In million years, under the pressure of natural selection, hominins acquired vocal learning, music, language, and intense cooperation, thanks to the efficacy of music in enhancing sociality. Thus, early in human evolution music became part of human life, a relevant activity, which required sophisticated perceptual and motor skills. It contributed to developing cultures and history, social bonding, and from the beginning of life strengthens the mother-baby relation while within the mother’s womb. Music existed in all known human cultures, although it varies in rhythmic and melodic complexity. It is art made of sounds capable of arousing emotions, evokes memories, engages multiple cognitive functions, and promotes attention, concentration, stimulates the imagination, creativity, and harmony of movement. Music and language share the same complex neural network. Music changes the chemistry of the brain activating the reward and prosocial systems, altruism, and allowing its use in therapy. This review explores "what" is music and illustrates the neural circuits that allow the production of music and language and those that transduce the sounds perceived by the ear, localize and archive them, allowing to recall them. Interestingly, songbirds share many commonalities with human music:, common neural pathways that shape vocal learning, and how they make sounds.

We have studied Juniperus oxycedrus subsp. badia in the central and southern Iberian Peninsula. Here, the macrobioclimate ranges from Mediterranean-pluviseasonal-oceanic and Mediterranean-pluviseasonal-continental, thermotype from thermomediterranean and supramediterranean. The relevés were taken following the Braun-Blanquet phytosociological methodology. A statistical treatment was applied to establish a separation among Juniperus communities. To understand the presence of Juniperus communities in territories dominated by species of the genus Quercus, we applied the formula of Thornthwaite to calculate potential evapotranspiration. The general cluster analysis clearly separates two groups of plant communities and separates the different associations in each group. All plant communities growing on rocky crests and in steeply extreme sloping areas are significantly influenced by the soil. The Ombroclimatic Index does not explain the presence of plant communities influenced by substrate: so, we propose a new Ombroedaphoxeric Index which explains the presence of the Juniperus communities in territories with a thermotype ranging from the thermo to the supramediterranean belt. The areas of distribution of Juniperus species are expanding due to the spread of rocky areas: this phenomenon causes a rise in edaphoxerophilous areas and a decrease in climatophilous one. We propose four new plant associations and with this update on their structures and floristic compositions, it is possible to make an efficient form of conservation in both territories studied (Spain and Portugal) with specific cross-border-cooperation projects.

The evolution of divaricate plants in New Zealand has been the subject of long-running debate among botanists and ecologists. Hypotheses about this remarkable case of convergent evolution have focused mainly on two different types of selective pressures: the Plio-Pleistocene advent of cool, dry climates, or browsing by now-extinct moa. Here, we review the scientific literature relating to the New Zealand divaricates, and present a list of 81 taxa whose architectures fall on the divaricate habit spectrum. We recommend a series of standardised terms to facilitate clear communication about these species. We identify potentially informative areas of research yet to be explored, such as the genetics underlying the establishment and control of this habit. We also review work about similar plants overseas, proposing a list of 47 such species as a first step towards more comprehensive inventories; these may motivate further studies of the ecology, morphology and evolutionary history of these overseas plants which could help shed light on the evolution of their New Zealand counterparts. Finally, we compile published divergence dates between divaricate species and their non-divaricate relatives, which suggest that the divaricate habit is fairly recent (< 10 My) in most cases.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an etiologic agent of the respiratory disease in humans that is known as coronavirus disease 2019 (COVID19). The first outbreak of the disease was initially documented in Wuhan, Hubei Province, China in late December 2019 where people had experienced SARS pneumonia-like symptoms with unknown etiology. Since then it has been observed that COVID-19 positive patients have been showing mild to severe upper respiratory illness symptoms. The type of virus is known to make its transfer from animals to humans and for the concerned virus; researchers have claimed its origin from bat coronavirus at whole-genome level with a 96 % sequence identity. The COVID-19 virus is very contagious and communicable in nature and has been spread throughout the globe since its first outbreak in China. On March 9, 2020, WHO declared it as a Pandemic, and within a month it was already reported to have shown its presence in 213 countries and territories or areas. As of April 29, 2020, this novel virus infected 3,218,183 people and caused 228,029 mortalities worldwide with a variable mortality rate from 3-13 % across the planet and also varied by age and gender. Diagnosis of the disease is a key component in understanding and controlling the spread of the virus and several techniques have been devised including RT-PCR, ELISA, and sequencing-based approaches. To cure COVID-19 patients as of now we do not have proven to be a safe and effective treatment. Therapeutic options currently under investigation in various parts of the world. However, there are various effective therapeutic targets to repurpose the present antiviral therapy for developing potential interventions against SARS-CoV-2. Boosting the immune system can also help to prevent and spread of COVID-19 using various medication and exercises. In this review, our goal to summarize and discussed the present scientific advancements to fight against this novel pandemic.

Abstract: The biological process of photosynthesis was critical in catalyzing the oxygenation of Earth’s atmosphere 2.5 billion years ago, changing the course of development of life on Earth. Recently, the fields of applied and synthetic photosynthesis have utilized the light-driven protein-pigment supercomplexes central to photosynthesis for the photocatalytic production of fuel and other various valuable products. The reaction center Photosystem I is of particular interest in applied photosynthesis due to its high stability post-purification, non-geopolitical limitation, and its ability to generate the greatest reducing power found in Nature. These remarkable properties have been harnessed for the photocatalytic production of a number of valuable products in the applied photosynthesis research field. These primarily include photocurrents and molecular hydrogen as fuels. The use of artificial reaction centers to generate substrates and reducing equivalents to drive non-photoactive enzymes for valuable product generation has been a long-standing area of interest of the synthetic photosynthesis research field. In this review, we cover advances in these areas and further speculate synthetic and applied photosynthesis as photocatalysts for the generation of valuable products.

Coatings of reliable materials of thickness in few atoms to several microns on a viable substrate is the basic need of society which attend regular attention of scientific community working in various fields. Decorative and protective coatings, transparent and insulating coatings, coatings of medical implants and surgical instruments, coatings for drug delivery and security purposes, ultra-precision machine coatings and coatings of other miscellaneous uses are in routine demand for research and commercial purposes. Different hard coatings develop with significant composition of different nature atoms where their force-energy behaviors when recovering certain transition states provide provision for electron of outer ring belonging to gas atom to react for another clamp of energy knot clamping unfilled state of outer ring belonging to solid atom. Set suitable process conditions regulate switching force-energy behaviors of different nature atoms, which are nearly opposite to the ones originally existing in them. Thus, different nature transition state atoms locate points of developing hard coating between their original ground points as the gaseous nature atoms increase their potential energy as per increasing the gravitational force exerting at electron level while the solid atoms decrease their potential energy as per decreasing the gravitational force exerting at electron level. Ti-atom to Ti-atom binding is taken place under the difference of expansion level of lattice in the just land atom and landed atom where the position of nitrogen atoms becomes nearly at their interstitial site. Thus, different nature transition state atoms accommodate to be deposited at substrate surface positioned in the deposition chamber under suitable set parameters. In random arc-based vapor deposition system, depositing different nature atoms at substrate surface depends on the supplied energy where non-conserved forces are remained engage to keep adherence. On undertaking electron (of gas atom), another clamp of energy knot (of solid atom) is being endorsed by the mutually adjusting expansion-contraction of lattices belonging to two different nature atoms developing structure in the form of hard coating, which is known since antiquity. Different properties and characteristics of hard coatings emerged as per engaged forces under the set conditions of involved energy. The present study sets new trends not only in the field of films and coatings but also in the diversified class of materials, wherever, atoms recall their roles.

Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional impacts on gene function and genome evolution, TEs participate in regulating the expression of genes nearby and even far away at transcriptional and post-transcriptional levels. There are two known principal ways by which TEs regulate expression of genes. First, TEs provide cis-regulatory sequences in the genome with their intrinsic regulatory properties for their own expression making them potential factors for regulating the expression of the host genes. TE-derived cis-regulatory sites are found in promoter and enhancer elements, providing binding sites for a wide range of trans-acting factors. Second, TEs encode for regulatory RNAs with their sequences showed to be present in a substantial fraction of miRNAs and long non-coding RNAs (lncRNAs), indicating the TE origin of these RNAs. Furthermore, TEs sequences were found to be critical for regulatory functions of these RNAs including binding to the target mRNA. TEs thus provide crucial regulatory roles by being part of cis-regulatory and regulatory RNA sequences. Moreover, both TE-derived cis-regulatory sequences and TE-derived regulatory RNAs, have been implicated to provide evolutionary novelty to gene regulation. These TE-derived regulatory mechanisms also tend to function in tissue-specific fashion. In this review, we aim to comprehensively cover the studies regarding these two aspects of TE-mediated gene regulation, mainly focusing on the mechanisms, contribution of different types of TEs, differential roles among tissue types, and lineage specificity, based on data mostly in humans.

That form and function relates, is the maxim to anatomy and physiology. Yet form-function relations can be difficult to establish. Human subjects with excessive trabeculated myocardium in the left ventricle, for example, are diagnosed with non-compaction cardiomyopathy, but the extent of trabeculations may be without relation to ejection fraction. Rather than rejecting a relation between form and function, we may ask whether the salient function is assessed; is there a relation to electrical propagation, mean arterial blood pressure, propensity to form blood clots, or all? And how should extent of trabeculated muscle be assessed? While reviewing literature on trabeculated muscle, we applied Tinbergen’s four types of causation - how does it work, why does it work, how is it made, and why did it evolve - to better parse what is meant by form and function. The paper is structured around cases that highlight advantages and pitfalls of applying Tinbergen’s questions. It further uses the evolution of lunglessness in amphibians to argue lung reduction can impact on chamber septation, and it considers the evolution of an arterial outflow in fishes to argue that reductions in energy consumption may drive structural changes with little consequences to function. Concerning trabeculations, we argue they relate to pump function in the embryo in the couple of weeks before the onset of coronary circulation. In fetal and postnatal stages, a spectrum of trabeculated-to-compact myocardium makes no difference to cardiac function and in this period form and function may appear unrelated.

Ruminants perhaps appeared about 50 million years ago (Ma). Five ruminant families had been extinct and about 200 species in 6 ruminant families are living today. The first ruminant family probably was small omnivore without functional ruminal microbiota to digest fiber. Subsequently, other ruminant families evolved around 18-23 Ma along with woodlands and grasslands. Probably, ruminants started to consume selective and highly nutritious plant leaves and grasses similar to concentrates. By 5-11 Ma, grasslands expanded and some ruminants used more grass in their diets with comparatively low nutritive values and high fibers. Historically, humans have domesticated 9 ruminant species that are mostly utilizer of low quality forages for human benefits. Thus, the non-functional rumen microbiota to predominantly concentrate fermenting microbiota, followed by predominantly fiber digesting microbiota had evolved for mutual complementary benefits of holobiont over the million years. The core microbiome of ruminant species seems the resultant of hologenome interaction in an evolutionary unit. The inertia and resilience properties of ruminal ecosystem seem to be due to this core microbiota, which makes the ecosystem most stable in response to perturbations because this core microbiota has evolutionary advantages with logically more generalists (i.e., wide metabolic versatile and redundancy). Also, a part of the ruminal microbiome shows highly plasticity, which is likely useful for evolutionary adaptability of holobiont. This review discusses ecological characteristics of ruminal microbial community in evolutionary perspectives. The updated understanding of ecological traits of ruminal microbiome would be helpful to better modulate the ruminal fermentation favorably for human benefits.

We have developed IrO_x/M-SnO₂ (M = Nb, Ta, and Sb) anode catalysts, IrO_x nanoparticles uniformly dispersed on M-SnO₂ supports with fused-aggregate structures, which make it possible to evolve oxygen efficiently, even with a reduced amount of noble metal (Ir) in proton exchange membrane water electrolysis. Polarization properties of IrO_x/M-SnO₂ catalysts for the oxygen evolution reaction (OER) were examined at 80 °C in both 0.1 M HClO₄ solution (half cell) and a single cell with a Nafion^® membrane (thickness = 50 μm). While all catalysts exhibited similar OER activities in the half cell, the cell potential (E_cell) of the single cell was found to decrease with the increasing apparent conductivities (σ_{app, catalyst}) of these catalysts: an E_cell of 1.61 V (voltage efficiency of 92%) at 1 A cm^-2 was achieved in a single cell by the use of an IrO_x/Sb-SnO₂ anode (highest σ_{app, catalyst}) with a low Ir-metal loading of 0.11 mg_Ir cm^-2 and Pt supported on graphitized carbon black (Pt/GCB) as the cathode, with 0.35 mg_Pt cm⁻². In addition to the reduction of the ohmic loss in the anode catalyst layer, the increased electronic conductivity contributed to decreasing the OER overpotential due to the effective utilization of the IrO_x nanocatalysts on the M-SnO₂ supports, which is an essential factor in improving the performance with low noble metal loadings.

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.

