rewarding than the first, thus making the mixed strategy effective, although people cooperate at a lower level with respect to the maximum allowed, as it is reasonably expected in real situations. Our findings highlight the importance of Stag-Hunt and Chicken games in understanding the emergence of cooperation in social networks.

The Stochastic Optimisation Software (SOS) is a Java platform facilitating the algorithmic design process and the evaluation of metaheuristic optimisation algorithms. It reduces the burden of coding miscellaneous methods for dealing with several bothersome and time-demanding tasks such as parameter tuning, implementation of comparison algorithms and testbed problems, collecting and processing data to display results, measuring algorithmic overhead, etc. SOS provides numerous off-the-shelf methods including 1) customised implementations of statistical tests, such as the Wilcoxon Rank-Sum test and the Holm-Bonferroni procedure, for comparing performances of optimisation algorithms and automatically generate result tables in PDF and LaTeX formats; 2) the implementation of an original advanced statistical routine for accurately comparing couples of stochastic optimisation algorithms; 3) the implementation of a novel testbed suite for continuous optimisation, derived from the IEEE CEC 2014 benchmark, allowing for controlled activation of the rotation operator. each testbed function. Moreover, this article comments on the current state of the literature in stochastic optimisation and highlights similarities shared by modern metaheuristics inspired by nature. It is argued that the vast majority of these algorithms are simply a reformulation of the same methods and that metaheuristics for optimisation should be simply treated as stochastic processes with less emphasis on the inspiring metaphor behind them.

The eastern subterranean termite, Reticulitermes flavipes, currently inhabits previously glaciated regions of the northeastern U.S., as well as the unglaciated southern Appalachian Mountains and surrounding areas. We hypothesized that Pleistocene climatic fluctuations have influenced the distribution of R. flavipes, and thus the evolutionary history of the species. We estimated contemporary and historical geographic distributions of R. flavipes by constructing Species Distribution Models (SDM). We also inferred the evolutionary and demographic history of the species using mitochondrial (cytochrome oxidase I and II) and nuclear (endo-beta-1,4-glucanase) DNA sequence data. To do this, genetic populations were delineated using Bayesian spatial genetic clustering, competing hypotheses about population divergence were assessed using approximate Bayesian computation (ABC), and changes in population size were estimated using Bayesian skyline plots. SDMs identified areas in the north with suitable habitat during the transition from the Last Interglacial to the Last Glacial Maximum, as well as an expanding distribution from the mid-Holocene to the present. Genetic analyses identified three geographically cohesive populations, corresponding with northern, central, and southern portions of the study region. Based on ABC analyses, divergence between the Northern and Southern populations was the oldest, estimated to have occurred 64.80 thousand years ago (kya), which corresponds with the timing of available habitat in the north. The Central and Northern populations diverged in the mid-Holocene, 8.63 kya, after which the Central population continued to expand. Accordingly, phylogeographic patterns of R. flavipes in the southern Appalachians appear to have been strongly influenced by glacial-interglacial climate change.

Understanding the evolutionary role of environmentally-induced phenotypic variation (i.e., environmental plasticity) is an important issue in developmental evolution. One of the major physiological responses to environmental changes is cellular stress, which is counteracted by a generic stress reaction that detoxifies the cell, refolds proteins, and repairs DNA damage. In this paper, we elaborate on a previous finding suggesting that the cell differentiation cascade of human decidual stromal cells, a cell type critical for embryo implantation and the maintenance of pregnancy, evolved from a cellular stress reaction. We hypothesize that the stress reaction in these cells was elicited ancestrally through the inflammation caused by embryo attachment and invasion. We describe a model, Stress-Induced Evolutionary Innovation (SIEI), whereby ancestral stress reactions and their corresponding pathways can be transformed into novel structural components of body plans, such as new cell types. After reviewing similarities and differences between SIEI and the “plasticity first hypothesis” (PFH) of evolution, we argue that SIEI is a distinct form of plasticity-based evolutionary change because it leads to the origin of novel structures rather than the adaptive transformation of a pre-existing character.

