Search Results (19)

This paper examines the extended evolutionary synthesis’s critique of the modern synthesis, and introduces the “survival of the luckiest” framework as a mediating perspective. This framework preserves the core principles of the modern synthesis, while incorporating an additional element of randomness arising from the interplay of natural and sexual selection. Although the extended synthesis emphasizes developmental processes, niche construction, epigenetic inheritance, and horizontal gene transfer, it also neglects the critical role of this additional randomness. By critically analyzing the evidence provided by proponents of the extended synthesis, we show that the survival of the luckiest framework offers compelling alternative explanations. In doing so, it bridges the modern synthesis with principles of self-organization and emergence, addressing key gaps while maintaining its foundational tenets. Full article

The evolution of the translation system is a fundamental issue in the quest for the origin of life. A feasible evolutionary scenario necessitates the autonomous emergence of a protoribosome capable of catalyzing the synthesis of the initial peptides. The peptidyl transferase center (PTC) region in the modern ribosomal large subunit is believed to retain a vestige of such a prebiotic non-coded protoribosome, which would have self-assembled from random RNA chains, catalyzed peptide bond formation between arbitrary amino acids, and produced short peptides. Recently, three research groups experimentally demonstrated that several distinct dimeric constructs of protoribosome analogues, derived predicated on the approximate 2-fold rotational symmetry inherent in the PTC region, possess the ability to spontaneously fold, dimerize, and catalyze the formation of peptide bonds and of short peptides. These dimers are examined, aiming at retrieving information concerned with the characteristics of a prebiotic protoribosome. The analysis suggests preconditions for the laboratory re-creation of credible protoribosome analogues, including the preference of a heterodimer protoribosome, contradicting the common belief in the precedence of homodimers. Additionally, it derives a dynamic process which possibly played a role in the spontaneous production of the first bio-catalyzed peptides in the prebiotic world. Full article

This paper introduces an application of the dandelion optimization (DO) algorithm in antenna arrays. This is the first time that the DO algorithm has been used for optimizing antenna arrays. For antenna array optimization, sidelobe level (SLL) and deep nulls are key technical indicators. A lower SLL can improve the signal-to-noise ratio and reduce the impact of clutter signals outside the main beam. Deep nulls need to be aligned with the direction of interference to eliminate the influence of interference sources. The combination of the two can effectively improve the anti-interference ability of the entire system. Therefore, antenna arrays with ultra-low sidelobes and ultra-deep nulls are currently hot in the field of antenna array design and are also some of the key technologies needed to achieve modern high-performance radar systems. As a new type of evolutionary algorithm inspired by nature, the DO algorithm is inspired by the wind propagation behavior of dandelions in nature. This algorithm iteratively updates the population from three stages of ascent, descent, and landing, ultimately finding the optimal position. It has good optimization ability in solving complex problems such as those involving nonlinearity, discreteness, and non-convexity, and the antenna array pattern synthesis optimization problem belongs to multivariate nonlinear problems. Therefore, the DO algorithm can be effectively applied in the field of antenna array optimization. In this work, we use the following method to obtain an optimized pattern of a linear array with the lowest sidelobe level (SLL), null placement in particular directions, and a lower notch in particular directions: by controlling the antenna array’s element spacing and leaving the phase unchanged to optimize the current amplitudes and by controlling the excitation current and phase fixation of the antenna array and changing the element spacing. In the first and second examples, different algorithms are used to reduce the SLL of the antenna. In the first example, the DO algorithm reduces the SLL to −33.37 dB, which is 2.67 dB, 2.67 dB, 3.77 dB, 2.74 dB, and 2.52 dB lower than five other algorithms. In the second example, the SLL optimized by the DO algorithm is −42.56 dB, which is 5.04 dB and 1.48 dB lower than two other algorithms. In both examples, the DO algorithm reduces the SLL lower than other algorithms when the main lobe of the antenna is not significantly widened. Examples 3, 4, and 5 use the DO algorithm to optimize the amplitude of the current, generating deep nulls and deep notches in specific directions. In Example 3, the DO algorithm obtains a depth of nulls equal to −187.6 dB, which is 66.7 dB and 44.3 dB lower than that of the flower pollination algorithm (FPA) and the chaotic colony predation algorithm (CCPA), respectively. In Example 4, the deep null obtained by the DO algorithm is as low as −98.69 dB, which is 6.67 dB lower than the deep null obtained by the grey wolf optimization (GWO) algorithm. In Example 5, the deep notch obtained by the DO algorithm is as low as −63.1 dB, which is 6.4 dB and 1.9 dB lower than the spider monkey optimization (SMO) algorithm and the grasshopper optimization algorithm (GOA), respectively. The data prove that the DO algorithm produces deeper nulls and notches than other algorithms. The last two examples involve reducing sidelobe levels and generating deep nulls by optimizing the spacing between elements. In Example 5, the SLL obtained using the DO algorithm is −22.8766 dB, which is 0.1998 dB lower than the lowest SLL of −22.6768 dB among other algorithms. In Example 6, the SLL obtained using the DO algorithm is −20.1012 dB, and the null depth is −125.1 dB, which is 1.592 dB lower than the SLL obtained by the cat swarm optimization (CSO) algorithm and 19.1 dB lower than the deep null obtained by the GWO algorithm, respectively. In summary, the results of six simulation experiments indicate that the DO algorithm has better optimization ability in linear array optimization than other evolutionary algorithms. Full article