A cosmological model was developed using the equation of state of photon gas, as well as cosmic time. The primary objective of this model is to see if determining the observed rotation speed of galactic matter is possible, without using dark matter (halo) as a parameter. To do so, a numerical application of the evolution of variables in accordance with cosmic time and a new state equation was developed to determine precise, realistic values for a number of cosmological parameters, such as energy of the universe , cosmological constant Λ, curvature of space k, energy density , age of the universe etc. Some assumptions were put forth in order to solve these equations. The current version of the model partially explains several of the observed phenomena that raise questions. Numerical application of the model has yielded the following results, among others: Initially, during the Planck era, at the very beginning of Planck time, , the universe contained a single photon at Planck temperature Planck energy in the Planck volume. During the photon inflation phase (before characteristic time ~10^-9 ), the number of original photons (alphatons) increased at each unit of Planck time and geometrical progression ~n³, where n is the quotient of cosmic time over Planck time . Then, the primordial number of photons reached a maximum of N~10⁸⁹, where it remained constant. It's primordial photons (alphatons) are still present today and represents the essential of the energy contained in the universe via the cosmological constante . Such geometric growth in the number of photons can bring a solution to the horizon problem through exchange and a photon energy volume that is in phase with that of the the volume energy of the universe. The age of the universe in cosmic time that is in line with positive energy conservation (in terms of conventional thermodynamics) and the creation of proton, neutron, electron, and neutrino masses, is ~76 [Gy] (observed . The predicted total mass (p, n, e and n), based on the Maxwell-Juttner relativistic statistical distribution, is ~7x10⁵⁰ . The predicted cosmic neutrino mass is ≤ 8.69x10^-32 (≤ 48.7 ) if based on observations of SN1987A. The temperature variation of the cosmic microwave background (CMB), as measured by Planck, can be said to be partially due to energy variations in the universe (DU/U) during the primordial baryon synthesis (energy jump from the creation of protons and neutrons). In this model, what is usually referred to as dark energy actually corresponds to the energy of the universe that has not been converted to mass, and which acts on the mass created by the energy-mass equivalence principle and the cosmological gravity field, , associated with the cosmological constant, which is high during primordial formation of the galaxies (<1 [Gy]). A look at the Casimir effect makes it possible to estimate a minimum Casimir pressure and thus determine our possible relative position in the universe at cosmic time 0,1813 (t₀/t_W=13,8 /76,1 ). Therefore, from the observed age of 13,8 [Gy], we can derive a possible cosmic age of 76,1 [Gy]. That energy of the universe, when taken into consideration during the formation of the first galaxies (< 1 [Gy]), provides a relatively adequate explanation of the non-Keplerian rotation of galactic masses. Indeed, such residual, non-baryonic energy, when considered in Newton’s gravity equation, adds the term , which can partially explain, without recourse to dark matter, the rotations of some galaxies, such as M33, UGC12591, UGC2885, NGC3198, NGC253, DDO161, UDG44, the MW and the Coma cluster. Today, in the MW, that cosmological gravity force is in the order of 10²⁶ times smaller than the conventional gravity force. The model predicts an acceleration of the mass in the universe (q~ 0,986); the energy associated with curvature is the driving force behind the expansion of the universe, rather than the energy associated with the cosmological constant . An equation to determine expansion is obtained using the energy form of the Friedmann equation relative to Planck power and cosmic time or Planck force acting at the frontier of the universe moving at c. This constant Planck force, from unknown sources, acts everywhere to the expansion of the universe as a stretching effect on the volume. Finally, the model partly explains the value a₀ of the MOND theory. Indeed, a₀ is not a true constant, but depends on the cosmological constant at the time the great structures were formed (~1 [Gy]), as well as an adjustment of the typical mass and dimension of those great structures, such as galaxies. The constant a₀ is a different expression of the cosmological gravity force as expressed by the cosmological constant, Λ, acting through the energy-mass equivalent during the formation of the structures. It does not put in question the value of G.

Photoelectrochemical water splitting is a promising field for sustainable energy production using hydrogen. Development of efficient catalysts is essential for resourceful hydrogen production. The most efficient catalysts reported to date have been extremely precious rare-earth metals. One of the biggest hurdles in this research area is the difficulty of developing highly efficient catalysts comparable to the noble metal catalysts. Here, we report that non-noble metal dichalcogenide (Co₃Se₄) catalysts made using a facile one-pot electrodeposition method, showed highly efficient photoelectrochemical activity on a Si photocathode. To enhance light collection and enlarge its surface area even further, we implemented surface nano-structuring on the Si surface. The nano-structured Si photoelectrode has an effective area greater than that of planar silicon and a wider absorption spectrum. Consequently, this approach exhibits reduced overvoltage as well as increased photo-catalytic activity. Such results show the importance of controlling the optimized interface between the surface structure of the photoelectrode and the electrodeposited co-catalyst on it to improve catalytic activity. This should enable other electrochemical reactions in a variety of energy conversion systems.

The properties of the charged dark matters are discussed in terms of the new three-dimensional quantized space model. Because of the graviton evaporations, the very small Coulomb’s constant (k(dd)) of 10 ⁻⁴⁸ k and large gravitation constant (G_N(dd)) of 10⁶ G_N for the charged dark matters at the present time are expected. The tentative values of G and k are used for the explanation purpose. Therefore, F_c(mm) > F_g(dd) > F_g(mm) > F_g(dm) > F_c(dd) > F_c(dm) = F_c(lq) = 0 for the proton-like particle. Also, the gravitation constant has been changed with increasing of the time because of the graviton evaporation. In the present work, the B1, B2 and B3 bastons with the condition of k(mm) = k >> k(dd) > k(dm) = 0 are explained as the good candidates of the dark matters. Also, the particle creation, dark matters and dark energy could be deeply associated with the changing gravitation constants (G). It is expected that the changing process of the gravitation constant between the matters from G_N(mm) ≈ 10³⁶ G_N to G_N(mm) = G_N happened mostly near the inflation period. Therefore, during most of the universe evolution the gravitation constant could be taken as G_N(mm) = G_N. And the effective charges and effective rest masses of the particles are defined in terms of the fixed Coulomb’s constant (k) and fixed gravitation constant (G_N). Then, the effective charge of the B1 dark matter with EC = −2/3 e is (EC)_eff = −2/3·10⁻²⁴ e. It is concluded that the photons, gravitons and dark matters are the first particles created since the big bang. The particles can be created from the decay of the matter universe and the pair production of the particle and anti-particle with decreasing of the gravitation constant (G_N(mm)). Also, the weak force, strong force and dark matter force bosons are created from the interactions of the elementary particles with the T fluctuations of the vacuum energy.

We develop and apply new physics theory. The theory suggests specific unfound elementary particles. The theory suggests specific constituents of dark matter. We apply those results. We explain ratios of dark matter amounts to ordinary matter amounts. We suggest details about galaxy formation. We suggest details about inflation. We suggest aspects regarding changes in the rate of expansion of the universe. The theory points to relationships between masses of elementary particles. We show a relationship between the strength of electromagnetism and the strength of gravity. The mathematics basis for matching known and suggesting new elementary particles extends mathematics for harmonic oscillators.

