Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: evolutionary stable strategies (ESS); Markov decision evolutionary games (MDEG); Hawk-Dove game; evolutionary dynamics; evolutionary game theory
Online: 24 June 2021 (08:38:13 CEST)
An evolutionary game is introduced which considers game-theoretic strategies in the context of non-linear population matrix models. This game considers the states and actions of the organisms of the evolving population, and a notion of dynamic equilibrium between strategies is described. The game’s formalism is expounded and a proof about equilibrium is given; specifically that any stable equilibrium can be described by proportions of pure strategies; particularly when population matrices are not defective.
ARTICLE | doi:10.20944/preprints201904.0266.v1
Subject: Biology And Life Sciences, Other Keywords: historical individuals, extended evolutionary synthesis, evolutionary innovation, culture
Online: 24 April 2019 (11:20:29 CEST)
Since its inception, evolutionary theory has experienced a number of extensions. The most important of these took the forms of the Modern Evolutionary Synthesis (MES), embracing genetics and population biology in the early 20th century, and the Extended Evolutionary Synthesis (EES) of the last thirty years, embracing, among other factors, non-genetic forms of inheritance. While we appreciate the motivation for this recent extension, we argue that it does not go far enough, since it restricts itself to widening explanations of adaptation by adding mechanisms of inheritance and variation. A more thoroughgoing extension is needed, one that widens the explanatory scope of evolutionary theory. In addition to adaptation and its various mechanisms, evolutionary theory must recognize as a distinct intellectual challenge the origin of what we call “historical kinds.” Under historical kinds we include any process that acquires a quasi-independent and traceable lineage-history in biological and cultural evolution. We develop the notion of a historical kind in a series of paradigmatic exemplars, from genes and homologues to rituals and music, and we propose a preliminary characterization.
ARTICLE | doi:10.20944/preprints202305.1427.v1
Subject: Engineering, Safety, Risk, Reliability And Quality Keywords: chemical enterprises; safety regulation; evolutionary game; evolutionary stable strategy
Online: 19 May 2023 (10:16:29 CEST)
Chemical safety is related to public health, safety and environmental concerns, and the dangerous chemicals safety problem is becoming the one that people commonly pay attention to. Strengthening chemical safety supervision not only involves safe production, but also is an important link to maintain social safety. Most related studies focus on chemical safety under normal regulation, this paper addresses the perspective of ‘special rectification’ and ‘normal regulation’, and establishes an evolutionary game model between chemical enterprises and government supervision departments under different supervision modes. Based on the evolutionary game theory, this paper studies the evolution process of the two game players' strategy choices, and compares and analyzes the evolution, stability and equilibrium between the chemical safety and the behavior strategies of government regulatory departments. The model is effectively analyzed based on numerical simulation, and the results show that: Under the ‘special rectification’ mode, the strategic choice of chemical enterprises engaging in safety without investment depends on the difference between the benefits and costs of safety without investment; In the ‘normal regulation’ mode, the choice of its safety non-investment strategy depends on the difference between the cost of engaging in safety investment and the cost of safety non-investment; Increasing the government's punishment will encourage chemical enterprises to take safety investment behavior under the two supervision modes. Increasing the punishment has a significant impact on the safety investment behavior of chemical enterprises under the ‘normal regulation’ mode, but it has no significant impact on the behavior of chemical enterprises under the ‘special rectification’ mode. At the same time, increasing the punishment will inhibit the strict supervision behavior of the government. The research conclusion provides important decision support for government departments to effectively supervise the safety production of chemical enterprises.
ARTICLE | doi:10.20944/preprints202112.0459.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: evolutionary transitions; multicellularity; cell adhesion; evolutionary preconditions; statistical physics
Online: 28 December 2021 (18:16:42 CET)
Multicellular life forms have evolved many times in our planet, suggesting that this is a common evolutionary innovation. Multiple advantages have been proposed for multicellularity (MC) to emerge. In this paper we address the problem of how the first precondition for multicellularity, namely "stay together" might have occurred under spatially limited resources exploited by a population of unicellular agents. Using a minimal model of evolved cell-cell adhesion among growing and dividing cells that exploit a localised resource with a given size, we show that a transition occurs at a critical resource size separating a phase of evolved multicellular aggregates from a phase where unicellularity (UC) is favoured. The two phases are separated by an intermediate domain where where both UC and MC can be selected by evolution. This model provides a minimal approach to the early stages that were required to transition from Darwinian individuality to cohesive groups of cells associated with a physical cooperative effect: when resources are present only in a localised portion of the habitat, MC is a desirable property as it helps cells to keep close to the available local nutrients.
ARTICLE | doi:10.20944/preprints201811.0312.v1
Subject: Physical Sciences, Mathematical Physics Keywords: constrains; Maxwell theory; evolutionary equations
Online: 13 November 2018 (11:03:45 CET)
The constraint equations in Maxwell theory are investigated. In analogy with some recent results on the constraints of general relativity it is shown, regardless of the signature and dimension of the ambient space, that the "divergence of a vector field" type constraints can always be put into linear first order hyperbolic form for which global existence and uniqueness of solutions to an initial-boundary value problem is guaranteed.
DATA DESCRIPTOR | doi:10.20944/preprints202306.0658.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Genetics and Genomics; Evolutionary Biology; Zoology
Online: 9 June 2023 (03:30:56 CEST)
Snakes are a vital component of wildlife resources and are widely distributed across the globe. Bungarus multicinctus, a highly venomous snake, is found in central and southern China. B. multicinctus is a highly venomous snake and is distributed in central and southern China. Snakes are an ancient group of reptiles, and their genome resources can provide important clues for understanding the evolutionary history of reptiles. Meanwhile, genomic resources play a crucial role in comprehending the evolution of species. So far, the genomic resources of snakes are a rarity. In 2021, a snake sample was collected from Beiliu Longgukeng, Guangxi, which was identified as B. multicinctus through morphological identification. In this study, we present a highly contiguous genome of B. multicinctus with a size of 1.51 Gb. The genome contains a repeat content of 40.15%, with a total length exceeding 620 Mb. Additionally, we annotated a total of 24,869 functional genes. This research is of great significance for comprehending the evolution of B. multicinctus and provides a genomic basis for the genes involved in venom gland function.
ARTICLE | doi:10.20944/preprints201812.0220.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: yeast, multicellularity, adhesion, major evolutionary transition
Online: 18 December 2018 (11:15:41 CET)
Understanding how and why cells cooperate to form multicellular organisms is a central aim of evolutionary biology. Multicellular groups can form through clonal development (where daughter cells stick to mother cells after division) or by aggregation (where cells aggregate to form groups). These different ways of forming groups directly affect relatedness between individual cells, which in turn influences the degree of cooperation and conflict within the multicellular group. It is hard to study the factors that favoured multicellularity by focusing only on obligately multicellular organisms, like complex animals and plants, because the factors that favour multicellular cooperation cannot be disentangled, as cells cannot survive and reproduce independently. We propose bakers yeast, Saccharomyces cerevisiae, as an ideal model for studying the very first stages of the evolution of multicellularity. This is because it can form multicellular groups both clonally and through aggregation and uses a family of proteins called ‘flocculins’ that determine the way in which groups form, making it particularly amenable to lab experiments. We briefly review current knowledge about multicellularity in S. cerevisiae and then propose a framework for making predictions about the evolution of multicellular phenotypes in yeast based on social evolution theory. We finish by suggesting outstanding questions and potentially fruitful avenues for future research.
ARTICLE | doi:10.20944/preprints202104.0058.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: evolutionary biology; astrobiology; philosophy of biology; epistemology
Online: 2 April 2021 (11:42:18 CEST)
The details of abiogenesis to date remain a matter of debate and constitute a key mystery in science and philosophy. The prevailing scientific hypothesis implies an evolutionary process of increasing complexity on earth starting from (self-) replicating polymers. Defining the cut-off point where life begins is another moot point beyond the scope of this article. We will instead walk through the known evolutionary steps that lead from these first exceptional polymers to the vast network of living biomatter that spans our world today, focusing in particular on perception, from simple biological feedback mechanisms to the complexity that allows for abstract thought. We then will project from the well-known to the unknown to gain a glimpse on what the universe aims to accomplish with living matter, just to find that if the universe had ever planned to be comprehended, evolution still has a long way to go.
Subject: Biology And Life Sciences, Other Keywords: historical kinds; individuation; cultural evolution; evolutionary innovation
Online: 22 September 2020 (08:45:54 CEST)
Two welcome extensions of evolutionary thinking have come to prominence over the last thirty years: the so-called “extended evolutionary synthesis” (EES) and debate about biological kinds and individuals. These two agendas have, however, remained orthogonal to one another. The EES has mostly restricted itself to widening the explanations of adaptation offered by the preceding “modern evolutionary synthesis” by including additional mechanisms of inheritance and variation; while discussion of biological kinds has turned toward philosophical questions of essential vs. contingent properties of life forms and realist vs. epistemological approaches to categorization and classification. Here we attempt to broaden the explanatory scope of evolutionary theory by linking these two agendas. We expand on the mechanistic orientation of the EES, using new understandings of networked systems of components in order to engage the distinct intellectual challenge of the origination of historical kinds. With this phrase we designate a subset of natural kinds that acquires, through evolutionary processes, a quasi-independent lineage-history. Such kinds emerge in both biology and culture, and we enlarge the limited number of historical kinds that have thus far been recognized in evolutionary biology in a series of paradigmatic exemplars, from genes and cell types to rituals and music. For each exemplar we discern specific mechanisms by which it arose and persists; comparing these, we suggest a general unity in the ways in which diverse historical kinds originate.
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: pregnancy; implantation; invasion; conflict; evolutionary innovation; feminism
Online: 14 April 2020 (15:17:44 CEST)
Embryo implantation is a hallmark of the female reproductive biology of eutherian (placental) mammals and does not exist in a sustainable form in any other vertebrate group. Implantation is the initial process that leads to a sustained fetal-maternal unit engendering a complex functional relationship between the mother and the embryo/fetus. The nature of this relationship is often portrayed as one of conflict between an aggressive embryo and a passive or defensive maternal organism. Recent progress in elucidating the evolutionary origin of eutherian pregnancy leads to a different picture. The emerging scenario suggests that the very initial stages in the evolution of embryo implantation require evolutionary changes to the maternal physiology, which modified an ancestral generic mucosal inflammation in response to the presence of the embryo into an active embedding process. This “female-first” evolutionary scenario also explains the role of endometrial receptivity in human pregnancy. On the marsupial side, where in most animals the fetal-maternal interaction is short and does not lead to a long term sustainable placentation, the relationship is mutual. In these mammals uterine inflammation is followed by parturition in short order. The inflammatory signaling pathways, however, are cooperative, i.e. they are performed by both the fetus and the mother and therefore we call this relationship “cooperative inflammation.” Based on these discoveries we reconceive the narrative of the maternal-fetal relationship.