The microbial biosynthesis of proteins, primary metabolites, and chemicals is gaining extraordinary momentum and is presently viewed as an advancing approach in the industrial research sector. Increased threats to the environment and the possibility of declining petroleum assets have switched the spotlight to microbial cell factories (MCFs). Aside from possessing various advantages over chemical synthesis, such as less toxicity, cheaper methodologies, and an environmentally benign nature, microbes can be cultivated in fermenters, resulting in an effective bioprocessing approach in terms of industrial relevance. As the overwhelming majority of biodiversity is microbial, this review first highlights the microbial biodiversity of industrially vital microorganisms. Then, the paper delineates the production pathways for generating valuable bioproducts via microbial workhorses. Many host cells synthesize bio-compounds as a part of their natural mechanism; however, several techniques have also been developed to attain the desired end product from non-native microbes with selected properties. The microbial biosynthetic pathways can be categorized as native-existing pathways, heterologous pathways, and artificial de novo pathways. Systems metabolic engineering, which integrates metabolic engineering with evolutionary engineering, synthetic biology, and systems biology, has further revolutionized the field of engineering robust phenotypes. The employment of these strategies improves the performance of the strain, eventually achieving high titer and productivity rates of bio-chemicals. Modern trends and tools for exploiting native pathways and designing non-native-created pathways are also briefly discussed in this paper. Finally, the review discusses the use of microbial workhorses for producing a myriad of materials and chemicals, including carboxylic acids, amino acids, plant natural products (PNPs), carotenoids, flavors, and fragrances, unveiling the efficacy of utilizing microbial species to generate sustainable bio-based products. Full article

The article presents the synthesis of a multi-layer group control system for a marine autonomous surface vessel with the use of modern control theory methods. First, an evolutionary programming algorithm for determining the optimal route path was presented. Then the algorithms—dynamic programming with neural state constraints, ant colony, and neuro-phase safe control algorithms—were presented. LMI and predictive line-of-sight methods were used for optimal control. The direct control layer is implemented in multi-operations on the principle of switching. The results of the computer simulation of the algorithms were used to assess the quality control. Full article