Eyes are quintessential complex traits and our understanding of their evolution guides models of trait evolution in general. A long-standing account of eye evolution argues natural selection favors morphological variations that allow increased functionality for sensing light (Darwin 1859; v. Salvini-Plawen and Mayr 1977; Nilsson and Pelger 1994; Nilsson 2013). While certainly true in part, this focus on visual performance does not entirely explain why diffuse photosensitivity persists even after eyes evolve, or why eyes evolved many times, each time using similar building blocks. Here we briefly review a vast literature indicating most genetic components of eyes historically responded to stress caused directly by light, including UV damage of DNA, oxidative stress, and production of aldehydes. We propose light-induced stress had a direct and prominent role in the evolution of eyes by bringing together genes to repair and prevent damage from light-stress, both before and during the evolution of eyes themselves. Stress-repair and stress-prevention genes were perhaps originally deployed as plastic responses to light and/or as beneficial mutations genetically driving expression where light was prominent. These stress-response genes sense, shield, and refract light but only as reactions to ongoing light stress. Once under regulatory-genetic control, they could be expressed before light stress appeared, evolve as a module, and be influenced by natural selection to increase functionality for sensing light, ultimately leading to complex eyes and behaviors. Recognizing the potentially prominent role of stress in eye evolution invites discussions of plasticity and assimilation and provides a hypothesis for why similar genes are repeatedly used in convergent eyes. Broadening the drivers of eye evolution encourages consideration of multi-faceted mechanisms of plasticity/assimilation and mutation/selection for complex novelties and innovations in general.

The success of many viruses depends upon cooperative interactions between viral genomes. For example, viruses that coinfect the same cell can share essential gene products, such as replicase, the enzyme that replicates the viral genome. However, when cooperation occurs, there is the potential for ‘cheats’ to exploit that cooperation. We suggest that: (1) the biology of viruses makes viral cooperation particularly susceptible to cheating; (2) cheats are common across a wide range of viruses, including viral entities that are already well studied, such as defective interfering genomes, and satellite viruses. Consequently, evolutionary theory developed to explain cheating offers a conceptual framework for understanding and manipulating viral dynamics. At the same time, viruses offer unique opportunities to study how cheats evolve, because cheating is relatively common in viruses, compared with taxa where cooperation is more usually studied, such as animals.

A general procedure is described, to generate material parameter sets to simulate fire propagation in horizontal cable tray installations. Cone Calorimeter test data is processed in an inverse modelling approach. Here, parameter sets are generated procedurally and serve as input for simulations conducted with the Fire Dynamics Simulator (FDS). The simulation responses are compared with the experimental data and ranked based on their fitness. The best fitness was found for a test condition of \SI{50}{\kilo\watt\per\meter^2}. Low flux conditions \SI{25}{\kilo\watt\per\meter^2} and less exhibited difficulties to be simulated accurately. As a validation step, the best parameter sets are then utilised to simulate fire propagation within a horizontal cable tray installation and are compared with experimental data. It is important to note, the inverse modelling process is focused on the Cone Calorimeter and not aware of the actual validation step. Despite this handicap, the general features in the fire development can be reproduced, however not exact. The fire in the tray simulation extinguishes earlier and the total energy release is slightly higher as compared to the experiment. The responses of the material parameter sets are briefly compared with a selection of state of the art procedures.

Wikipedia, as "social machine", is a privileged place to observe the collective construction of concepts without central control. Based on Dahlberg's theory of concept, and anchored in the pragmatism of Hjørland - in which the concepts are socially negotiated meanings - the evolution of the concept of Semantic Web (SW) was analyzed in the English version of Wikipedia. An exploratory, descriptive and qualitative study was designed and we identified 26 different definitions (between 7-12-2001 and 12/31/2017) of which 8 are of particular relevance for their duration, with the latter being the two recorded at the end of the analyzed period. According to them, SW: "is a extension of the web"and "is a Web of Data"; the latter, used as a complementary definition, links to Berners-Lee's publications. In Wikipedia, the evolution of the SW concept appears to be based on the search for the use of non-technical vocabulary and the control of authority carried out by the debate. As a space for collective bargaining of meanings, the Wikipedia study may bring relevant contributions to a community's understanding of a particular concept and how it evolves over time.

Fructan, a fructose polymer, is used as carbohydrate reserve in many plants. The nutritional and therapeutic benefits of fructans have attracted increasing interest by consumers and food industry. In the course of evolution, many plants have developed the ability of regulating plant frunctan metabolism genes to produce different structures and chain length fructans, which are strongly correlated with their survival in harsh environments. De nevo domestication of fructan-rich plants based on genome editing is a viable and promising approach to improve human dietary quality and reduce the risk of chronic disease. These advances will greatly facilitate breeding and production of tailor-made fructans as a healthy food ingredient from wild plants such as polygonati rhizoma. The purpose of this review is to broaden our knowledge on plant fructan biosynthesis, evolution and beneficial applications for human health.

We discuss the role of the opposing principles of order and disorder in physical and biological systems in determining stability, growth and evolution and bring forth the potential role of a cosmic ordering agency. We analyze its role in decreasing entropy by coarse-graining and hence in determining the initial low entropy state of the big bang universe. Since all physical and biological systems have either cycles of order and disorder alternating, or may have chaotic evolution with non-linear laws, the same is expected of the dynamics of the whole universe as well. The entropy of the initial state of the universe could be low because of the reduction of degrees of freedom (DoF) as one moves from physical encoding to neural encoding and then on to psychic encoding of information in a nested manner by coarse-graining. It is by such encoding that this cosmic agency enables the universe to pass through the big crunch phase and then rolls it out as the big bang universe from the initial state of low entropy.

Silicon-based photoelectrochemical (PEC) conversion system has recently gained attention with its ability to provide cost-efficient and superior photoresponsive behavior in regard to other various semiconductor photoelectrodes. Carbon-based co-catalysts have always shared the spotlight for being rendered as alternative metal-free electrocatalysts intended for hydrogen evolution reaction (HER). In particular, a representative carbon-derived material, reduced Graphene Oxide (rGO) has attracted much attention as a non-metal catalyst for efficient and durable HER. Herein, we have deposited rGO on silicon nanowire (SiNW) structure which shows the highest reduction in the overpotential for HER up to date. This could be attributed to the synergistic effects of rGO and SiNW with unique anisotropic morphology, facile tuning capabilities, and scalable fabrication methods. Combined with nanostructured photocathode, rGO deposited SiNW showed better applied bias photon to current conversion efficiency of 3.16%, which is 158 times higher than that of bare planar Si system. In regard to this development we believe that rGO-SiNW photoelectrodes would pave the way for state-of-the-art highly efficient non-metal catalysts for energy conversion technologies.

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.

Phylostratigraphic analysis is a way to look anew on phylogenetic data in the evolutionary aspect. It allows counting the evolutionary age based on the analysis of genes, their orthologs and finding the last common ancestor. We performed phylostratigraphic analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) determined by the Gene Ontology annotation. Comparison of the distributions of ages of genes associated with stresses of different type has shown the heat stress to involve older genes while the light stress – younger genes. At the same time, all types of stress are characterized by a significantly higher proportion of old genes (common to all eukaryotes) compared to the whole set of A.thaliana genes. This can be explained by the involvement of basic molecular processes in plant cells into the stress response. Reconstruction and graphical analysis of the gene network of the heat stress educed several clusters associated with different response functions. Some of these clusters contain only ancient genes. The results obtained show that the phylostratigraphic analysis reveals the fundamental features of the organization of gene networks and their evolution.