REVIEW | doi:10.20944/preprints202306.0244.v1
Subject: Medicine And Pharmacology, Clinical Medicine Keywords: antibiotics; antibiotic therapy; antibiotic resistance; evolutionary medicine; ethics
Online: 5 June 2023 (05:32:00 CEST)
The first half of the 20th century was noteworthy for the introduction of a unique group of drugs – antibiotics. It drastically changed concepts of infectious diseases treatment, which for centuries remained a scourge of the human population. With improvement of the antibiotic treatment efficacy, humanity has faced the problem of a dramatic increase in antibiotic resistance in bacteria. The COVID-19 pandemic has only exacerbated the problem and posed a new challenge to the medical community in finding solutions, both clinical and organizational and methodological, to fight antibiotic resistance widespread all over the globe. This publication covers some aspects of evolutionary processes in either pathogens or diseases, including ethical perspective.
REVIEW | doi:10.20944/preprints202203.0170.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: cancer; DNA informational entropy; cell compartmentation; evolutionary Biology; lactate dehydrogenase (LDH); lactic acid; metabolism; thermodynamic entropy; Warburg effect
Online: 17 March 2022 (03:37:53 CET)
Attempts to find and quantify the supposed low entropy of organisms and its preservation are revised. Absolute entropy of the mixed components of non-living biomass (around -1.6 x 103 J K-1 L-1) is the reference to which other entropy decreases would be ascribed to life. Compartmentation of metabolites and departure from the equilibrium of metabolic reactions account for 1 and 40-50 J K-1 L-1, respectively, decreases of entropy and, though small, are distinctive features of living tissues. DNA and proteins do not supply significant decreases of thermodynamic entropy, but their low informational entropy is relevant for life and its evolution. No other living feature contributes significantly to the low entropy associated to life. The photosynthetic conversion of radiant energy to biomass energy accounts for the most of entropy (2.8 x 105 J K-1 carbon kg-1) produced by living beings. The comparative very low entropy produced in other processes (around 4.8 x102 J K-1 L-1 day-1 in human body) must be rapidly exported outside as heat to preserve the low entropy decreases due to compartmentation and non-equilibrium metabolism. Enzymes and genes are described whose control minimize the rate of production of entropy and could explain selective pressures in biological evolution and the rapid proliferation of cancer cells.
BRIEF REPORT | doi:10.20944/preprints202103.0755.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: evolutionary divergence; phylogenetic analysis; transporter proteins; Leishmania major
Online: 31 March 2021 (09:55:35 CEST)
Transporter proteins, P-glycoprotein (P-gp) and P4ATPase-CDC50, are responsible for the transport of Miltefosine drug across cell membrane of a protozoan parasite Leishmania major. Mutations or change in activity of these proteins may lead to emergence of resistance in the parasite. Owing to the structural and functional importance of these transporter proteins, in this ppaper, we have tried to decipher the evolutionary divergence of these Miltefosine transporter proteins across different forms of life including Protists, Fungi, Plants and Animals. We retrieved 96, 207, and 189 sequences of P-gp, P4ATPase and CDC50 proteins respectively, across diverse variety of organisms for the conserved analysis. Phylogenetic trees were constructed for these three transporter proteins based on Bayesian posterior probability inference. The evolutionary analysis concluded that these proteins remain highly conserved throughout the species diversity but still substantial differences in the proteins for host (Homo sapiens) and parasite (L. major) were observed which have led in targeting these Miltefosine transporter proteins in a parasite specific manner.
ARTICLE | doi:10.20944/preprints202011.0536.v1
Subject: Engineering, Automotive Engineering Keywords: Stabilization; control constraints; evolutionary algorithms; switched linear system
Online: 20 November 2020 (11:07:03 CET)
In this paper, we address the problem of stabilization of switched linear systems. The idea is to look for a state feedback control law using evolutionary algorithms (EA) in order to assure the stability of the switched linear systems under control constraints. In some cases when states are not available and only outputs are measurable, the previous method is applied to design an output feedback controller which stabilizes the system. Both stabilizing controllers are developed using deferential evolution and genetic algorithm. Two numerical examples illustrate our proposed theory and point out the effectiveness of our proposed approaches.
COMMUNICATION | doi:10.20944/preprints202005.0428.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: evolutionary genomics; Gasterosteus aculeatus; gene flow; hybridization; phylogeny
Online: 26 May 2020 (08:44:35 CEST)
Where genetic variation promoting speciation originates is a crucial question in evolutionary genomics. In a recent article, Marques et al. (2019) seek to address this question in lake and stream threespine stickleback fish from the Lake Constance (hereafter LC) basin in Central Europe. Based on population genetic methods, they conclude that incipient speciation between lake and stream stickleback was facilitated by the mixing of genetic variation from old lineages evolved in isolation (i.e., admixture following secondary contact). In this comment, I discuss conceptual and methodological problems and unrecognized conflicts with existing evidence that cast doubt on Marques et al.’s conclusion.
REVIEW | doi:10.20944/preprints202002.0068.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: cis-regulatory element; developmental modularity; evolutionary modularity; Heliconius
Online: 5 February 2020 (14:02:51 CET)
Developmental modularity has long been viewed as a hierarchical organization that facilitates evolution over macro-evolutionary time through modification or co-option of preexisting modules. More recently, developmental modularity has been proposed as a micro-evolutionary mechanism capable of driving rapid evolution of novel color pattern phenotypes between closely related taxa. In this scenario, swapping allelic variants of modular cis-regulatory elements (CREs) via recombination generates novel phenotypes by shuffling preexisting color pattern modules into new arrangements. Recent evidence from Drosophila and butterflies, however, provides a series of examples in which pleiotropic CREs function in multiple developmental contexts. The potential prevalence of pleiotropy in CRE function is a major barrier to the proposed evolutionary role of CRE modules and encourages us to reconsider the relative importance of modularity for microevolutionary change. Here we first review the case for the apparent frequent exchange of modular color pattern phenotypes as a mechanism facilitating diversification. We then contrast this with recent evidence of CRE pleiotropy and argue that exchange of CRE modules should not be the default assumption, even when phenotypes look modular. Finally, we review experimental data on Heliconius butterfly wing patterns—which appear modular—and introduce the concept of evolutionary modularity as an alternative to developmental modularity. Evolutionary modularity reconciles the appearance of modularity in comparative genomic studies of Heliconius color patterns with experimental data supporting a non-modular architecture. We propose that evolutionary modularity provides a potentially important pathway for exchange of phenotypic elements between hybridizing taxa independent of the underlying developmental architecture.
REVIEW | doi:10.20944/preprints202304.0614.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: varietal mixture; evolutionary population; resilient; informal seed system; landrace
Online: 20 April 2023 (07:13:09 CEST)
Crop genetic diversity is most for the long-term sustainable production system. The breeding and production strategies of developing and growing uniform and homogenous varieties have created many different problems. Such populations are static and very sensitive to unpredictable stresses. In Nepal, more than 80% of seed system is informal s which has contributed greatly to creating and maintaining genetic diversity within the field particularly contributing to landrace diversity. This paper aims to assess and present the approaches and advantages of increased crop genetic diversity in the fields. The paper is developed based on experiences of implementing on-farm conservation activities carried out in Nepal since last two decades. Some of the evidences have been derived from on-going evolutionary plant breeding project being implemented in Nepal. The information is supplemented with field assessment, focus group discussion, and literature review. The major approaches to increase crop genetic diversity are evolutionary plant breeding, cultivar mixture, landrace enhancement, informal seed system, bulk method, diversifying the sources, participatory plant breeding, open pollination, etc. EPB and cultivar mixture are very simple and effective approaches to increase crop genetic diversity at field level. The involvement of farmers in these approaches helps to accelerate the population improvement particularly for landraces. The major advantages of increased crop genetic diversity are: seed maintenance by farmers themselves, minimal risk of crop failure, resilience to unpredictable stresses, increased amount of diversified nutrition, production increment each year, ease to produce organically, etc. However, there are some issues and problems associated with mixtures and diverse varieties, for example, not being able to harvest by machine, mature at a different date, difficulty in maintaining seeds and registration, etc. Crop genetic diversity should be considered for a climate-resilient and self-dependent production system. The higher the genetic diversity in farming land, the more chance of getting the multiple benefits in the agriculture system (Vernooy 2022).
ARTICLE | doi:10.20944/preprints202208.0471.v1
Subject: Business, Economics And Management, Economics Keywords: carbon sequestration; evolutionary game theory; organic fertilizer; food security
Online: 29 August 2022 (07:29:22 CEST)
The application of organic fertilizers plays a crucial role in achieving carbon sequestration in the agricultural sector. This paper discusses how farmers can more smoothly promote organic fertilizer extension services. An evolutionary game model is developed to describe the conflicting interests of Chinese farmers and local governments in organic fertilizer extension services, and the dynamic evolution of the game players and the influence of parameter adjustment on the strategic choices of both parties is presented. In this paper, the game model and the main results are validated with the help of simulation tools, and a sensitivity analysis of the selected parameters is performed. The results show that (1) the implementation of subsidy policy is less helpful for organic fertilizer extension services; (2) The ideal event probability of the game was found to be positively related to the cost of applying inorganic fertilizers, additional benefits to farmers, political returns to local governments, and penalties for not using organic fertilizers; (3) This is important for improving the performance of local governments, reducing government regulatory costs, improving policy support for organic fertilizer extension services, and reducing the cost of implementing organic fertilizer extension services.
ARTICLE | doi:10.20944/preprints202208.0315.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Transcription Factors; Evolutionary progression; Pearl millet; Phytohormones; Abiotic stress
Online: 17 August 2022 (09:50:48 CEST)
Transcription factors (TFs) are the regulatory proteins that act as molecular switches in controlling stress responsive gene expression. Among them MYB transcription factor family is one of the largest TF family in plants, playing a significant role in plant growth, development, phytohormone signaling and stress-responsive processes. Pearl millet (Pennisetum glaucum L.) is one of the most important C4 crop plant of the arid and semi-arid regions of Africa and South-east Asia for sustaining food and fodder productions. To explore the evolutionary mechanism and functional diversity of the MYB family in pearl millet, we conducted a comprehensive genome-wide survey and identified 279 MYB TFs (PgMYB) in pearl millet and distributed unevenly across seven chromosomes of pearl millet. Phylogenetic analysis of identified PgMYBs classified them into 18 subgroups and members of the same group showed a similar gene structure and conserved motif/s pattern. Further, duplication events were identified in pearl millet that indicated towards evolutionary progression and expansion of the MYB family. Transcriptome data and relative expression analysis by qRT-PCR identified differentially expressed candidate PgMYBs (PgMYB2, PgMYB9, PgMYB88 and PgMYB151) under dehydration, salinity, heat and phytohormones (ABA, SA and MeJA) treatment. Taken together, this study provides valuable information for a prospective functional characterization of MYB family members of pearl millet and genetic improvement of crop plants.