Obesity is a common, serious, and costly disease. More than 1 billion people worldwide are obese—650 million adults, 340 million adolescents, and 39 million children. The WHO estimates that, by 2025, approximately 167 million people—adults and children—will become less healthy because they are overweight or obese. Obesity-related conditions include heart disease, stroke, type 2 diabetes, and certain types of cancer. These are among the leading causes of preventable, premature death. The estimated annual medical cost of obesity in the United States was nearly $173 billion in 2019 dollars. Obesity is considered the result of a complex interaction between genes and the environment. Both genes and the environment change in different populations. In fact, the prevalence changes as the result of eating habits, lifestyle, and expression of genes coding for factors involved in the regulation of body weight, food intake, and satiety. Expression of these genes involves different epigenetic processes, such as DNA methylation, histone modification, or non-coding micro-RNA synthesis, as well as variations in the gene sequence, which results in functional alterations. Evolutionary and non-evolutionary (i.e., genetic drift, migration, and founder’s effect) factors have shaped the genetic predisposition or protection from obesity in modern human populations. Understanding and knowing the pathogenesis of obesity will lead to prevention and treatment strategies not only for obesity, but also for other related diseases. Full article

A historical Christmas card connecting two pioneers of modern chronobiology (Colin Pittendrigh and Jürgen Aschoff) brings together key evolutionary facets of the field at Christmas time. The importance of the field to physiology and medicine is conveyed by the Nobel Prize award in 2017 for discoveries of how body clocks facilitate the temporal organization of physiology across days and nights. Temporal organization can have relevance for dietary Christmas excesses and dietary New Year resolutions. Herein, we examine how diet around Christmas and New Year has been targeted in human health research and we examine published opinion on dietary practice concerning Christmas and New Year using a systematized literature review approach. Thereafter, via a selective literature synthesis regarding time-restricted eating, we explore the chronobiological notion that “when” we eat and drink may make differences in terms of whether we experience weight gain and adverse health effects during and after the festive days. Overall, current Christmas eating is typically detrimental to health in terms of “how much” we consume of “what”. Regarding New Year’s goal-setting, chronobiology-based advice could be considered insofar as “when” we eat may be a healthier and more sustainable nutritional habit alternative. While we need further studies in humans, individual and public health may benefit during and after Christmas by adhering to plausible principles of chrononutrition. That detrimental nutritional excesses over Christmas may encourage individuals to tackle their eating habits should not be left untapped. Full article

The New Evolutionary Synthesis (NES) groups a series of theories that, departing from the gene-centric approach of Modern Synthesis evolutionary theory (MS), place the organism as the central agent of evolution. Two versions of NES, each one with advantages and disadvantages, can be distinguished in this regard; the restrictive NES and the comprehensive NES. Comparatively, the comprehensive NES is a more robust theoretical construction than the restrictive one because it comes grounded on a general, thermodynamically informed theory of living beings (something that the restrictive NES lacks). However, due to its strong teleological commitments, the comprehensive NES has serious problems fitting with modern science’s methodological framework; a problem that the restrictive version, with no explicit commitment to teleology, does not face. In this paper, we propose the autopoietic approach to evolution as a way of integrating these two versions of NES, combining the theoretical robustness of the comprehensive view with the methodological appropriateness of the restrictive one. The autopoietic approach, we show, offers a non-teleological, organism-centered theory of evolution, namely the natural drift theory (NDT), and a grounding on a thermodynamic theory of living beings, namely the embodied autopoietic theory (EAT). We conclude that, from the programmatic point of view, an autopoietic (NDT plus EAT) approach to evolution offers a promising way to develop the NES project. Full article

Polycystic ovary syndrome (PCOS) is increasingly recognized as a complex metabolic disorder that manifests in genetically susceptible women following a range of negative exposures to nutritional and environmental factors related to contemporary lifestyle. The hypothesis that PCOS phenotypes are derived from a mismatch between ancient genetic survival mechanisms and modern lifestyle practices is supported by a diversity of research findings. The proposed evolutionary model of the pathogenesis of PCOS incorporates evidence related to evolutionary theory, genetic studies, in utero developmental epigenetic programming, transgenerational inheritance, metabolic features including insulin resistance, obesity and the apparent paradox of lean phenotypes, reproductive effects and subfertility, the impact of the microbiome and dysbiosis, endocrine-disrupting chemical exposure, and the influence of lifestyle factors such as poor-quality diet and physical inactivity. Based on these premises, the diverse lines of research are synthesized into a composite evolutionary model of the pathogenesis of PCOS. It is hoped that this model will assist clinicians and patients to understand the importance of lifestyle interventions in the prevention and management of PCOS and provide a conceptual framework for future research. It is appreciated that this theory represents a synthesis of the current evidence and that it is expected to evolve and change over time. Full article