In this paper we first provide a primer on SARS-CoV-2 and Covid-19 delineating the etiopathogenesis, epidemiology, clinical manifestations and the natural history of the disease. We then trace the evolution of the Covid-19 pandemic highlighting the characteristics of the epidemic in China where the pandemic originated, select countries of Europe which peaked during April, and Brazil, US and India where the pandemic has taken serious turns recently. We also project some possible trajectories for the mega cities of India based on the demographic characteristics of these cities in comparison to New York city. This is an updated version of the article from mid-April published online.

Human language is a prime example of a complex system characterized by multiple scales of description. Understanding its origins and distinctiveness has sparked investigations with very different approaches, ranging from the Universal Grammar to statistical analyses of word usage, all of which highlight, from different angles, the potential existence of universal patterns shared by all languages. Yet, a cohesive perspective remains elusive. In this paper we address this challenge. First, we provide a basic structure of universality, and define recursion as a special case thereof. We cast generative grammars of formal languages, the Universal Grammar and the Greenberg Universals in our basic structure of universality, and compare their mathematical properties. We then define universality for writing systems and show that only those using the rebus principle are universal. Finally, we examine Zipf's law for the statistics of word usage, explain its role as a complexity attractor, and explore its relation to universal writing systems as well as its similarities with universal Turing machines. Overall, we find that there are two main kinds of universality, termed {\it mechanistic} and {\it emergent}, and unveil some connections between them.

Since matter, energy and information are the three major components of the world, is there an interaction between information and matter? In the present work, the coevolution of human language and brain is taken as a case of interaction between information and brain. Some evidence that may show interactions between human language and brain revealed by previous researches is summarized in this paper, such as the language areas in the cerebral cortex of the modern human brain, the evolution of human language and brain in human history, and the genetic basis for the evolution of language. Based on the evidence, a dynamic model is developed to investigate the possible mechanism of coevolution of human language and brain. In the model, human language development and brain development reinforce each other: the developmental level of language can be promoted by advances in brain function due to language-related gene mutations, in turn, whether such mutations are selected positively can be influenced by the current developmental level of language. The coevolution of human language and brain can be taken as a case of interaction between information and matter.

Physics theory has yet to settle on specific descriptions for new elementary particles, for dark matter, and for dark energy forces. Our work extrapolates from the known elementary particles. The work suggests well-specified candidate descriptions for new elementary particles, dark matter, and dark energy forces. This part of the work does not depend on theories of motion. This work embraces symmetries that correlate with motion-centric conservation laws. The candidate descriptions seem to explain data that prior physics theory seems not to explain. Some of that data pertains to elementary particles. Our theory suggests relationships between masses of elementary particles. Our theory suggests a relationship between the strengths of electromagnetism and gravity. Some of that data pertains to astrophysics. Our theory seems to explain ratios of dark matter effects to ordinary matter effects. Our theory seems to explain aspects of galaxy formation. Some of that data pertains to cosmology. Our theory suggests bases for inflation and for changes in the rate of expansion of the universe. Generally, our work proposes extensions to theory in three fields. The fields are elementary particles, astrophysics, and cosmology. Our work suggests new elementary particles and seems to explain otherwise unexplained data.

In addition to the risk of vaccine failure caused by strain mismatch, the production of inactivated FMD vaccines is dangerous if adequate biosafety cannot be maintained. Using a high-throughput sequencing protocol optimized for short nucleic acid fragments, the composition of a local inactivated vaccine was analyzed in depth. The serotype O strain identified in the vaccine was genetically identical to viruses found in recent FMD outbreaks in Egypt.

Technological advances made Virtual and Mixed Reality (VMR) accessible at our fingertips. However, only recently VMR has been explored for the teaching of biology. Here, we highlight how VMR applications can be useful in biology education, discuss about caveats related to VMR use that can interfere with learning, and look into the future of VMR applications in the field. We then propose that the combination of VMR with Machine Learning and Artificial Intelligence can provide unprecedented ways to visualise how species evolve in self-sustained immersive virtual worlds, thereby transforming VMR from an educational tool to the centre of biological interest.

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.

Delve into the ebb and flow of human ingenuity as the researcher traces the evolution of writing from papyrus to pixels. Discover how humble instruments like quill pens and typewriters have propelled human into the digital frontier, forever reshaping the art of expression in the modern age. This article examines the evolution of writing tools from traditional pen and paper to digital writing in the modern age. It explores the development of writing materials such as papyrus, parchment, and paper, as well as the invention of writing tools including quill pens, fountain pens, and typewriters. The rise of digital writing tools, including word processing software and smartphones, is also discussed, along with their benefits such as increased efficiency and productivity, enhanced collaboration and sharing capabilities, and greater accessibility and flexibility. However, the article also highlights the challenges of writing in the digital age, including the impact of digital distractions on writing focus and quality, the issue of online plagiarism and copyright infringement, and the potential loss of traditional writing skills. The article concludes with recommendations for educators, school administrators, students, and researchers to strike a balance between digital and traditional writing practices, to embrace digital writing tools while preserving traditional writing skills, and to understand the importance of the evolution of writing. The theoretical frameworks of Social Construction of Technology (SCOT) Theory, Media Ecology Theory, and Activity Theory are also discussed in relation to the evolution of writing tools. Overall, this article provides valuable insights into the history, benefits, and challenges of writing in the digital age, as well as suggestions for navigating the future of writing and its tools.

We propose a novel interpretation of consciousness and an enlarged definition of locality, which provide a solution to the problem of the consistency of measurements in quantum mechanics: consciousness is a characteristics of the Universe as a whole. Besides its physical consequences, this interpretation has also moral implications: individuality comes out naturally to be just an accident functional to evolution which shaped past and present history through competition, and realizing this fact should enforce cooperation.

Nickel foam substrates are frequently utilised for renewable energy applications as porous 3D-substrates. Preparation of these substrates usually includes an acid washing step, however the degree to which this step affects the final electrochemical performance after spray coating a catalyst ink is unreported. Herein, we report the effect of acid washing through physicochemical and electrochemical characterisation. The electrochemical performance was determined by repeated measurements of catalyst-coated nickel foam substrates both with and without the initial step of acid washing. Acid washing increased current density by 17.9% for the acid treated, MoS2-coated nickel foam electrode. This increment was affiliated with an electrochemically active surface area which increased by 87.1%, where Tafel analysis indicated that the acid treated, MoS2-coated electrodes facilitates the initial water dissociation step of the hydrogen evolution reaction with greater ease. Similar effects were also discovered for acid treated PtIr(1:3)/C-coated nickel foam substrates, albeit with less pronounced effects. Stability was also improved where the degradation rate was reduced by 18.9% for the acid treated, MoS2-coated electrodes. This proves the utility of acid washing nickel foam electrodes.