Manufacturing systems need to meet I4.0 guidelines to deal with uncertainty in scenarios of turbulent demand for products. The engineering concepts to define the service’s resources to manufacture the products will be more flexible, ensuring the possibility of re-planning in operation. These can follow the engineering paradigm based on capabilities. The virtualization of industry components and assets achieves the RAMI 4.0 guidelines and (I4.0C), which describes the Asset Administration Shell (AAS). However, AAS are passive components that provide information about I4.0 assets. The proposal of specific paradigms is exposed for managing these components, as is the case of multi-agent systems (MAS) that attribute intelligence to objects. The implementation of resource coalitions with evolutionary architectures (EAS) applies cooperation and capabilities’ association. Therefore, this work focuses on designing a method for modeling the asset administration shell (AAS) as virtual elements orchestrating intelligent agents (MAS) that attribute cooperation and negotiation through contracts to coalitions based on the engineering capabilities concept. The systematic method suggested in this work is partitioned for the composition of objects, AAS elements, and activities that guarantee the relationship between entities. Finally, Production Flow Schema (PFS) refinements are applied to generate the final Petri net models (PN) and validate them with Snoopy simulations. The results achieved demonstrate the validation of the procedure, eliminating interlocking and enabling liveliness to integrate elements behavior.

Particle Swarm Optimization (PSO) is a metaheuristic global optimization paradigm that has gained prominence in the last two decades due to its ease of application in unsupervised, complex multidimensional problems which cannot be solved using traditional deterministic algorithms. The canonical particle swarm optimizer is based on the flocking behavior and social co-operation of birds and fish schools and draws heavily from the evolutionary behavior of these organisms. This paper serves to provide a thorough survey of the PSO algorithm with special emphasis on the development, deployment and improvements of its most basic as well as some of the very recent state–of-the-art implementations. Concepts and directions on choosing the inertia weight, constriction factor, cognition and social weights and perspectives on convergence, parallelization, elitism, niching and discrete optimization as well as neighborhood topologies are outlined. Hybridization attempts with other evolutionary and swarm paradigms in selected applications are covered and an up-to-date review is put forward for the interested reader.

During the past few years unexpected developments have driven studies in the field of clinical immunology. One driver of immense impact was the outbreak of a pandemic caused by the novel virus SARS-CoV-2. Excellent recent reviews address diverse aspects of immunological re-search into cardiovascular diseases. Here, we specifically focus on selected studies taking ad-vantage of advanced state-of-the-art molecular genetic methods ranging from genome-wide epi/transcriptome mapping and variant scanning to optogenetics and chemogenetics. First, we discuss emerging clinical relevance of advanced diagnostics for cardiovascular diseases - includ-ing those associated with COVID-19 - with a focus on the role of inflammation in cardiomyopa-thies and arrhythmias. Second, we consider newly identified immunological interactions at or-gan and systems level which affect cardiovascular pathogenesis. Thus, studies into immune in-fluences arising from the intestinal system are moving towards therapeutic exploitation. Fur-ther, powerful new research tools have enabled novel insight into brain – immune system inter-actions at unprecedented resolution. This latter line of investigation emphasizes the strength of influence of emotional stress - acting through defined brain regions - upon viral and cardiovas-cular disorders. Several challenges need to be overcome before the full impact of these far-reaching new findings will hit the clinical arena.

A few empirical examples document fixed alternative male mating strategies in animals. Here we focus on the polymorphism of male mating strategies in the ruff (Calidris pugnax, Aves Charadriiformes). In ruffs, three fixed alternative male mating strategies coexist and are signaled by extreme plumage polymorphism. We first present relevant data on the biology of the species. Then we review the available knowledge of the behavioral ecology of ruffs during the breeding season and we detail the characteristics of each of the three known fixed male mating strategies. We next turn to the exceptional quality results accumulated on both the structural and functional genomics of the ruff over the past few years. We show how much these genomic data can shed a new, mechanistic light on the evolution and maintenance of the three fixed alternative male mating strategies. We then look if there are sufficient indication to support frequency-dependent selection as key mechanism in maintaining these three strategies. Specifically, we search for evidences of equal fitness among individuals using each of the three strategies. Finally, we propose three lines of research avenues that will help to understand the eco-evolutionary dynamics of phenotypic differences within natural populations of this iconic model species.