ARTICLE | doi:10.20944/preprints202201.0427.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: Cooperative localization; Vehicle network; Game theory; Evolutionary coalitional game
Online: 28 January 2022 (07:31:21 CET)
Cooperative localization under complex urban environments has become a solution to replace the Global Navigation Satellite System (GNSS) positioning. Due to utilizing distance measured and information exchanged between vehicles, cooperative localization results in high computational complexity and heavy communication overhead. This paper proposes a cooperative localization method based on evolutionary coalitional game theory, which implements vehicles' location estimation with less communication cost. We select the neighboring vehicles to form a coalition based on the node's square position error bound and communication cost. The location is obtained via exchanging information between vehicles. It is evident from the simulations and results that the proposed method holds low communication overhead while maintaining localization accuracy.
ARTICLE | doi:10.20944/preprints202111.0113.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Body-size; Cerrado; Evolutionary history; Nymphalidae; Phylogeny; Species traits
Online: 5 November 2021 (10:35:29 CET)
Introduction: Body size is correlated with many aspects of an animal species' natural history, such as life span, abundance, dispersal capacity and diet breadth. However, contrasting trends have been reported for the relationship between body size and these ecological traits. Methods: Butterfly species from fruit-feeding guilds were used to investigate whether body size correlates with species abundances, dispersal, permanence, and diet breadth in a Neotropical savanna in Brazil (Cerrado). We used Blomberg’s K and Phylogenetic Generalized Least Squares models (PGLS) to measure phylogenetic signal strength in species traits, and to estimate size-dispersal-diet breadth associations while taking shared ancestry into account. Results: 539 individuals from 27 species were captured, and 190 individuals were recaptured, representing a 35% recapture rate. We found that body size negatively influenced butterfly abundance. In contrast, body size was positively associated with dispersal levels, distance traveled, number of traps visited, individual permanence, and diet breadth. These results indicate that larger butterflies have a greater proportion of dispersing individuals over longer distances, as they permanence were detected over longer periods than their smaller relatives. Moreover, larger butterflies are more generalized, based on the number of host plant families and genera they consume. Smaller butterflies demand fewer resources, which is reflected in their higher survival in small patches, and may explain their lower dispersal ability, and higher diet specialization. Nevertheless, lower dispersal ability, if not compensated by large population sizes, may threaten small-bodied species inhabiting environments with intense deforestation rates, such as the Cerrado. Conclusions: Body size positively influences dispersal and diet breadth in the fruit-feeding butterflies collected in this study.
Subject: Business, Economics And Management, Accounting And Taxation Keywords: evolutionary game theory; social conventions; costly acquisition of information
Online: 17 June 2021 (12:01:05 CEST)
We consider an evolutionary model of social coordination in a 2x2 game where two groups of players prefer to coordinate on different actions. Players can pay a cost to learn their opponent's group: if they pay it, they can condition their actions on the groups. We assess the stability of outcomes in the long-run using stochastic stability analysis. We find that three elements matter for the equilibrium selection: the group size, the strength of preferences, and the information's cost. If the cost is too high, players never learn the group of their opponents in the long-run. If one group is stronger in preferences for its favorite action than the other, or its size is sufficiently large compared to the other group, every player plays that group's favorite action. If both groups are strong enough in preferences, or if none of the group's size is large enough, players play their favorite actions and miscoordinate in inter-group interactions. Lower levels of the cost favor coordination. Indeed, when the cost is low, in inside-group interactions, players always coordinate on their favorite action, while in inter-group interactions, they coordinate on the favorite action of the group that is stronger in preferences or large enough.
ARTICLE | doi:10.20944/preprints201912.0409.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: design optimization; evolutionary computation; finite element analysis; power transformers
Online: 31 December 2019 (10:42:23 CET)
Since large power transformers are custom-made, and their design process is a labor-intensive task, their design process is split into different parts. In tendering, the price calculation is based on the preliminary design of the transformer. Due to the complexity of this task, it belongs to the most general branch of discrete, non-linear mathematical optimization problems. Most of the published algorithms are using a copper filling factor based winding model to calculate the main dimensions of the transformer during this first, preliminary design step. Therefore, these cost optimization methods are not considering the detailed winding layout and the conductor dimensions. However, the knowledge of the exact conductor dimensions is essential to calculate the thermal behaviour of the windings and make a more accurate stray loss calculation. The paper presents a novel, evolutionary algorithm-based transformer optimization method which can determine the optimal conductor shape for the windings during this examined preliminary design stage. The accuracy of the presented FEM method was tested on an existing transformer design. Then the results of the proposed optimization method have been compared with a validated transformer design optimization algorithm.
ARTICLE | doi:10.20944/preprints201809.0350.v1
Subject: Business, Economics And Management, Business And Management Keywords: Environmental incident; Information disclosure; Social media; Evolutionary game model
Online: 18 September 2018 (12:44:56 CEST)
Despite the expectation that social media use in the public sector contributes to enhancing government's transparency, few studies have been investigated whether social media use actually leads to more disclosure during environmental incidents in practice and how social media influence local governments and their officials' information disclosure. In this article, we model information disclosure during environmental incidents as an evolutionary game process between the central government and local government in social media context, and examine the internal mechanism that how social media influence the progress of information disclosure during environmental incidents. The findings indicate that social media plays an active constructive role in central-local government game relations. Specific- ally, social media can provides an efficient information channels for the central government supervise regional officials in environmental incidents, and thus improves its supervision efficiency, and it also provides an important means for internet mobilization and online-offline interaction by encouraging the public exchange information and express their views, and in turn forces local governments and their officials tend to disclosure ahead.
ARTICLE | doi:10.20944/preprints201611.0070.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: bees algorithm; swarm intelligence; evolutionary optimization; grouped bees algorithm
Online: 14 November 2016 (04:48:54 CET)
As with many of the non-deterministic search algorithms, particularly those are analogous to complex biological systems, there are a number of inherent difficulties, and the Bees Algorithm (BA) is no exception. Basic versions and variations of the BA have their own drawbacks. Some of these drawbacks are a large number of parameters to be set, lack of methodology for parameter setting and computational complexity. This paper describes a Grouped version of the Bees Algorithm (GBA) addressing these issues. Unlike its conventional version, in this algorithm bees are grouped to search different sites with different neighbourhood sizes rather than just discovering two types of sites, namely elite and selected. Following a description of the GBA, the results gained for 12 benchmark functions are presented and compared with those of the basic BA, enhanced BA, standard BA and modified BA to demonstrate the efficacy of the proposed algorithm. Compared to the conventional implementations of the BA, the proposed version requires setting of fewer parameters, while producing the optimum solutions much faster.
ARTICLE | doi:10.20944/preprints202304.0054.v1
Subject: Engineering, Energy And Fuel Technology Keywords: new energy vehicles; “dual carbon” targets; evolutionary games; government subsidies
Online: 5 April 2023 (10:15:18 CEST)
To promote low-carbon and green travel, this study proposes a tripartite evolutionary game model among new energy vehicle manufacturers, consumers, and government agencies. The game strategy combinations of each party and the stability conditions of the equilibrium point in the evolutionary game system are analyzed, and the validity of the conclusions is verified through simulation results. The study shows a strong correlation between the three parties in the evolutionary game system. From the perspective of car manufacturers, the probability of producing new energy vehicles is positively proportional to the subsidy received from new energy policy, the additional revenue gained from the management of the carbon trading scheme, and the fine received for producing conventional fuel vehicles. However, from the consumer perspective, the likelihood that consumers purchase new energy vehicles is positively related to the utility value to consumers and the coverage of public charging points in the city, and inversely related to the sales price of new energy vehicles. From the government perspective, a combination of direct subsidy policies and indirect support strategies should be considered to stimulate the rapid development of the new energy vehicle industry.
BRIEF REPORT | doi:10.20944/preprints202112.0368.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Raccoon dog parvovirus; Epidemiology; VP2 gene; NS1 gene; Evolutionary analysis.
Online: 22 December 2021 (12:52:50 CET)
To understand the epidemiological status of parvovirus (RDPV) in raccoon dogs, intestinal tissues of raccoon dogs in Liaoning Province of China were collected and evaluated. Three strains of raccoon dog parvovirus were successfully isolated from 12 intestinal tissues. Nine samples were positive for RDPV, with a positive rate of 75%. The VP2 and NS1 genes of the viruses were cloned and subjected to sequencing for analysis. The nucleotide sequences of the VP2 gene showed 99.94% similarity to the CPV-2a/Racoon dog/QHD/2/19(MT183665) strain, and the nucleotide sequences of the NS1 gene showed 99.75% similarity to RDPV-DP1 NS1(MF996335) strain. The three isolates belonging to the CPV-2a cluster were further confirmed by amino acid sequence alignment and phylogenetic analysis. Our study enriched the epidemiological data of parvovirus in raccoon dogs in the investigating region, and the results will be helpful for future investigation of the variations and transmission of raccoon dog parvoviruses.
Subject: Chemistry And Materials Science, Biomaterials Keywords: plastics thermoforming; sheet thickness distribution; evolutionary algorithms; multi-objective optimization
Online: 1 June 2021 (09:41:57 CEST)
The practical application of a multi-objective optimization strategy based on evolutionary algorithms was proposed to optimize the plastics thermoforming process. For that purpose, the various steps of the process were considered individually and the optimization strategy was applied to the determination of the final part thickness distribution with the aim of demonstrating the validity of the methodology proposed. The preliminary results obtained considering three different theoretical initial sheet shapes indicates clearly that the methodology proposed is valid, as it provides solutions with physical meaning and with a great potential to be applied in real practice.