The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host adhesion like type 1 fimbriae. The extent to which non-pathogenic gut E. coli and infectious ST131 share AMR genes and key associated plasmids remains understudied at a genomic level. Here, we examined AMR gene sharing between gut E. coli and ST131 to discover an extensive shared preterm infant resistome. In addition, individual ST131 show extensive AMR gene diversity highlighting that analyses restricted to the core genome may be limiting and could miss AMR gene transfer patterns. We show that pEK499-like segments are ancestral to most ST131 Clade C isolates, contrasting with a minority with substantial pEK204-like regions encoding a type IV fimbriae operon. Moreover, ST131 possess extensive diversity at genes encoding type 1, type IV, P and F17-like fimbriae, particular within subclade C2. The type, structure and composition of AMR genes, plasmids and fimbriae varies widely in ST131 and this may mediate pathogenicity and infection outcomes.

A recent report in PNAS that Candidatus Nanohaloarchaeum antarcticus requires haloarchaeon Halorubrum lacusprofundi for growth expands the list of known symbiotic or parasitic associations between the members of DPANN archaea, which are relatively small cells with reduced genomes and limited metabolic capacity, and free-living archaea. In line with previous studies addressing the enigmatic mechanism(s) for the transfer of metabolites from Ignicoccus hospitalis to Nanoarchaeum equitans, this new study presents additional evidence supporting a direct cytoplasmic connection facilitated by the fusion of parasite’s membrane with that of its host. Here I show that this novel mechanism for accessing the host resources by a membrane fusing mechanism, which eliminates the need for sophisticated multivalent transport systems, is fundamentally similar to that employed by several viral lineages. These new findings support an evolutionary model on the origin of incipient viral lineages from parasitic cellular lineages that started their parasitic life cycle by fusing with their host cells.

The biology of sexual orientations has intrigued people for generations. Many models have been providing insights to that topic, but there are still unanswered questions. In humans, sexual orientation has a learned component. Humans have to learn cues by which they identify the sex of their mates, and cues of the emotional messages that those mates broadcast. Many of those cues depend on arbitrary societal conventions. The cues are learned automatically and subconsciously during childhood, based on non-sexual experiences. When sexual orientation emerges at puberty, the youngsters cannot tell how and when they have acquired it. A model that deals with those phenomena is presented. A basic tenet of the model is that a sexual orientation is determined by the innate wirings of the brain. The model describes how the brain learns cues for identifying the sex of the mate, and cues for identifying emotional messages that the mate broadcasts. The learning mechanism is conditioning. The unconditioned stimulus is human voice. The unconditioned responses are the triggers of the physical and emotional manifestations of sexual activity. The model suggests that innate connections from auditory detectors of men’s and women’s voice onto brain centers that trigger sexual activities, such as the hypothalamus, determine the sexual orientation that emerges at puberty. Innate connections from those auditory centers to emotional centers, such as the amygdala, determine the learned emotional cues. It is also proposed that during evolution, the roles of the chemosensory system in identifying mates were taken over by the auditory system.

The fundamental question in the field of sensor research is new directions of scientific fields, which play a vital role in the progress of science and technology. This study confronts this question here by developing a bibliometric analysis, which endeavors to explain the evolution of sensor research and new technologies that are critical to science and society. The database of Scopus concerning scientific documents and patents is used for statistical and computational analyses in these topics. Results suggest that emerging technological trajectories in sensors are wireless sensor networks, wearable sensors and biosensors. Main characteristics of these growing research fields and technologies in sensors are described for fruitful implications of research and innovation policy directed to science advances and technological change in society.

We remind about the dogma initially established with the nucleic acid double helix, i.e. the DNA structure as the primary source of life. However, we bring into the discussion those additional processes that were crucial to enable life and cell evolution. Studying chemosensory proteins (CSPs) and odor binding proteins (OBPs) of insects, we have found a high level of pinpoint mutations on the RNA and peptide sequences. Many of these mutations are found to be tissue-specific and induce subtle changes in the protein structure, leading to a new theory of cell multifunction and life evolution. Here, attention is given to RNA and peptide mutations in small soluble protein families known for carrying lipids and fatty acids as fuel for moth cells. A new phylogenetic analysis of mutations is presented and provides even more support to the pioneer work, i.e. the finding that mutations in binding proteins have spread through moths and various groups of insects. Then, focus is given to specific mechanisms of mutations that are not random, change α-helical profilings and bring new functions at the protein level. In conclusion, RNA and peptide mutations are not seen as representative of a multitude of diseases, but rather as an alternative way by which protocells developed to acquire multifunction and totipotency. This provides a basis for the theory of RNA/peptide mutations for birth and evolution of life on earth’s crust proposed here.

Viruses are the most prevalent infectious agents, populating almost every ecosystem on earth. Most viruses carry only a handful of genes supporting their replication and the production of capsids. It came as a great surprise in 2003 when the first giant virus was discovered and found to have a >1Mbp genome encoding almost a thousand proteins. Following this first discovery, dozens of giant virus strains across several viral families have been reported. Here, we provide an updated quantitative and qualitative view on giant viruses and elaborate on their shared and variable features. We review the complexity of giant virus proteomes, which include functions traditionally associated only with cellular organisms. These unprecedented functions include components of the translation machinery, DNA maintenance, and metabolic enzymes. We discuss the possible underlying evolutionary processes and mechanisms that might have shaped the diversity of giant viruses and their genomes, highlighting their remarkable capacity to hijack genes and genomic sequences from their hosts and environments. This leads us to examine prominent theories regarding the origin of giant viruses. Finally, we present the emerging ecological view of giant viruses, found across widespread habitats and ecological systems, with respect to the environment and human health.

The paper is concerned with a class of stochastic differential equations in infinite dimensional Hilbert space with random coefficients driven by Teugel's martingales which are more general processes. and its optimal control problem. Here Teugels martingales are a family of pairwise strongly orthonormal martingales associated with L\'{e}vy processes (see Nualart and Schoutens). There are three major ingredients. The first is to prove the existence and uniqueness of the solutions by continuous dependence theorem of solutions combining with the parameter extension method. The second is to establish the stochastic maximum principle and verification theorem for our optimal control problem by the classicconvex variation method and dual technique.The third is to represent an example of a Cauchy problem for a controlled stochastic partial differential equation driven by Teugels martingales which our theoretical results can solve.

Micro channel tube (MCT) is widely employed in industry due to its excellent efficiency in heat transfer. An MCT is commonly produced through extrusion within a porthole die, where severe plastic deformation is inevitably involved. Moreover, the plastic deformation, which dramatically affects the final property of the MCT, varies significantly from location to location. In order to understand the development of the microstructure and its effect on the final property of the MCT, the viscoplastic self-consistent (VPSC) model, together with the finite element analysis and the flow line model, is employed in the current study. The flow line model is used to reproduce the local velocity gradient within the complex porthole die, while VPSC model is employed to predict the evolution of the microstructure accordingly. In addition, electron backscatter diffraction (EBSD) measurement and mechanical tests are used to characterize the evolution of the microstructure and the property of the MCT. The simulation results agree well with the corresponding experimental ones. The influence of the material’s flow line on the evolution of the orientation and morphology of the grains, and the property of the produced MCT are discussed in detail.