The present paper reviews evidence for ecological evolution of Montiaceae. Montiaceae (Portulacineae) comprise a family of ca. 275 species and ca. 25 subspecific taxa of flowering plants distributed mainly in extreme western America, with additional endemism elsewhere, including other continents and islands. They have diversified repeatedly across steep ecological gradients. Based on narrative analysis, I argue that phylogenetic transitions from annual to perennial life history have been more frequent than suggested by computational phylogenetic reconstructions. I suggest that a reported phylogenetic correlation between the evolution of life history and temperature niche is coincidental and not causal. I demonstrate how statistical phylogenetic comparative analysis (PhCA) missed evidence for marked moisture niche diversification among Montiaceae. I discount PhCA evidence for the relation between Montiaceae genome duplication and ecological diversification. Based on the present analysis of Montiaceae evolution, I criticize the premise of the prevalent statistical approach to PhCA, which tests Darwinian deterministic hypotheses against stochastic evolutionary null models. I discuss theoretical/empirical evidence that evolution is neither stochastic, nor Darwinistically-determined, but idiosyncratic. Idiosyncraticity describes the outcome of a stochastically perturbed nonlinear chaos-like process. The Principle of Evolutionary Idiosyncraticity (PEI) is based on the evolutionary theory of Natural Drift, which maintains that determinism in evolution is a property of the organism and not, as maintained by the theory of Natural Selection, its traits or its milieu. This determinism is characteristic of chaotic functions, which are absolutely determinate, generate self-similarity, but remain absolutely unpredictable. PEI explains precisely observations that evolution proceeds not linearly, but chaotically, producing both quasi-linear fractal-like patterns and non-linear jumps. PEI has ramifications for all areas of macroevolutionary research. In particular, it demonstrates both the fallacy and futility of the statistical PhCA approach that interprets evolutionary causes in terms of evolutionary correlations. However, statistical methods of PhCA can be applied heuristically and fruitfully to reveal idiosyncraticity and discover evolutionary novelty. This, in turn, is demonstrated by the emergence of statistical anomalies in evolutionary analyses of Montiaceae.

Appropriate governance structures are extremely important for the fishery dependent communities to develop integrated territorial development strategies and adaptive capacity to change, including the climate one. This paper assesses to what extent fisheries co-management schemes (e.g Fisheries LAGs, being regional/local governance instruments in fishing communities) are strengthening sustainability. The latter includes improving energy efficiency, promoting renewable energy sources (RES), coping with climate crisis, minimizing environmental impacts, and promoting sustainable blue economy. For detecting policy aspects of aligning climate neutrality and sustainable blue economy, the research lens focuses on the Greek Fisheries Local Action Groups (FLAGs) given that these are mostly located in coastal/marine and insular territories with significant blue growth potential. To map and assess their capacity and efficiency in pursuing Green Deal objectives, a co-development process with FLAG managers was put in place. The results and findings of this process reveal the scarcity of sustainability and blue economy related strategies. Key conclusion is that transition to a post-carbon blue economy on a local level, requires the understanding of the evolutionary dynamics of fisheries co-management schemes. The latter, being multi-sectoral structures, may boost dialogue and cooperation to harmonize local development strategies and EU policies. Maritime Spatial Planning (MSP) as an evolutionary governance process itself, can be a driver for making FLAGs evolve, and strengthen commonization and blue justice and equity for fishers.

The corona (COVID-19) pandemic offers an opportunity for dealing with persistent problems, through a transformative recovery process. It is a crisis that offers opportunities for dealing with three interrelated crises: the ecological crisis (climate change, loss of biodiversity, resource depletion, pollution and ecosystem destruction), the confidence crisis (people losing trust in government, politics, companies, regular news channels, science, each other and the future), and the inequality crisis (the widening of the gap between rich and poor). Our argument is that sustainability transitions will not succeed without a different economy and another social contract with the associated rights and duties of care (for the environment and the well-being of others, including future generations). A different social contract is not only desirable from the point of view of sustainability and fairness, justice and equality, but is also necessary to restore citizens' trust in politics, government, companies and each other. In the paper we discuss mechanisms towards a Natural Social Contract, systemic leverage points for system transformations and possibilities for co-evolutionary governance by actor coalitions interested in transformative change. The combination of those three elements helps to synchronize different agendas and reduce the chance that they will work against each other.