REVIEW | doi:10.20944/preprints201911.0387.v2
Subject: Social Sciences, Behavior Sciences Keywords: evolutionary bottleneck; evolution of sleep; sleep variability; function of sleep
Online: 20 July 2020 (10:31:23 CEST)
The Nocturnal Bottleneck explains how mammals evolved from their reptilian ancestors after inverting the chronotype, form diurnal to nocturnal. Pre-mammals traded-off the excellent visual system of their ancestors for improvements in audition and in olfactory telencephalon, needed for efficient orientation in the dark. This was how the mammalian nocturnal telencephalic wakefulness was born. However, the modified visual system of those pre-mammals became sensitive to the dangerous diurnal light and the exposure would involve a high risk of blindness and death. Therefore, pre-mammals had to remain immobile with closed eyes hidden in lightproof burrows during light time. This was the birth of the mammalian sleep. Typical reptiles distribute their wake time cycling between Basking Behavior, to attain the preferred body temperature, and poikilothermic Goal Directed Behavior, to perform life sustaining tasks. These cycles persisted during the new mammalian sleep. However, as the behavioral output had to be blocked during light time, the paralyzed reptilian Basking Behavior and Goal Directed Behavior cycles became the NREM and REM cycles, respectively. This was how NREM and REM cycles remained incorporated within the mammalian sleep. After the Cretaceous-Paleogene extinction, the environmental pressure for nocturnal life was softened, allowing high variability in chronotype and sleeping patterns. This permitted some mammalian groups, e.g., primates, to begin the quest for diurnal wake.Concluding, sleep constituted an additional bottleneck in the mammalian evolution. The reduced population of pre-mammals that was able to develop sleep during light time, including NREM and REM, became full mammals and survived; the remainder perished.
ARTICLE | doi:10.20944/preprints201902.0181.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: Power factor compensation; non-sinusoidal circuits; geometric algebra; evolutionary algorithms.
Online: 19 February 2019 (12:01:39 CET)
Non-linear loads in circuits cause the appearance of harmonic disturbances both in voltage and current. In order to minimize the effects of these disturbances and, therefore, to control over the flow of electricity between the source and the load, they are often used passive or active filters. Nevertheless, determining the type of filter and the characteristics of their elements is not a trivial task. In fact, the development of algorithms for calculating the parameters of filters is still an open question. This paper analyzes the use of genetic algorithms to maximize the power factor compensation in non-sinusoidal circuits using passive filters, while concepts of geometric algebra theory are used to represent the flow of power in the circuits. According to the results obtained in different case studies, it can be concluded that the genetic algorithm obtain high quality solutions that could be generalized to similar problems of any dimension.
ARTICLE | doi:10.20944/preprints201810.0420.v1
Subject: Engineering, Energy And Fuel Technology Keywords: District Heating; multi-objective evolutionary optimization; distributed cogeneration; optimal operation.
Online: 18 October 2018 (11:53:15 CEST)
The paper deals with the modelization and optimization of an integrated multi-component energy system. On-off operation and presence-absence of components must be described by means of binary decision variables, besides equality and inequality constraints; furthermore, the synthesis and the operation of the energy system should be optimized at the same time. In this paper a hierarchical optimization strategy is used, adopting a genetic algorithm in the higher optimization level, to choose the main binary decision variables, whilst a MILP algorithm is used in the lower level, to choose the optimal operation of the system and to supply the merit function to the genetic algorithm. The method is then applied to a distributed generation system, which has to be designed for a set of users located in the center of a small town in the North-East of Italy. The results show the advantage of distributed cogeneration, when the optimal synthesis and operation of the whole system are adopted, and significant reduction in the computing time by using the proposed two-level optimization procedure.
REVIEW | doi:10.20944/preprints202208.0452.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: lactate; lactic acid; glycolysis; carcinogenesis; malignant tumor; evolutionary oncology; Warburg effect
Online: 26 August 2022 (07:13:46 CEST)
The role of lactic acid (lactate) in cell metabolism has been significantly revised in recent dec-ades. Initially, lactic acid was attributed to the role of a toxic end product of metabolism, which accumulation in the cell and extracellular space leads to acidosis, muscle pain and other adverse effects. However, it has now become obvious that lactate is not only a universal fuel molecule and the main substrate for gluconeogenesis, but also one of the most ancient metabolites with signaling function, which has a wide range of regulatory activity. The Warburg effect described 100 years ago (that means intensification of glycolysis associated with high lactate production), which is characteristic of many malignant tumors, confirms the key role of lactate not only in physiological conditions, but also in pathologies. The study of lactate’s role in the malignant transformation becomes more relevant in the light of the “atavistic theory of carcinogenesis,” which suggests that tumor cells return to a more primitive hereditary phenotype during micro-evolution. In this review, we attempted to summarize the accumulated knowledges about the functions of lactate in cell metabolism and its role in the process of carcinogenesis, and to con-sider the possible evolutionary significance of the Warburg effect.
REVIEW | doi:10.20944/preprints202111.0509.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: hox genes; gene cluster; larva; evolutionary novelties; Spiralia; Lophotrochozoa; Annelida; Rotifera
Online: 26 November 2021 (13:28:22 CET)
The decoding of genomes of a larger number of animal species have provided further insights into the genomic Hox gene organization and with this indicated the evolutionary changes during the radiation of several clades. The expansion of gene expression studies during development and life history stages of more species, complete the picture of the relationship between cluster organisation and temporal and spatial correlation of the Hox activity. Now these results open the opportunity to look deeper into the regulatory pathways that form these patterns and identify what exact changes caused the evolution of the application of this iconical gene set for the evolution of new larval forms and new structures. Here we review recent progress of Hox gene related research in the large clade Spiralia, that comprises Annelida, Mollusca, Lophophorata, Platyhelminthes, Nemertea and others. Albeit their relationship to each other is not resolved yet, there are emerging patterns that indicate that Hox genes are mainly used for patterning late, adult body parts and that Hox genes are often not expressed on the larval stages. Hox genes seem also often recruited for the formation of morphological novelties. Together with the emerging genomic information Hox genes show a much more dynamic evolutionary history than previously assumed.
ARTICLE | doi:10.20944/preprints202106.0219.v1
Subject: Physical Sciences, Applied Physics Keywords: Evolutionary algorithms, shape of aerofoil, optimization of shape, Bezier-PARSEC model
Online: 8 June 2021 (12:17:22 CEST)
This work deals with aerofoil aerodynamic features optimization, not only to improve flight features, but also to improve economy, ecology and safety of parameters of flight technique. In cruise mission, occupying the most flight time, the most important parameter is aerodynamic drag, which directly influences the aeroplane operational economy of transportation. Drag reduction is adequately reflected in the fuel consumption reduction. Consumption reduction is also adequately reflected in the flight ecology. In take-off and landing mission, the safety is priority and directly influences the aerofoil geometry. For cruise mission the new modified evolutionary algorithms (EA) are used to parameters incoming to Bezier-PARSEC 3434 parametrization. Such aerofoil is processed and evaluated by the Xfoil program. The change of model parameters results to optimal aerofoil shape. The DCAG (Direct Control Aerofoil Geometry) is unique developed mechanical device, makes possible the change of curvature of aerofoil, and also aerofoil geometry. DCAG is based on the rotary principle, which makes it possible to define the curvature of aerofoil for every roll as well as defining the geometry in the variable parts of aerofoil. For take-off and landing mission the best combination of slots and flaps is choosed. To improve of laminarity and reduce turbulent flow the DCAG is used. The work results to optimization, which is 50 times faster in comparison to ordinary optimization, with minimum of input parameters (flight speed, chord length, range of angles of attack and fitness function). The optimized aerofoil can achieve savings in fuel consumption up to 44% in comparison with unoptimized aerofoil, the aerodynamic drag reduction up to 44%. The output was checked by ANSYS Fluent simulation.
ARTICLE | doi:10.20944/preprints202106.0148.v1
Subject: Engineering, Aerospace Engineering Keywords: Evolutionary algorithms; shape of aerofoil; optimization of shape; Bezier-PARSEC model
Online: 7 June 2021 (07:54:50 CEST)
AbstractThis work deals with aerofoil aerodynamic features optimization, not only to improve flight features, but also to improve economy, ecology and safety of parameters of flight technique.In cruise mission, occupying the most flight time, the most important parameter is aerodynamic drag, which directly influences the aeroplane operational economy of transportation. Drag reduction is adequately reflected in the fuel consumption reduction. Consumption reduction is also adequately reflected in the flight ecology. In take-off and landing mission, the safety is priority and directly influences the aerofoil geometry.For cruise mission the new modified evolutionary algorithms (EA) are used to parameters incoming to Bezier-PARSEC 3434 parametrization. Such aerofoil is processed and evaluated by the Xfoil program. The change of model parameters results to optimal aerofoil shape.The DCAG (Direct Control Aerofoil Geometry) is unique developed mechanical device, makes possible the change of curvature of aerofoil, and also aerofoil geometry. DCAG is based on the rotary principle, which makes it possible to define the curvature of aerofoil for every roll as well as defining the geometry in the variable parts of aerofoil.For take-off and landing mission the best combination of slots and flaps is choosed. To improve of laminarity and reduce turbulent flow the DCAG is used.The work results to optimization, which is 50 times faster in comparison to ordinary optimization, with minimum of input parameters (flight speed, chord length, range of angles of attack and fitness function).The optimized aerofoil can achieve savings in fuel consumption up to 44% in comparison with unoptimized aerofoil, the aerodynamic drag reduction up to 44%.The output was checked by ANSYS Fluent simulation.
ARTICLE | doi:10.20944/preprints202003.0126.v1
Subject: Engineering, Architecture, Building And Construction Keywords: change order; pricing; game theory; evolutionary stable strategy (ESS); system dynamics
Online: 8 March 2020 (01:19:49 CET)
Change orders have received considerable attention from researchers thus far, but none have considered pricing strategies of change orders through the interaction between general contractors and subcontractors. Previous studies found that contractors’ opportunistic bidding considering beyond-contractual reward (BCR) in the execution stage can be reduced by improving the construction management system and strengthening the supervision of contractors’ performance. However, the BCR remains in ecology of construction engineering. This study proposes an integrated evolutionary game theory-system dynamics model (ET-SD model) and simulates the pricing strategy of change orders between general contractors and subcontractors to explore the root cause of BCR phenomenon. Sensitivity analysis on the evolutionary dynamics of payoff is explored. Results reveal that change orders with BCR maintain Nash equilibrium and evolutionary stable strategy (ESS) unless changing the payoff structure between general and subcontractors’ pricing strategies. This study presents important managerial insights from the evolutionary game perspectives, nature of change orders, and payoff of the alternative.