The stellar winds of the central stars of planetary nebulae play an essential role in planetary nebulae shaping. In the interacting stellar winds model, the fast stellar wind injects energy and momentum which are transfered to the nebular envelope through an X-ray-emitting hot bubble. Together with other physical processes, such as the ionization of the nebular envelope, the asymmetrical mass-loss in the AGB, and the action of collimated outflows and magnetic fields, the presurized hot gas determines the expansion and evolution of planetary nebulae. \emph{Chandra} and \emph{XMM-Newton} have provided us with detailed information of this hot gas. Here in this talk I will review our current understanding of the effects of the fast stellar wind in the shaping and evolution of planetary nebulae and give some hints of the promissing future of this research.

The current framework of evolutionary theory postulates that evolution relies on random mutations generating a diversity of phenotypes on which natural selection acts. This framework was established using a top-down approach as it originated from Darwinism, which is based on observations made on complex multicellular organisms, and then modified to fit a DNA-centric view. In this article, I argue that, based on a bottom-up approach starting from the physicochemical properties of nucleic and amino acid polymers, we should reject the facts that: i) natural selection plays a dominant role in evolution, and ii) the probability of mutations is independent of the generated phenotype. I will show that the adaptation of a phenotype to an environment does not correspond to organism fitness but rather corresponds to maintaining the genome stability and integrity. In a stable environment, the phenotype maintains the stability of its originating genome, and both (genome and phenotype) are reproduced identically. In an unstable environment (i.e., corresponding to variations in physicochemical parameters above a physiological range), the phenotype no longer maintains the stability of its originating genome but instead influences its variations. Indeed, environment- and cellular-dependent physicochemical parameters define the probability of mutations in terms of frequency, nature and location in a genome. Evolution is non-deterministic because it relies on probabilistic physicochemical rules, and evolution is driven by a bidirectional interplay between genome and phenotype, the phenotype ensuring the stability of the genotype in a cellular and environment physicochemical parameter-depending manner.

Amid global energy challenges, hydrogen evolution reaction (HER) is gaining traction for green hydrogen production. While catalyst research is ongoing, recognizing electrolyte effects remains crucial for sustainable hydrogen production via renewable-powered water electrolysis. This review delves into the intricate effects of electrolytes on the kinetics of HER. It examines key factors, including pH, cations, anions, impurities, and electrolyte concentration. It is discussed that electrolyte pH alters catalyst-electrolyte interactions and proton concentrations, thereby influencing factors such as hydrogen binding energy, water adsorption, and the overall reaction kinetics. Moreover, it is briefed that electrolyte cations, such as Li+, can impact HER positively or negatively, offering opportunities for improvement based on the metal substrate. Interestingly, there is a potential that HER can be tuned using Li+ ions to modify M-H bond energy, demonstrating flexibility beyond pH levels and counter ions. Varied adsorption energies of metal cations on metal electrodes are also found to influence HER kinetics. The effects of electrolyte anions and impurities are also discussed, emphasizing both positive and negative impacts on HER kinetics. Moreover, it is pointed out that the electrolyte engineering approach enhances the HER kinetics of both metal and carbon-based electrodes without permanent catalyst surface modifications. This review underscores the importance of electrolyte composition, highlighting both challenges and potential solutions in advancing HER research for sustainable energy production.

We try to solve three decades-old physics challenges. List all elementary particles. Describe dark matter. Describe mechanisms that govern the rate of expansion of the universe. We propose new modeling. The modeling uses extensions to harmonic oscillator mathematics. The modeling points to all known elementary particles. The modeling suggests new particles. Based on those results, we do the following. We explain observed ratios of dark matter amounts to ordinary matter amounts. We suggest details about galaxy formation. We suggest details about inflation. We suggest aspects regarding changes in the rate of expansion of the universe. We interrelate the masses of some elementary particles. We interrelate the strengths of electromagnetism and gravity. Our work seems to offer new insight regarding applications of harmonic oscillator mathematics. Our work seems to offer new insight regarding three branches of physics. The branches are elementary particles, astrophysics, and cosmology.

Viruses were classically named after the very same Latin word virus, originally meaning poison or venom. Public understanding of viruses reinforces their “malign” aspects, especially nowadays under the COVID-19 global pandemic. It is our aim here to propose a new way to view viruses and understand their origins and evolution. First, viruses are the most abundant biological systems found on Earth. They can be found almost everywhere and form a subtle biological layer named virosphere. Second, viruses are probably the most important drivers of molecular evolution and they are active agents of ecosystems maintenance and homeostasis, allowing and driving their dynamic modification. A significant number of eukaryotic genomes are composed by genome elements similar to viruses and these endogenous viruses are continuously acting for our equilibrium and fitness. They are responsible for the origin of species-specific orphan genes that allow adaptation through the development of specific traits in separate lineages of eukaryotes. Accumulated evidence indicate that a viral infection was responsible to create the eukaryotic nucleus and, also, it is a syncytium structure caused by viral replication that allows the formation of the placenta. Therefore, viruses were fundamental for the evolutionary fate of eukaryotes and mammals. The presence of virus-specific genes that are absent in cellular organisms indicates that viruses existed before cells. Besides, such as progenotes, viruses are simply ribonucleoproteic entities and their capsids are orders of magnitude simpler than proteolipidic membranes. Here, we (i) propose a complete scenario to describe the major transitions in prebiotic evolution, (ii) present the possibility that viruses emerged before LUCA, and (iii) suggest that viruses originated at the age of progenotes. However, viruses do not form a monophyletic clade. They should be seen as an evolutionary stable strategy recurrently achieved by biological systems to survive. We propose that the word “VIRUS”, known as venom, is historically mistaken and introduce a new interpretation for their name as an acronym for “Very Important Replicator Unit and Symbiont”. But more than being “very important”, viruses are of “Utmost” relevance for the maintenance of life in biosphere, by which reason we suggest referring to them as “UIRUS” to reinforce their incredible role in symbiosis and their beneficial characteristics over the infectious ones.

The implementation of One Health/EcoHealth/Planetary Health approaches has been identified as key (i) to address the strong interconnections between risk for pandemics, climate change and biodiversity loss, and (ii) to develop and implement solutions to these interlinked crises. As a response to the multiple calls of scientists in that direction, we have put forward seven long term research questions regarding COVID-19 and emerging infectious diseases (EIDs) that are based on an effective integration of environmental, ecological, evolutionary, and social sciences to better anticipate and mitigate EIDs. Research needs cover the social-ecology of infectious disease agents, their evolution, the determinants of susceptibility of humans and animals to infections, and the human and ecological factors accelerating infectious disease emergence. For comprehensive investigation, they include the development of nature-based solutions to interlinked global planetary crises, addressing ethical and philosophical questions regarding the relationship of humans to nature and regarding transformative changes to safeguard the environment and human health. In support of this research, we propose the implementation of innovative multidisciplinary facilities embedded in social-ecosystems locally: the “ecological health observatories” and the “living laboratories”. This work has been carried out in the frame of the EC project HERA (www.HERAresearchEU.eu) that aims to set the priorities for an environment, climate and health research agenda in the EU by adopting a systemic approach in the face of global environmental change.