Newly characterising 245 Italian and Albanian HCV-2 NS5B sequences collected between 2001 and 2016 was used to reconstruct the origin and dispersion pathways of HCV-2c. The tree of a subset of these sequences aligned with 247 publicly available sequences was reconstructed in spatio-temporal scale using the Bayesian approach, and the effective replication number (Re) was estimated using the birth-death model. Our findings show that HCV-2c was the most prevalent subtype in Italy and Albania, and that GT2 originated in Guinea Bissau in the XVI century and spread to Europe in the XX century. The HCV-2c subtype had two internal nodes respectively dating back to the 1930s and 1950s having as most probable locations Ghana and Italy, respectively. Phylodynamic analysis revealed an exponential increase in the effective number of infections and Re in both Italy between the 1950s and 1980s, and Albania between the 1990s and the early 2000s. It seems very likely that HCV-2c reached Italy from Africa at the time of the second Italian colonisation (1936-1941), but did not reach Albania until the period of dramatic migration to Italy in the 1990s.

In this paper, I give readers an idea of what some scholars are interested in, what I found interesting, and what may be of future interest in the philosophy of emotion. I begin with a brief overview of the general topics of interests in the philosophy of emotion. I then discuss what I believe to be some of the most interesting topics in the contemporary discourse, including questions about how philosophy can inform the science of emotion, conceptions of the mind and the mind-body problem, concerns about perception, cognition, and emotion, along with questions about the place of 4E approaches and meta-semantic pluralist approaches in the embodied cognitive tradition. Finally, I discuss the emerging field of cultural evolution, the import of a dual-inheritance theory in this emerging field, and I propose a possible way to integrate the frameworks of dual-inheritance theory and meta-semantic pluralism to demonstrate at least one way in which the philosophy of emotion can contribute to the emerging field of cultural evolution.

Both SARS-CoV-2 (COVID-19) and SARS coronaviruses (CoVs) are members of the subgenus Sarbecovirus. To understand the origin of SARS-CoV-2, protein sequences from sarbecoviruses were analyzed to identify highly-specific molecular markers consisting of conserved inserts or deletions (termed CSIs) in the spike (S) and nucleocapsid (N) proteins that are specific for either particular clusters/lineages of these viruses or are commonly shared by specific lineages. Three novel CSIs in the N-terminal domain of the spike protein S1-subunit (S1-NTD) are uniquely shared by the SARS-CoV-2, BatCoV-RaTG13 and most pangolin CoVs, distinguishing this cluster of viruses (SARS-CoV-2r) from all others. In the same positions, where these CSIs are found, related CSIs are also present in two other sarbecoviruses (viz. CoVZXC21 and CoVZC45 forming CoVZC cluster), which form an out group of the SARS-CoV-2r cluster. These three CSIs are not found in the SARS-CoVs. However, both SARS and SARS-CoV-2r CoVs contain two large CSIs in the C-terminal domain of S1 (S1-CTD), which binds the human ACE-2 receptor, that are absent in the CoVZC cluster of CoVs. These results indicate that while the S1-NTD of the SARS-CoV-2r viruses possesses the sequence characteristics of the CoVZC cluster of CoVs, their S1-CTD resembles the SARS viruses. Thus, the spike protein of SARS-CoV-2r viruses has likely originated from a recombination event between the S1-NTD of the CoVZC viruses and the S1-CTD of SARS viruses. This inference is also supported by the amino acid sequence similarity of the S1-NTD and S1-CTD from SARS-CoV-2 compared to the CoVZC and SARS CoVs. We also present evidence that one of the pangolin-CoV_MP789, whose receptor-binding domain is most similar to the SARS-CoV-2, is also derived by a recent recombination between the S1-NTD of the CoVZC CoVs and the S1-CTD of a SARS-CoV-2 related virus. Several other identified CSIs are specific for others clusters of sarbecoviruses including a clade consisting of bat SARS-CoVs (BM48-31/BGR/2008 and SARS_BtKY72). Structural mappings studies show that the identified CSIs are located within surface-exposed loops and form distinct patches on the surface of the spike protein. These surface loops/patches are predicted to interact with other host components and play important role in the biology/pathology of SARS-CoV-2 virus. Lastly, the CSIs specific for the SARS-CoV-2r clade provide novel means for development of new diagnostic and therapeutic targets for these viruses.