ARTICLE | doi:10.20944/preprints201809.0096.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Montiaceae; phylogeny; phylogeography; long-distance dispersal; idiosyncrasy; Principal of Evolutionary Idiosyncraticity
Online: 5 September 2018 (12:02:42 CEST)
Montiaceae comprise a clade of at least 270 species plus about 20 accepted subspecific taxa, primarily of western America and Australia. The present paper is the first of a two-part work that seeks to evaluate evolutionary theory via metadata analysis of Montiaceae. In particular, it uses metadata analysis to evaluate the theory in theory-laden methods that have been applied in evolutionary analyses of Montiaceae. This part focuses on phylogeny and phylogeography. The second part focuses on phenotypic and ecological diversification. An emergent theme in this paper is the degree to which historical idiosyncrasy during Montiaceae evolution misleads quantitative methods of evolutionary reconstruction and phylogeographic interpretation. This suggests that idiosyncraticity itself is a fundamental property of evolution. The second part of this work elaborates this notion as the Principle of Evolutionary Idiosyncraticity. The present part describes idiosyncraticity in molecular phylogenetic and phylogeographic data and uses this notion to refine ideas on Montiaceae evolution. Phylogenetic metadata conflicts and conflicting phylogeographic interpretations are discussed. I conclude that, owing to PEI, quantitative methods of evolutionary analysis cannot be globally accurate, though they are useful heuristically. In contrast, classical narrative analysis is robust in the face of PEI.
ARTICLE | doi:10.20944/preprints202305.1278.v1
Subject: Engineering, Transportation Science And Technology Keywords: shared private charging pile; low-carbon urban transport; evolutionary game; policy making
Online: 18 May 2023 (05:31:18 CEST)
Choosing new energy vehicles for travel, especially electric vehicles, is an important component of building a low-carbon urban transportation system. However, the charging need of electric vehicle users is still constrained by the unreasonable layout and insufficient supply of public charging piles in the city. Private charging pile sharing as an alternative policy tool can play a very good role in solving this problem. But it needs decision-makers in urban transportation to take corresponding measures to promote. This paper constructs an evolutionary game model to study the decision behavior of participants in private piles sharing platform. Through numerical simulation analysis, it is found that under most parameter conditions, the government tends to establish a shared charging pile platform based on public interests. Private charging pile owners are influenced by the relationship between the cost of supply modification and revenue, and they tend to join the shared platform when they expect to recover the modification cost. The research conclusions of this paper will provide support for exploring how participants make decisions to maximize overall benefits in the development of low-carbon urban transportation.
Subject: Engineering, Automotive Engineering Keywords: Evolutionary Algorithms; differential evolution; constraints handling techniques; optimal power flow; renewable energy
Online: 10 May 2021 (10:22:10 CEST)
In this paper, a multi-operator differential evolution algorithm (MODE) is proposed to solve the Optimal Power Flow (OPF) problem and is called MODE-OPF. The MODE-OPF utilizes the strengths of more than one differential evolution (DE) operator in a single algorithmic framework. Additionally, an adaptive method (AM) is proposed to update the number of solutions evolved by each DE operator based on both the diversity of population and quality of solutions. This adaptive method has the ability to maintain diversity at the early stages of the optimization process and boost convergence at the later ones. The performance of the proposed MODE-OPF is tested by solving OPF problems for both small and large IEEE bus systems (i.e., IEEE-30 and IEEE-118) while considering the intermittent solar and wind power generation. To prove the suitability of this proposed algorithm, its performance has been compared against several state-of-the-art optimization algorithms, where MODE-OPF outperforms other algorithms in all experimental results and thereby improving a network's performance with lower cost. MODE-OPF decreases the total generation cost up to 24.08%, the real power loss up to 6.80% and the total generation cost with emission up to 8.56%.
HYPOTHESIS | doi:10.20944/preprints202004.0286.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; domain-fold; evolutionary fingerprint; conserved domain; point mutation; recombination
Online: 16 April 2020 (16:13:13 CEST)
The high transmissibility and replication of SARS-CoV-2 have been attributed to enhanced protein functions which are dependent on protein folding. Our in silico study endeavored to scrutinize SARS-CoV-2 ORF1ab by analyzing the conserved folding patterns of its transcribed proteins. Accordingly, the findings indicated that SARS-CoV-2 ORF1ab shares domain-specific fold-fingerprints with a spectrum of unrelated organisms. Closer observation revealed slight changes in folding patterns engendered with small variation in the intrinsic amino acid sequence. By correlating with the evolvability-potential of RNA-viruses and COVID-19 pandemic, we hypothesize that SARS-CoV-2 could undergo fast recombination with the host, SARS-CoV-2 minor variants and other viral species resulting in a reservoir of SARS-CoV-2 quasispecies. It is highly possible that natural selection will cause a future emergence of evolved SARS-CoV-2-descendants. Nonetheless, we hope that this insightful study will assist in elucidating SARS-CoV-2 protein functionalities, development of vaccines, and the possibility and nature of future emergence.
ARTICLE | doi:10.20944/preprints201912.0401.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: microbial eukaryotes; phylogeography; marine-freshwater transitions; evolutionary radiation; species flocks; Lake Baikal
Online: 31 December 2019 (03:57:14 CET)
Ancient lakes are among the most interesting models for evolution studies, because their biodiversity is the result of a complex combination of migration and speciation. Here, we investigate the origin of single celled planktonic eukaryotes from the oldest lake in the world – Lake Baikal. By using 18S rDNA metabarcoding we recovered 1,427 Operational Taxonomic Units (OTUs) belonging to protists populating surface waters (1-50 meters) and belonging to pico- and nano-plankton size fractions. The recovered communities resembled other lacustrine freshwater assemblages found elsewhere, especially the unclassified protists. However, our results suggest that a fraction of Baikal protists originated evolutionary recently from marine/brackish ancestors. Moreover, our results suggest that rapid radiation may have occurred among some protist taxa, partially mirroring what was already shown for multicellular organisms in Lake Baikal. We found potential species flocks in Stramenopiles, Alveolata, Opisthokonta, Archaeplastida, Rhizaria and Hacrobia. Putative flocks predominated in Chrysophytes, which are highly diverse in Lake Baikal. Some of the species, especially those from these flocks, may be endemic from Lake Baikal, because their 18S rDNA differed > 10% from known DNA. Overall, our study points to novel diversity of planktonic protists in Lake Baikal, some of which may have emerged in situ after evolutionary diversification.
ARTICLE | doi:10.20944/preprints201903.0047.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Gender Recognition; Speech Signal; Deep Learning; Evolutionary Search; PSO search; Wolf Search
Online: 4 March 2019 (13:42:02 CET)
The speech entailed in human voice comprises essentially para-linguistic information used in many voice-recognition applications. Gender voice-recognition is considered one of the pivotal parts to be detected from a given voice, a task that involves certain complications. In order to distinguish gender from a voice signal, a set of techniques have been employed to determine relevant features to be utilized for building a model from a training set. This model is useful for determining the gender (i.e, male or female) from a voice signal. The contributions are involved in two folds: (i) providing analysis information about well-known voice signal features using a prominent dataset, (ii) studying various machine learning models of different theoretical families to classify the voice gender, and (iii) using three prominent feature selection algorithms to find promisingly optimal features for improving classification models. Experimental results show the importance of sub-features over others, which are vital for enhancing the efficiency of classification models performance. Experimentation reveals that the best recall value is equal to 99.97%; 99.7% of two models of Deep Learning (DL) and Support Vector Machine (SVM) and with feature selection the best recall value is 100% for SVM techniques.
ARTICLE | doi:10.20944/preprints202304.0669.v1
Subject: Business, Economics And Management, Economics Keywords: Government intervention; Pest and disease control outsourcing; Evolutionary game; Simulation analysis; Policy instruments
Online: 21 April 2023 (03:55:43 CEST)
Abstract: The purpose of this study is to explore, from the perspective of government interven-tion, behavioral logic and game relationship among farmers, service organizations and the gov-ernment in the pest and disease control outsourcing system, as well as the endogenous motiva-tion of each subject. The results indicate that the stronger the willingness of each subject, the faster the stable state of joint pest and disease control among the three parties can be formed; In the case of implementing a single policy tool, the convergence rate of each party that imple-ments the regulatory policy alone is fast but may be unstable, while the rate is slow but more stable when a guidance- or incentive-based policy is solely applied; The effect of policy tool combination is much better than that of a single policy tool applied. The simultaneous imple-mentation of the three types of policy tools can form a policy system with both positive and negative mechanisms, which can maximize complementary and superposition effect.
ARTICLE | doi:10.20944/preprints202211.0103.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: multi-objective optimization; hypervolume indicator; Newton method; evolutionary algorithms; constraint handling; hypervolume scalarization
Online: 7 November 2022 (04:20:09 CET)
Recently, the Hypervolume Newton method (HVN) has been proposed as fast and precise indicator-based method for solving unconstrained bi-objective optimization problems with objective functions that are at least twice continuously differentiable. The HVN is defined on the space of (vectorized) fixed cardinality sets of decision space vectors for a given multi-objective optimization problem (MOP) and seeks to maximize the hypervolume indicator adopting the Newton-Raphson method for deterministic numerical optimization. To extend its scope to non-convex optimization problems the HVN method was hybridized with a multi-objective evolutionary algorithm (MOEA), which resulted in a competitive solver for continuous unconstrained bi-objective optimization problems. In this paper, we extend the HVN to constrained MOPs with in principle any number of objectives. We demonstrate the applicability of the extended HVN on a set of challenging benchmark problems and show that the new method can be readily be applied to solve equality constraints with a high precision problems, and to some extend also inequalities. We finally use HVN as local search engine within a MOEA and show the benefit of this hybrid method on several benchmark problems.
ARTICLE | doi:10.20944/preprints202210.0404.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2 Omicron; tMRCA; evolutionary rate; mutational profiling; selection pressure
Online: 26 October 2022 (08:15:25 CEST)
The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic antibodies and has undergone a sustained genetic evolution, resulting in the emergence of five distinct sub-lineages. However, the evolutionary dynamics of initially identified Omicron BA.1 and BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, and selection pressure analysis to track virus genetic changes that drive the early evolutionary dynamics of the Omicron. Based on the Omicron dataset chosen for the improved temporal signals and sampled globally between November 2021 and January 2022, most recent common ancestor (tMRCA) and substitution rates for BA.1 were estimated to be 18 September 2021 (95% highest posterior density (HPD) 04 August – 22 October 2021) and 1.435×10-3 (95% HPD = 1.021×10-3 – 1.869×10-3) substitution/site/year, respectively, whereas 03 November 2021 (95% highest posterior density (HPD) 26 September – 28 November 2021) and 1.074×10-3 (95% HPD = 6.444×10-4 – 1.586×10-3) substitution/site/year for BA.2 sub-lineage. The findings of this study suggest that the Omicron BA.1 and BA.2 sub-lineages originated independently and evolved over time. Furthermore, we identified multiple sites in spike protein undergoing continued diversifying selection that may alter the neutralization profile of BA.1. This study shed light on the ongoing global genomic surveillance and Bayesian molecular dating analyses to better understand the evolutionary dynamics the virus and, as a result, mitigate the impact of emerging variants on public health.