Either stereo reactants or stereo catalysis from achiral or chiral molecules are a prerequisite to obtain pure enantiomeric lipid derivatives. We reviewed a few plausibly organic syntheses of phospholipids under prebiotic conditions with special attention paid to the starting materials as pro-chiral dihydroxyacetone and dihydroxyacetone phosphate (DHAP), which are the key molecules to break symmetry in phospholipids. The advantages of homochiral membranes compared to those of heterochiral membranes were analysed in terms of specific recognition, optimal functions of enzymes, membrane fluidity and topological packing. All biological membranes contain enantiomerically pure lipids in modern bacteria, eukarya and archaea. The contemporary archaea, comprising of methanogens, halobacteria and thermoacidophiles, are living under extreme conditions reminiscent of primitive environment and may indicate the origin of one ancient evolution path of lipid biosynthesis. The analysis of the known lipid metabolism reveals that all modern cells including archaea synthetize enantiomerically pure lipid precursors from prochiral DHAP. Sn-glycerol-1-phosphate dehydrogenase (G1PDH), usually found in archaea, catalyses the formation of sn-glycerol-1-phosphate (G1P), while sn-glycerol-3-phosphate dehydrogenase (G3PDH) catalyses the formation of sn-glycerol-3-phosphate (G3P) in bacteria and eukarya. The selective enzymatic activity seems to be the main strategy that evolution retained to obtain enantiomerically pure lipids. The occurrence of two genes encoding for G1PDH and G3PDH served to build up an evolutionary tree being the basis of our hypothesis article focusing on the evolution of these two genes. Gene encoding for G3PDH in eukarya may originate from G3PDH gene found in rare archaea indicating that archaea appeared earlier in the evolutionary tree than eukarya. Archaea and bacteria evolved probably separately, due to their distinct respective genes coding for G1PDH and G3PDH. We propose that prochiral DHAP is an essential molecule since it provides a convergent link between G1DPH and G3PDH. The synthesis of enantiopure phospholipids from DHAP appeared probably firstly in the presence of chemical catalysts, before being catalysed by enzymes which were the products of later Darwinian selection. The enzymes were probably selected for their efficient catalytic activities during evolution from large libraries of vesicles containing amino acids, carbohydrates, nucleic acids, lipids, and meteorite components that induced symmetry imbalance. Full article

Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction form the building blocks of the (Neo-)Darwinian research program, and several of these have been called “Darwinian principles”. Here, we suggest that caution should be taken in calling these principles Darwinian because of the important role played by reticulate evolutionary mechanisms and processes in also bringing about these phenomena. Reticulate mechanisms and processes include symbiosis, symbiogenesis, lateral gene transfer, infective heredity mediated by genetic and organismal mobility, and hybridization. Because the “Darwinian principles” are brought about by both vertical and reticulate evolutionary mechanisms and processes, they should be understood as foundational for a more pluralistic theory of evolution, one that surpasses the classic scope of the Modern and the Neo-Darwinian Synthesis. Reticulate evolution moreover demonstrates that what conventional (Neo-)Darwinian theories treat as intra-species features of evolution frequently involve reticulate interactions between organisms from very different taxonomic categories. Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction therefore cannot be understood as “traits” or “properties” of genes, organisms, species, or ecosystems because the phenomena are irreducible to specific units and levels of an evolutionary hierarchy. Instead, these general principles of evolution need to be understood as common goods that come about through interactions between different units and levels of evolutionary hierarchies, and they are exherent rather than inherent properties of individuals. Full article