A revitalized practice of natural philosophy can help people to live a better life and promote a flourishing ecosystem. Such a philosophy is natural in two senses. First, it is natural by seeking to understand the whole of nature, including mental phenomena, In particular, a comprehensive natural philosophy should address the phenomena of sentience by embracing first- and second-person methods of investigation. Moreover, to expand our understanding of the world, natural philosophy should embrace a full panoply of explanations, similar to Aristotle’s four causes. Second, such a philosophy is natural by being grounded in human nature, taking full account of human capacities and limitations. Future natural philosophers should also make use of all human capacities, including emotion and intuition as well as reason and perception, to investigate nature. Finally, since the majority of our brain's activities are unconscious, natural philosophy should explore the unconscious mind with the aim of deepening our relation to the rest of nature and enhancing well-being.

The hybridization of conventional thermal power plants by incorporation of renewable energy systems has witnessed widespread adoption in recent years. This trend aims not only to mitigate carbon emissions but also to enhance the overall efficiency and performance of these power generation facilities. However, calculating the performance of such intricate systems using fundamental thermodynamic equations proves to be both laborious and time-intensive. Nevertheless, possessing accurate and real-time insights into their performance is of utmost significance to ensure optimal plant operation, facilitate decision-making, and streamline power production planning. In this paper, we delve into the application of machine learning techniques, particularly hybrid methodologies, to predict the performance of power plants. Specifically, we employ three approaches: the Adaptive Neuro-Fuzzy Inference System (ANFIS), the ANFIS optimized via Particle Swarm Optimization (ANFIS-PSO), and the ANFIS optimized through Genetic Algorithm (ANFIS-GA). These techniques are alternatively applied to a complex hybrid thermal power plant, namely an Integrated Solar Combined Cycle Power Plant (ISCCPP). This ISCCPP comprises a steam turbine section, a gas turbine section, and a concentrated solar power system utilizing troughs as collectors. The energy transfer fluid, in conjunction with exhaust from the gas turbine section, heats water within a vessel or steam generator, producing steam to propel the steam turbine's rotor. Electricity generation is facilitated by both gas and steam turbines, which are coupled to a generator. The findings of this study underscore the accuracy and appropriateness of ANFIS-based models in evaluating and predicting the performance of intricate hybrid power plants. The ANFIS model exhibited an impressive overall coefficient of correlation of 0.9991. Notably, the integration of evolutionary algorithms (PSO and GA) into the ANFIS framework elevated model performance, yielding correlation coefficients of 0.9994 for ANFIS-PSO and 0.9997 for ANFIS-GA. It is noteworthy that ANFIS-GA demonstrated superior predictive capability. The modeling framework developed in this research offers valuable support to designers, energy managers, and decision-makers. It provides a robust and dependable tool to assess the performance of hybrid thermal power plants, which are poised for a global surge in numbers amid the ongoing energy transition.

We introduce the Transformation Flower Approach (TFA), a Theory of Change that attends to multiple value creation and institutional change as a dual design challenge. We highlight how the TFA integrates social scientific theories and models relevant for transformative change (in particular focusing on pathways, leverage points, governance, power, and values) and demonstrate its practical value by an application to the ongoing transformation of the Dutch food system. By providing a holistic, transdisciplinary and practically relevant approach that aims to support new social contract formation, the TFA goes beyond other transformative change approaches. Based on the notion of pathways, it offers a toolbox that aids in working towards desired futures, involving both incumbents and challengers in an effort to harness untapped yet proximal potentials in a forward-looking way. By embracing an innovation approach, it not only promises to circumvent resistance to change, but also serves as a step-by-step approach to identify options for multiple value creation and effective cooperation. We demonstrate the analytical and practical value of the TFA by discussing action perspectives at various levels and scales in the context of the Dutch food system transition, including (1) area-oriented approaches, (2) acceleration agendas for specific transformation pathways, and (3) actor-specific transformation flowers. In developing these, we emphasize the importance of interdependencies between leverage points. Our approach helps to identify opportunities to link transformative options (the what), actors (the who) and levers (the how) in dynamic interaction to embark on transformative pathways.