ARTICLE | doi:10.20944/preprints202208.0314.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: Differential Evolution; APGSK algorithm; Constrained Optimization; transformation; parameter adaptation; multi-operator; Evolutionary Algorithms
Online: 17 August 2022 (09:47:59 CEST)
Real-world optimization problems are often gov- erned by one or more constraints. Over the last few decades, extensive research has been performed in Constrained Opti- mization Problems (COPs) fueled by advances in computational power. In particular, Evolutionary Algorithms (EAs) are a preferred tool for practitioners for solving these COPs within practicable time limits. We propose a novel hybrid Evolutionary Algorithm based on the Differential Evolution algorithm and Adaptive Parameter Gaining Sharing Knowledge-based algo- rithm to solve global real-world constrained parameter space. The proposed CHAGSKODE algorithm leverages the power of multiple adaptation strategies concerning the control parameters, search mechanisms, as well as uses knowledge sharing between junior and senior phases. We test our method on the benchmark functions taken from the CEC2020 special session & competition on real-world constrained optimization. Experimental results indicate that CHAGSKODE is able to achieve state-of-the- art performance on real-world constrained global optimization when compared against other well-known real-world constrained optimizers.
ARTICLE | doi:10.20944/preprints202208.0307.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: constrained optimization; multi-operator; multi-parameter adaptation; ensemble constraint handling techniques; Evolutionary Algorithms
Online: 17 August 2022 (08:35:44 CEST)
Real-world optimization problems are often governed by one or more constraints. Over the last few decades, extensive research has been performed in Constrained Optimization Problems (COPs) fueled by advances in computational intelligence. In particular, Evolutionary Algorithms (EAs) are a preferred tool for practitioners for solving these COPs within practicable time limits. We propose an ensemble of multi- method hybrid EA framework with four mutation operators, two crossover operators, multi-search [Differential Evolution (DE) & Gaining Sharing Knowledge (GSK)] optimization algorithm, and ensemble of constraint handling techniques to solve global real- world constrained optimization problem. The proposed frame- work FEPEA has an ascendancy of multiple adaptation strategies concerning the control parameters, search mechanisms, two sub-populations as well as uses knowledge sharing mechanism between junior and senior phases. The algorithm also combines the power of four popular constraint handling techniques (CHT) and uses a voting mechanism to select any particular CHT. On top of that, this algorithm also uses both linear and non- linear population size reduction in every step of the evolutionary process. We test our method on 57 real-world problems provided as part of the CEC 2020 special session & competition on real- world constrained optimization benchmark suite. Experimental results indicate that FEPEA is able to achieve state-of-the- art performance on real-world constrained global optimization when compared against other well-known real-world constrained optimizers.
ARTICLE | doi:10.20944/preprints202112.0506.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: multi-objective; evolutionary algorithms; Pareto optimality; Wasserstein distance; network vulnerability; resilience; sensor placement.
Online: 31 December 2021 (11:01:51 CET)
This paper is focused on two topics very relevant in water distribution networks (WDNs): vulnerability assessment and the optimal placement of water quality sensors. The main novelty element of this paper is to represent the data of the problem, in this case all objects in a graph underlying a water distribution network, as discrete probability distributions. For vulnerability (and the related issue of re-silience) the metrics from network theory, widely studied and largely adopted in the water research community, reflect connectivity expressed as closeness centrality or, betweenness centrality based on the average values of shortest paths between all pairs of nodes. Also network efficiency and the related vulnerability measures are related to average of inverse distances. In this paper we propose a different approach based on the discrete probability distribution, for each node, of the node-to-node distances. For the optimal sensor placement, the elements to be represented as dis-crete probability distributions are sub-graphs given by the locations of water quality sensors. The objective functions, detection time and its variance as a proxy of risk, are accordingly represented as a discrete e probability distribution over contamination events. This problem is usually dealt with by EA algorithm. We’ll show that a probabilistic distance, specifically the Wasserstein (WST) distance, can naturally allow an effective formulation of genetic operators. Usually, each node is associated to a scalar real number, in the optimal sensor placement considered in the literature, average detection time, but in many applications, node labels are more naturally expressed as histograms or probability distributions: the water demand at each node is naturally seen as a histogram over the 24 hours cycle. The main aim of this paper is twofold: first to show how different problems in WDNs can take advantage of the representational flexibility inherent in WST spaces. Second how this flexibility translates into computational procedures.
HYPOTHESIS | doi:10.20944/preprints202105.0234.v2
Subject: Physical Sciences, Applied Physics Keywords: Theory of Life; Definition of Life; Evolutionary Theory; Origin of Life; Electron Bifurcation; Hydrothermal Vents; Biophysics; Biological Physics
Online: 17 May 2021 (09:46:37 CEST)
The definition, origin and recreation of life remain elusive. As others have suggested, only once we put life into reductionist physical terms will we be able to solve those questions. To that end, this work proposes the phenomenon of life to be the product of two dissipative mechanisms. From them, one reinterprets extant biological life and deduces a testable scenario for its origin. The proposed theory of life allows its replication, reinterprets ecological evolution, brings new constraints to astrobiology and lays the foundations for groundbreaking technologies.
REVIEW | doi:10.20944/preprints202009.0091.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Evolutionary dynamics; life-history stages; mating systems; biotic interactions; climatic variability; ecological genomics
Online: 4 September 2020 (08:13:40 CEST)
Contemporary climate change is exposing plant populations to novel combinations of temperatures, drought stress, [CO2] and other abiotic and biotic conditions. These changes are rapidly disrupting the evolutionary dynamics of plants. Despite the multifactorial nature of climate change, most studies typically manipulate only one climatic factor. In this opinion piece, we seek to explore how climate change factors interact with each other and with biotic pressures to alter evolutionary processes. We first explore the ramifications of climate change for key life history stages (germination, growth and reproduction). We then examine how mating system variation influences population persistence under rapid environmental change and propose that mixed mating could be advantageous in future climates. Furthermore, we discuss how spatial and temporal mismatches between plants and their mutualists and antagonists could promote or constrain adaptive responses to climate change. For example, plant-virus interactions vary from highly pathogenic to mildly facilitative, and are partly mediated by temperature, moisture availability and [CO2]. Will host plants exposed to novel, stressful abiotic conditions be more susceptible to viral pathogens? Finally, we propose novel experimental approaches that could illuminate how plants will cope with unprecedented global change, such as resurrection studies combined with experimental evolution, genomics or epigenetics.
CONCEPT PAPER | doi:10.20944/preprints202008.0648.v1
Subject: Biology And Life Sciences, Virology Keywords: Covid-19; case fatality rate; infection fatality rate; evolution of virulence; evolutionary medicine
Online: 30 August 2020 (10:26:58 CEST)
In the ongoing Covid-19 pandemic, in the global data on the case fatality ratio and other indices reflecting death rate, there is a consistent downward trend from mid-April to mid-August. The downward trend can be an illusion caused by biases and limitations of data or it could faithfully reflect a declining death rate. A variety of explanations for this trend are possible, but a systematic analysis of the testable predictions of the alternative hypotheses has not yet been attempted. We state six testable alternative hypotheses, analyse their testable predictions using public domain data and evaluate their relative contributions to the downward trend. We show that a decline in the death rate is real; changing age structure of the infected population and evolution of the virus towards reduced virulence are the most supported hypotheses and together contribute to major part of the trend. The testable predictions from other explanations including altered testing efficiency, time lag, improved treatment protocols and herd immunity are not consistently supported, or do not appear to make a major contribution to this trend although they may influence some other patterns of the epidemic.
HYPOTHESIS | doi:10.20944/preprints202008.0459.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: colonial life-history; major evolutionary transition (MET); cooperation; modularity; biological information; heterochrony; tunicate
Online: 20 August 2020 (13:05:33 CEST)
The diversification of life-histories is mediated by cooperation, innovations of biological information, modularity, and heterochrony in developmental processes. These processes are defined, contextualized, and exemplified, studying the evolution of coloniality (i.e. life-history involving modularization of the multicellular individual) in the family of benthic tunicates Styelidae. This study proposes that in these colonial tunicates there is an inter-generational division of labor, where one generation is feeding, a second is developing by morphogenetic processes, and a third is aging by programmed cell death and phagocytosis. The communication system developed in these colonies is mediated, by changes in proportion, location, and gene expression of specialized blood cells. Colonial life-history in animals is related to the reduction of individual size; development of extra-corporeal tissues to interconnect zooids; the inter-generational division of labor; and the reduction of zooid’s individuality. Processes analogous with the widely accepted major evolutionary transitions (METs), suggesting that coloniality could be studied as a MET. The understanding of colonial life-histories could provide information about key mechanisms for life diversification.
ARTICLE | doi:10.20944/preprints201710.0104.v1
Subject: Computer Science And Mathematics, Applied Mathematics Keywords: evolutionary dynamics; quantitative trait; Manhattan norm; Euclidean norm; Chebyshev norm; parasitism; exploitation; egalitarianism
Online: 16 October 2017 (07:35:46 CEST)
Various distance metrics and their induced norms are employed in the quantitative modeling of evolutionary dynamics. Minimization of these distance metrics when applied to evolutionary optimization are hypothesized to result in different outcomes. Here, we apply the different distance metrics to the evolutionary trait dynamics brought about by the interaction between two competing species infected by parasites (exploiters). We present deterministic cases showing the distinctive selection outcomes under the Manhattan, Euclidean and Chebyshev norms. Specifically, we show how they differ in the time of convergence to the desired optima (e.g., no disease), and in the egalitarian sharing of carrying capacity between the competing species. However, when randomness is introduced to the population dynamics of parasites and to the trait dynamics of the competing species, the distinctive characteristics of the outcomes under the three norms become indistinguishable. Our results provide theoretical cases when evolutionary dynamics using different distance metrics exhibit similar outcomes.
REVIEW | doi:10.20944/preprints202301.0271.v1
Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: evolutionary mismatch; diagnosis of labor; prospective diagnosis; cervical dilatation; uterine contractions; pain intensity; metabolomic.
Online: 16 January 2023 (07:25:19 CET)
The difficulty in the clinical diagnosis of labor is due to an evolutionary mismatch. The ability to hide the signs and symptoms of labor is an evolutionary trait that was once advantageous, but became maladaptive due to environmental changes. Prospective diagnosis of labor is not possible with certainty using only clinical criteria; however, by analyzing the urinary metabolome of women in labor, this diagnosis is likely possible in all cases. In this review, we explain why the two methods (clinical and metabolomic) differ in efficacy and sensitivity, and we try to fit this difference into an evolutionary framework that explains these discrepancies considering evolutionary mismatch. The study of metabolomics allows the truth to emerge from the past, and the diffusion of metabolomic techniques and their application to clinical reality in the form of POC (Point of Care) could change the management of labor and childbirth in the future.