Nutrigenomics studies how environmental factors, such as food intake and lifestyle, influence the expression of the genome. Vitamin D₃ represents a master example of nutrigenomics, since via its metabolite 1α,25-dihydroxyvitamin D₃, which binds with high-affinity to the vitamin D receptor, the secosteroid directly affects the epigenome and transcriptome at thousands of loci within the human genome. Vitamin D is important for both cellular metabolism and immunity, as it controls calcium homeostasis and modulates the response of the innate and adaptive immune system. At sufficient UV-B exposure, humans can synthesize vitamin D₃ endogenously in their skin, but today’s lifestyle often makes the molecule a true vitamin and micronutrient that needs to be taken up by diet or supplementation with pills. The individual’s molecular response to vitamin D requires personalized supplementation with vitamin D₃, in order to obtain optimized clinical benefits in the prevention of osteoporosis, sarcopenia, autoimmune diseases, and possibly different types of cancer. The importance of endogenous synthesis of vitamin D₃ created an evolutionary pressure for reduced skin pigmentation, when, during the past 50,000 years, modern humans migrated from Africa towards Asia and Europe. This review will discuss different aspects of how vitamin D interacts with the human genome, focusing on nutritional epigenomics in context of immune responses. This should lead to a better understanding of the clinical benefits of vitamin D. Full article

Venoms are evolutionary key adaptations that species employ for defense, predation or competition. However, the processes and forces that drive the evolution of venoms and their toxin components remain in many aspects understudied. In particular, the venoms of many smaller, neglected (mostly invertebrate) organisms are not characterized in detail, especially with modern methods. For the majority of these taxa, even their biology is only vaguely known. Modern evolutionary venomics addresses the question of how venoms evolve by applying a plethora of -omics methods. These recently became so sensitive and enhanced that smaller, neglected organisms are now more easily accessible to comparatively study their venoms. More knowledge about these taxa is essential to better understand venom evolution in general. The methodological core pillars of integrative evolutionary venomics are genomics, transcriptomics and proteomics, which are complemented by functional morphology and the field of protein synthesis and activity tests. This manuscript focuses on transcriptomics (or RNASeq) as one toolbox to describe venom evolution in smaller, neglected taxa. It provides a hands-on guide that discusses a generalized RNASeq workflow, which can be adapted, accordingly, to respective projects. For neglected and small taxa, generalized recommendations are difficult to give and conclusions need to be made individually from case to case. In the context of evolutionary venomics, this overview highlights critical points, but also promises of RNASeq analyses. Methodologically, these concern the impact of read processing, possible improvements by perfoming multiple and merged assemblies, and adequate quantification of expressed transcripts. Readers are guided to reappraise their hypotheses on venom evolution in smaller organisms and how robustly these are testable with the current transcriptomics toolbox. The complementary approach that combines particular proteomics but also genomics with transcriptomics is discussed as well. As recently shown, comparative proteomics is, for example, most important in preventing false positive identifications of possible toxin transcripts. Finally, future directions in transcriptomics, such as applying 3rd generation sequencing strategies to overcome difficulties by short read assemblies, are briefly addressed. Full article

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification. Full article

As the prime unification of Darwinism and genetics, the Modern Synthesis continues to epitomize mainstay evolutionary theory. Many decades after its formulation, its anchor assumptions remain fixed: conflict between macro organic organisms and selection at that level represent the near totality of any evolutionary narrative. However, intervening research has revealed a less easily appraised cellular and microbial focus for eukaryotic existence. It is now established that all multicellular eukaryotic organisms are holobionts representing complex collaborations between the co-aligned microbiome of each eukaryote and its innate cells into extensive mixed cellular ecologies. Each of these ecological constituents has demonstrated faculties consistent with basal cognition. Consequently, an alternative hologenomic entanglement model is proposed with cognition at its center and conceptualized as Pervasive Information Fields within a quantum framework. Evolutionary development can then be reconsidered as being continuously based upon communication between self-referential constituencies reiterated at every scope and scale. Immunological reactions support and reinforce self-recognition juxtaposed against external environmental stresses. Full article