Appropriate estimation of soil settlement is of significant importance since it directly influences the performance of building and infrastructures that are built on soil. In particular, the settlement of fine-grained soils is critical because of low permeability and continuous settlement with time. Coefficient of consolidation (Cc) is a key parameter to estimate settlement of fine-grained soil layers. However, estimation of this parameter is time consuming, needs skilled technicians, and specific equipment. In this study, Cc was estimated using several soil parameters such as liquid limit (LL), plastic limit (PL), and initial void ratio (e0). Estimating such parameters in laboratory is straight forward and needs substantially less time and cost compared to conventional tests to estimate Cc such as Oedometer test. This study presents a novel prediction model for Cc of fine-grained soils using gene-expression programming (GEP). GEP is a biologically inspired technique capable of offering closed-form solution for the optimal solution. A database consisted of 108 different data points was used to develop the model. A closed-form equation solution was derived to estimate Cc based on LL, PL, and e0. The performance of developed GEP-based model was evaluated through coefficient of determination (R2), root mean squared error (RMSE), and mean average error (MAE). High R2 and low error values indicated the descent performance of the model. Furthermore, the model was evaluated using the additional performance measures and met all the suggested criteria. Furthermore, the model had a better performance in terms of R2, RMSE, and MAE compared to most of existing models. It is expected that the developed model will decrease the time and cost associate with determining Cc of fine-grained soils.

Appropriate estimation of soil settlement is of significant importance since it directly influences the performance of building and infrastructures that are built on soil. In particular, the settlement of fine-grained soils is critical because of low permeability and continuous settlement with time. Coefficient of consolidation (C_c) is a key parameter to estimate settlement of fine-grained soil layers. However, estimation of this parameter is time consuming, needs skilled technicians, and specific equipment. In this study, C_c was estimated using several soil parameters such as liquid limit (LL), plastic limit (PL), and initial void ratio (e₀). Estimating such parameters in laboratory is straight forward and needs substantially less time and cost compared to conventional tests to estimate C_c such as oedometer test. This study presents a novel prediction model for C_c of fine-grained soils using gene-expression programming (GEP). GEP is a biologically inspired technique capable of offering closed-form solution for the optimal solution. A database consisted of 108 different data points was used to develop the model. A closed-form equation solution was derived to estimate C_c based on LL, PL, and e₀. The performance of developed GEP-based model was evaluated through coefficient of determination (R²), root mean squared error (RMSE), and mean average error (MAE). High R² and low error values indicated the descent performance of the model. Furthermore, the model was evaluated using the additional performance measures and met all the suggested criteria. Furthermore, the model had a better performance in terms of R², RMSE, and MAE compared to most of existing models. It is expected that the developed model will decrease the time and cost associate with determining C_c of fine-grained soils.Keywords: evolutionary model, gene-expression programming (GEP), prediction, soil compression index, estimation, soil engineering, soil informatics, civil engineering, machine learning, data science, big data, soft computing, deep learning, forecasting, subject classification codes, construction informatics, computational intelligence (CI), artificial intelligence (AI), estimation

SARS-CoV-2 Omicron variant spike RBD epitopes in complex with spike (S) -protein D614G mutations now predominate globally and increase infectivity by assembling more functional S proteins into the virion. On average, homeopathic medicine contains less than one molecule per dose on average. Single variable SphericalHarmonicY, LaguerreL, WhittakerM, SphericalBesselJ, LegendreP, LegendreQ, LaguerreL, ChebyshevT, and Hypergeometric1F1 Functions pFqarise in connection with the power series solution of the Schrodinger equation or in the summation of perturbation expansions in quantum mechanics. A quantum interpretation of the homeopathic method is presented here through a novel algebraic topology approach to supersymmetry and symmetry breaking in quantum fields and quantum gravity theory with the aim of developing a wide range of physical-based drug design applications in a Small Molecule Quantized Water Memory Network suggesting that the Hidden Black Hole Paradox of Information Loss might be solved under suitable conditions.