ARTICLE | doi:10.20944/preprints202206.0413.v1
Subject: Engineering, Electrical And Electronic Engineering Keywords: Simulated annealing quasi-Affine Transformation Evolutionary (SA-QUATRE); Coordinated optimization design; Power system stabilizer
Online: 30 June 2022 (03:48:32 CEST)
This paper proposes a parameter coordination optimization design of Power System Stabilizer (PSS) based on an improved Quasi-Affine Transformation Evolutionary (QUATRE) algorithm to suppress low-frequency oscillation and improve the dynamic stability of power system. To begin, the Simulated Annealing (SA) algorithm randomly updates the globally optimal solution of each QUATRE iteration and matches the inferior solution with a certain probability to escape the local extreme point. This new algorithm is first applied to power system. Second, Since damping ratio is one of the criteria to measure the dynamic stability of power system, this paper sets the objective function according to the principle of maximization of damping coefficient of electromechanical mode, and uses SA-QUATRE to search a group of global optimal PSS parameter combinations to improve the stability margin of the system as much as possible. Finally, the method's rationality and validity were validated by applying it to the simulation examples of IEEE 4-machine 2-area system with different operation states. The comparison with the traditional optimization algorithm shows that the proposed method has more advantages for multi-machine PSS parameter coordination optimization, and can restrain the low-frequency oscillation of power system more effectively and enhance the system stability.
CONCEPT PAPER | doi:10.20944/preprints202105.0767.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: evidential integration; causal explanation; early animal evolution; phylogenetics; macroevolution; evolutionary scenario; cross-disciplinary research
Online: 31 May 2021 (12:25:44 CEST)
Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have collectively transformed our understanding of the evolutionary history of animals. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and traditional phylogenies. Here, I argue that tackling this multifaceted problem lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent developments in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence and theory. I then argue that integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond.
HYPOTHESIS | doi:10.20944/preprints202012.0069.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: aging; anti-inflammaging helminth hypothesis; evolutionary medicine; helminth therapy; hygiene theory; inflammaging; old friends
Online: 2 December 2020 (15:25:37 CET)
Evolutionary medicine argues that disease can arise because modern conditions do not match those in which we evolved. For example, a decline in exposure to commensal microbes and gastrointestinal helminths in developed countries has been linked to increased prevalence of allergic and autoimmune inflammatory disorders (the hygiene hypothesis). Accordingly, microbial and helminthic probiotic therapies have been explored as Darwinian treatments for these disorders. A further possibility is that loss of old friend commensals also increases the sterile, aging-associated inflammation known as inflammaging, that contributes to a range of age-related diseases, including cardiovascular disease, dementia and cancer. Interestingly, Crowe et al. (2020) recently reported that treatment with a secreted glycoprotein from a parasitic nematode can protect against murine aging by induction of anti-inflammatory mechanisms. Here, we explore the hypothesis that restorative helminth therapy would have anti-inflammaging effects. Could worm infections provide broad-spectrum protection against age-related disease?
ARTICLE | doi:10.20944/preprints202011.0002.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: adaptive security; evolutionary game; Internet of Things; Smart grid; advanced metering infrastructure; smart home
Online: 2 November 2020 (08:08:12 CET)
We applied evolutionary game theory to extend a resource constrained security game model for confidentiality attacks in an Advanced Metering Infrastructure (AMI), which is a component of IoT-enabled Smart Grids. The AMI is modelled as a tree structure where each node aggregates the information of its children before encrypting it and passing it on to its parent. As a part of the model, we developed a discretization scheme for solving the replicator equations. The aim of this work is to explore the space of possible behaviours of attackers and to develop a framework where the AMI nodes adaptively select the most profitable strategies. Using this model, we simulated the evolution of a population of attackers and defenders on various cases resembling the real life implementation of AMI. We discuss in depth how to enhance security in AMI using evolutionary game theory either by a priori analysis or as a tool to run dynamic and adaptive infrastructure defence.
ARTICLE | doi:10.20944/preprints201909.0325.v1
Subject: Arts And Humanities, Philosophy Keywords: speciesism; intuition; evolutionary debunking arguments; experimental philosophy; species-egalitarianism; conservation; singer; williams; kagan; jacquet
Online: 29 September 2019 (06:07:31 CEST)
This article argues for five correctives to the current ethical debate about speciesism, and proposes normative, conceptual, methodological and experimental avenues to move this debate forward. Firstly, it clarifies the Principle of Equal Consideration of Interests and points out limitations of its scope. Secondly, it disambiguates between ‘favouritist’ and ‘species-relative’ views about moral treatment. Thirdly, it argues that not all moral intuitions about speciesism should be given equal weight. Fourthly, it emphasizes the importance of empirical research to corroborate statements about ‘folk speciesism’. Fifthly, it disambiguates between the moral significance of species and the moral status of their individual members. For each of these issues, it is shown that they have either been overlooked, or been given inapt treatment, in recent contributions to the debate. Building on the correctives, new directions are proposed for ethical inquiry into the moral relevance of species and species membership.
ARTICLE | doi:10.20944/preprints202105.0504.v1
Subject: Business, Economics And Management, Accounting And Taxation Keywords: livestreaming e-commerce; evolutionary game; multi-party behavior; replicator dynamics equation; three-party game theory
Online: 21 May 2021 (08:32:45 CEST)
With the diversified development of media forms, livestreaming e-commerce has become a new sales model. Unlike the traditional sales model, this paper constructs a three-party game model composed of manufacturers, social media influencers and consumers based on the livestreaming model. It explores the equilibrium strategy selections of each participant in the supply chain system. In analyzing the evolutionary game stability of each participant, this paper obtains the equilibrium strategy and stability factors by analysis of the income and expenditure matrix. It uses the simulation model to analyze reasons for strategy selections of different game participants in the livestreaming e-commerce model. The results show that the strategies of manufacturers, social media influencers and consumers' selections have different impacts on their decision-making mechanism, and man-ufacturers are more sensitive to consumers' active participation in livestreaming e-commerce.
ARTICLE | doi:10.20944/preprints202010.0168.v2
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Genetic Programming; Evolutionary Computation; Machine Learning; Classification; Multiclass Classification; Feature Construction; Hyper-features; Spectral Indices
Online: 24 December 2020 (08:59:19 CET)
Genetic Programming (GP) is a powerful Machine Learning (ML) algorithm that can produce readable white-box models. Although successfully used for solving an array of problems in different scientific areas, GP is still not well known in Remote Sensing. The M3GP algorithm, a variant of the standard GP algorithm, performs Feature Construction by evolving hyper-features from the original ones. In this work, we use the M3GP algorithm on several sets of satellite images over different countries to create hyper-feature from satellite bands to improve the classification of land cover types. We add the evolved hyper-features to the reference datasets and observe a significant improvement of the performance of three state-of-the-art ML algorithms (Decision Trees, Random Forests and XGBoost) on multiclass classifications and no significant effect on the binary classifications. We show that adding the M3GP hyper-features to the reference datasets brings better results than adding the well-known spectral indices NDVI, NDWI and NBR. We also compare the performance of the M3GP hyper-features in the binary classification problems with those created by other Feature Construction methods like FFX and EFS.
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: artificial intelligence; bioinformatics; computational biology; data mining & machine learning; evolutionary studies; mathematical biology; animal behavior
Online: 6 November 2019 (05:07:24 CET)
Industrial pig farming is associated with negative technological pressure on the bodies of pigs. Leg weakness and lameness are the sources of significant economic loss in raising pigs. Therefore, it is important to identify predictors of limb condition. This work presents assessments of the state of limbs using indicators of growth and meat characteristics of pigs based on machine learning algorithms. We have evaluated and compared the accuracy of prediction for several ML classification algorithms (Random Forest, K-Nearest Neighbors, Artificial Neural Networks, C50Tree, Support Vector Machines, Naive Bayes, Generalized Linear Models, Boost, and Linear Discriminant Analysis) and have identified the Random Forest and K-Nearest Neighbors as the best performing algorithms for predicting pig leg weakness using a small set of simple measurements that can be taken at an early stage of animal development. Muscle Thickness, Back Fat amount, and Average Daily Gain serve as significant predictors of conformation of pig limbs. Our work demonstrates the utility and relative ease of using machine learning algorithms to assess the state of limbs in pigs based on growth rate and meat characteristics.
ARTICLE | doi:10.20944/preprints201812.0205.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Diminished fitness return, mutation rate tuning, Darwinian evolution; neutral evolution; punctuated equilibrium; unified evolutionary theory
Online: 17 December 2018 (16:10:52 CET)
I propose a dynamic evolution hypothesis regarding the evolution of organisms by incorporating both diminished fitness returns and mutation rate tuning during adaptation to a constant environment. Basically, accumulating evidence from life history studies conducted over the past 70 years suggests that the evolution of individual fitness is subject to ecological constraints, leading to the evolutionary existence of an upper limit of individual fitness (ULIF). Given the existence of the ULIF, organismal evolution, which might initially have relatively great fitness returns through primarily Darwinian evolution, will eventually be subject to diminished fitness returns towards zero. With the diminished fitness return, Darwinian selection strength may eventually become smaller than the power of random genetic drift, leading to the occurrence of neutral evolution at both phenotypic and molecular levels. Meanwhile, mutation rates may change from an initial increase, due to the relatively strong fitness return, to subsequent decreases, due to both the diminished fitness return of beneficial mutations and the cost of deleterious mutations. The diminished fitness returns with subsequently reduced mutation rates are two potential evolution barriers leading to eventual evolutionary stasis. These findings provide important insights for understanding the conditions for the occurrences of different evolutionary patterns. Darwinian evolution theory, neutral evolution theory and punctuated equilibrium theory can be unified in the context of the dynamic evolution hypothesis formulated in this study.
ARTICLE | doi:10.20944/preprints202302.0064.v1
Subject: Engineering, Civil Engineering Keywords: Riparian vegetation; Experimental meandering channel; Scour pit; Downstream scroll bars; Inner-bank cutting; evolutionary spectral analysis
Online: 3 February 2023 (08:50:20 CET)
We conducted the meander evolution experiments incorporating the effects of riparian vegetation and the series of upper vortex flow disturbances induced by a scour pit simultaneously. Two employed nonlegume plants with salinity and alkalinity resistance, had uniform degrees of seedling normal growth and different lengths of root networks. Our results show that riparian vegetation in general can consolidate the single-thread channel planform without branching outward under the flooding flow conditions. Transverse point bars on inner banks were instead by downstream scroll bars in overall channel for long, unless the coupling of riparian vegetation and flood scour. Shallow-rooted plant was inadequate to resist the inner-bank cutting effect brought by the upper vortex flow. Deep-rooted plant can stabilize the bank-lines and thalweg significantly, but that was susceptible to locally low vegetation coverage. Using evolutionary spectral analysis based on thalweg, we found streamwise high-frequency distribution of bed topography mainly concentrated downstream the bifurcation interface in unvegetated scenario when faced with a flood, shrank to the upper isolated turning interface in shallow-rooted scenario, and conversely stood out along the bare roots disturbed region in deep-rooted scenario. This experimental study expands a much wider understanding of vegetation effects in hydro-bio-geomorphological systems engineering.
CONCEPT PAPER | doi:10.20944/preprints202108.0416.v1
Subject: Physical Sciences, Fluids And Plasmas Physics Keywords: Natural selection; individuality; levels of selection; evolutionary biology; physics; philosophy of biology; exobiology; origins of life
Online: 20 August 2021 (13:42:15 CEST)
Natural selection is commonly seen not just as an explanation for adaptive evolution, but as the inevitable consequence of “heritable variation in fitness among individuals”. Although it remains embedded in biological concepts, such a formalisation makes it tempting to explore whether this precondition may be met not only in life as we know it, but also in other physical systems. This would imply that these systems are subject to natural selection and may perhaps be investigated in a biological framework, where properties are typically examined in light of their putative functions. Here we relate the major questions that were debated during a three-day workshop devoted to discussing whether natural selection may take place in non-living physical systems. We start this report with a brief overview of research fields dealing with “life-like” or “proto-biotic” systems, where mimicking evolution by natural selection in test tubes stands as a major objective. We contend the challenge may be as much conceptual as technical. Taking the problem from a physical angle, we then discuss the framework of dissipative structures. Although life is viewed in this context as a particular case within a larger ensemble of physical phenomena, this approach does not provide general principles from which natural selection could be derived. Turning back to evolutionary biology, we ask to what extent the most general formulations of the necessary conditions or signatures of natural selection may be applicable beyond biology. In our view, such a cross-disciplinary jump is in large part impeded by reliance on individuality as a central yet implicit and loosely defined concept. Overall, these discussions thus lead us to conjecture that understanding, in physico-chemical terms, how individuality emerges and how it can be recognised, will be essential in the search for instances of evolution by natural selection outside of living systems.  Natural Selection Beyond Life? Observing the physico-chemical world through Darwinian glasses; 12-15 November 2019 - Institut d'Etudes Scientifiques, Cargèse, France
ARTICLE | doi:10.20944/preprints201907.0285.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: extended evolutionary synthesis; inheritance of acquired characters; stress-induced mutagenesis; fitness-dependent sex; horizontal gene transfer
Online: 25 July 2019 (08:24:32 CEST)
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.
REVIEW | doi:10.20944/preprints202011.0302.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: evolutionary cell biology; evo-devo; animal origins; choanoflagellates; history of science; Haeckel; Metchnikoff; Blastaea; origin of multicellularity
Online: 10 November 2020 (11:18:25 CET)
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 19th 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.
ARTICLE | doi:10.20944/preprints201902.0233.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: deep neural network architectures; supervised learning; unsupervised learning; testing neural networks; applications of deep learning; evolutionary computation
Online: 26 February 2019 (04:02:00 CET)
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.
ARTICLE | doi:10.20944/preprints201808.0330.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ancestry of orthogs, ancestry of gene families; gene genealogy; FUCA; LUCA; origins of life; gradualism; evolutionary biology
Online: 18 August 2018 (08:24:09 CEST)
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.
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: D-Glutamate and D-Glutamate racemase; Mitochondria; evolutionary approach; gut microbiota; Amyotrophic Lateral Sclerosis (ALS); Motor neurone disease (MND)
Online: 30 September 2019 (03:13:27 CEST)
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.
ARTICLE | doi:10.20944/preprints201901.0282.v1
Subject: Computer Science And Mathematics, Robotics Keywords: artificial intelligence; neuro-evolution; swarm intelligence; robotic swarm; cooperative robotics; free-energy principle; active inference; evolutionary computation; novelty search
Online: 28 January 2019 (15:51:25 CET)
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.
ARTICLE | doi:10.20944/preprints201712.0041.v1
Subject: Arts And Humanities, Archaeology Keywords: conceptual model; Evolutionary Determinants of Health; greened city; human evolution; Palaeolithic genome; urban greenspace; urban wellbeing; Western Lifestyle Diseases
Online: 7 December 2017 (07:15:37 CET)
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’.
REVIEW | doi:10.20944/preprints201911.0265.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: craft brewing; saccharomyces cerevisiae; saccharomyces eubayanus; hybrids; 4-vinyl guaiacol; non-conventional yeasts; evolutionary engineering; artisanal fermented food; natural biodiversity
Online: 24 November 2019 (04:35:23 CET)
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.
ARTICLE | doi:10.20944/preprints202107.0343.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Evolutionary Games; Cooperation; Consensus; Dynamics on Networks; Stag-Hunt Game; Chicken Game; Mixed Nash Equilibrium; Self-regulation; Stable Equilibrium; Complex Systems
Online: 15 July 2021 (09:26:30 CEST)
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.
ARTICLE | doi:10.20944/preprints202003.0381.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: algorithmic design; metaheuristic optimisation; evolutionary computation; swarm intelligence; memetic computing; parameter tuning; fitness trend; Wilcoxon Rank-Sum; Holm-Bonferroni; benchmark suite
Online: 26 March 2020 (04:03:41 CET)
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.
ARTICLE | doi:10.20944/preprints201902.0041.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Approximate Bayesian computation; demographic history; distributional shift; evolutionary history; machine learning; phylogeography; range contraction; range expansion; Reticulitermes flavipes; species distribution modeling
Online: 4 February 2019 (16:47:40 CET)
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.
ARTICLE | doi:10.20944/preprints201809.0193.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: evolutionary innovation, cell type evolution, cellular stress response, evolution of gene regulation, gene regulatory network evolution, decidual cell, evolution of pregnancy
Online: 11 September 2018 (11:41:34 CEST)
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.
ARTICLE | doi:10.20944/preprints202111.0083.v2
Subject: Engineering, Control And Systems Engineering Keywords: RAMI4.0; Asset Administration Shell (AAS); Multi-Agent Systems (MAS); Evolutionary Assembly Systems (EAS); Engineering Capabilities Based, Production Flow Scheme (PFS); Petri Net (PN).
Online: 18 November 2021 (14:26:42 CET)
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.
REVIEW | doi:10.20944/preprints201809.0007.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: Particle Swarm Optimization; Swarm Intelligence; Evolutionary Computation; Intelligent Agents; Optimization; Hybrid Algorithms; Heuristic Search; Approximate Algorithms; Robotics and Autonomous Systems; Applications of PSO
Online: 2 September 2018 (15:29:55 CEST)
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.
REVIEW | doi:10.20944/preprints202209.0487.v2
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Immunology; innate immunity; immunogenetics; noncoding genome; tRNA biology; evolutionary genetics (list 3-10 specific to the article yet reasonably common within the subject discipline)
Online: 1 November 2022 (09:55:10 CET)
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.
REVIEW | doi:10.20944/preprints202203.0388.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: phenotypic polymorphism; structural genomics; chromosomal inversion; supergene; functional genomics; hormonal plasticity; frequency-dependent selection; cryptic female choice of sperm; sexual selection; eco-evolutionary dynamics
Online: 30 March 2022 (10:15:55 CEST)
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.
ARTICLE | doi:10.20944/preprints201809.0566.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Montiaceae; life history; climate niche; polyploidy; phylogenetic comparative analysis (PhCA); natural selection (NS); natural drift (ND); chaos; stochasticity; determinism; principle of evolutionary idiosyncraticity (PEI)
Online: 2 October 2018 (12:06:57 CEST)
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.
ARTICLE | doi:10.20944/preprints202304.0498.v2
Subject: Social Sciences, Geography, Planning And Development Keywords: Maritime Spatial Planning (MSP); Green Deal; blue economy; fishing communities; fisheries co-management; climate change; local development; evolutionary governance; commonisation; blue equity; blue justice; Greece
Online: 29 April 2023 (05:06:02 CEST)
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.
ARTICLE | doi:10.20944/preprints202202.0079.v1
Subject: Social Sciences, Political Science Keywords: Natural Social Contract; Co-evolutionary governance; Transformative governance; Institutional change; Policy mixes; Transformative Social-Ecological Innovation; Transformative Social Innovation; Social Innovation; Sustainability Transition; Societal Transition
Online: 7 February 2022 (11:43:04 CET)
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.
ARTICLE | doi:10.20944/preprints202101.0198.v1
Subject: Biology And Life Sciences, Virology Keywords: epidemiological history of HCV-2; HCV-2 subtypes; evolutionary demography of HCV-2; phylodynamics of HCV-2 in Italy and Albania; HCV-2 Re estimation
Online: 11 January 2021 (13:10:30 CET)
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.
ARTICLE | doi:10.20944/preprints202207.0084.v1
Subject: Arts And Humanities, Philosophy Keywords: philosophy of emotion; science of emotion; meta-semantic pluralism; embodied cognition; mind; mind-body problem; perception; cognition; emotion; cultural evolution; dual-inheritance theory; evolutionary norm psychology
Online: 6 July 2022 (03:55:00 CEST)
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.
ARTICLE | doi:10.20944/preprints202006.0165.v2
Subject: Biology And Life Sciences, Virology Keywords: Conserved signature indels (CSIs) specific for SARS and SARS-CoV-2-related viruses. Molecular markers distinguishing different clades of Sarbecovirus, Evolutionary relationships between SARS and SARS-CoV-2-related viruses, Origin of SARS-CoV-2 and Pangolin CoV_MP789 viruses, Novel sequence and structural features of spike and nucleocapsid proteins. Genetic recombination.
Online: 26 August 2020 (10:17:16 CEST)
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.
ARTICLE | doi:10.20944/preprints201810.0628.v1
Subject: Arts And Humanities, Philosophy Keywords: natural philosophy; philosophy of science; Jungian psychology; depth psychology; analytical psychology; phenomenological psychology; evolutionary psychology; active imagination; Aristotle’s four causes; aesthetics in science; philosophy as a way of life
Online: 26 October 2018 (11:30:46 CEST)
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.
Subject: Engineering, Civil Engineering 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
Online: 25 March 2019 (10:25:18 CET)
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.
Subject: Engineering, Civil Engineering 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
Online: 25 March 2019 (10:21:45 CET)
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.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