It is desirable to upgrade previous evolutionary theories, which have remained incomplete and controversial for decades. Here we employ the concept of carbon-based entities (CBEs), which include methane, amino acids, proteins, organisms, and other entities containing relatively many carbon atoms. We deduce the driving force, mechanisms, steps, modes, tempos of CBE evolution, through integration of biology, physics, and chemistry using logics for complex issues. We hence establish the Carbon-Based Evolutionary Theory (CBET). The CBET suggests that evolution is the increase in hierarchy, diversity, fitness of CBEs under natural selection and driven by thermodynamics due to the chemical effect of the thermodynamic features of the Earth on CBEs. It provides better explanations for life origin, macroevolution events, natural selection, sympatric speciation, and evolution tempos than previous evolutionary theories. It reveals the evolutionary basis of multiple important social notions, including diversity, collaboration, altruism, obeying rules, and proper increase in freedom. It refutes some wrong notions in thermodynamics, including negative entropy (negentropy) and that biological order is equal to thermodynamic order, which have misled many people. The CBET is supported by its deduction and application. It could be a rare bridge linking laws of thermodynamics, evolution of life, and development of human society, and could have great significance in various sciences.

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.

Intermediate-luminosity-optical-transients (ILOTs) are stellar outbursts with luminosity between those of classical novae and supernovae. They are divided into a number of sub-groups depending on the erupting progenitor and the properties of the eruption. Many of the ILOTs sit on the slanted Optical Transient Stripe (OTS) in the Energy-Time Diagram (ETD) that shows their total energy vs. duration of their eruption. We describe the different kinds of ILOTs that populate the OTS and other parts of the ETD. We also stand on similarities between Planetary Nebulae (PN) to ILOTs, and suggest that some PNe were formed in an ILOT event. The high energy part of the OTS is reserved to the supernova impostors -- giant eruption of very massive stars. We show results of 3D hydrodynamical simulations of supernova impostors that expose the mechanism behind these giant eruptions, and present new models for recent ILOTs. We stand on the connection between different kinds of ILOTs, and suggest that they are powered by a similar source of energy -- gravitational energy released by mass transfer.

This paper investigates a range of popular differential evolution (DE) configurations to identify components responsible for emergence of structural bias – a recently identified tendency of algorithms to prefer some regions of search space over others, for reasons unrelated to objective function values. Previous work has explored this tendency for genetic algorithms (GA) and particle swarm optimisation (PSO), finding a relationship between population size and extent of structural bias, hence highlighting potential weaknesses of those algorithms. In current article, we focus on DE, extend the investigation to include consideration of an algorithmic component that is often overlooked – constraint handling mechanism. Towards this end, a wide range of DE configurations was tested here. Results suggest that DE is generally robust to structural bias. Unlike the case with GA and PSO, population size seems to have no influence on DE structural bias. Only one of variants studied – DE/current-to-best/1/bin – shows clear signs of bias, however, we show that this effect is mitigated by a judicious choice of constraint handling technique. These findings contribute towards explaining widespread success of DE variants in algorithm comparison studies; its robustness to structural bias represents the absence of a factor that may confound other algorithms.

In extant biology, biopolymers perform multiple crucial functions. The biopolymers are synthesized by enzyme-controlled biosystems that would not have been available at the earliest stages of chemical evolution and consist of correctly sequenced and/or linked monomers. Some of the abiotic “messy” polymers approximate some functions of biopolymers. Condensation polymers are an attractive search target for abiotic functional polymers since principal polymers of life are produced by condensation and since condensation allows for the accurate construction of high polymers. Herein the formation of hyperbranched polyesters that have been previously used in the construction of enzyme-like catalytic complexes is explored. The experimental setup compares between the branched polyesters prepared under mild continuous heating and the wet-dry cycle conditions. The results reveal that period wetting during which partial hydrolysis of the polyester occurs, helps control the chain growth and retards the gel transition. It is significant to the origin of life studies that environmental, prebiotically plausible conditions could achieve such control without enzymes or a skilled chemist. As expected in marginally controlled systems, the identification of each component of the heterogeneous system has proved challenging, but it is not crucial for drawing the conclusions.

Ability of quantitative structure – property / activity relationships (QSPRs/QSARs) to serve for epistemological processes in natural sciences is discussed. Some weirdness of QSPR/QSAR state-of-art are listed. There are some contradictions in the research results in this area. Sometimes, these should be classified as paradoxes or weirdness. These points often are ignored. Here these are listed and briefly commented. In addition, hypothesises on the future evolution of the QSPR/QSAR theory and practice are suggested.

Cellular communications play pivotal roles in multi-cellular species, but they do so also in uni-cellular species. Moreover, cells communicate with each other not only within the same individual but also with cells in other individuals belonging to the same or other species. These communications occur between two unicellular species, two multicellular species, or between unicellular and multicellular species. The molecular mechanisms involved exhibit diversity and specificity, but they share common basic features which allow common pathways of communication between different, and sometimes very different species. These interactions have been made possible by the high degree of conservation of the basic molecular mechanisms of interaction of many ligand-receptor pairs in evolutionary remote species. These inter-species cellular communications played crucial roles during Evolution and must have been positively selected, particularly when collectively beneficial in hostile environments. We think that communications between cells did not arise after their emergence but was part of the very nature of first cells. Synchronization of populations of non-living protocells through chemical communications may have been a mandatory step towards their emergence as populations of living cells and explain the large commonality of cell communication mechanisms among microorganisms, plants, and animals.

In 1984, Susumu Ohno hypothesized that the nylon-degrading enzyme NylB arose de novo via a frameshift mutation within a hypothetical precursor protein (PR.C). However, Ohno never tested his hypothesis or provided supporting biological evidence. For decades, Ohno’s famous frame-shift hypothesis has been uncritically accepted as the correct explanation for the origin of NylB and has been used to illustrate how simple it is for a totally new enzyme to arise spontaneously. In this paper we test Ohno’s hypothesis in light of data not available in 1984. We searched multiple protein databases and found that the NylB protein is widely occurring, has thousands of homologs, and is found in diverse organisms and diverse habitats. Conserved domain searches showed that the NylB sequence is homologous to beta lactamases - a family of highly conserved enzymes. However, our searches showed that there is no evidence for the existence of Ohno’s hypothetical PR.C protein, nor any credible homolog. Our results effectively falsify Ohno's frameshift hypothesis. We extended this analysis to other nylonases and found all the nylonases we examined had large numbers of homologs throughout the biosphere. This falsifies the long-held assumption that all nylonases evolved after the invention of nylon in 1935.

For decades, sepsis research has been motivated by the idea of a dangerous overreaction of the immune system in sepsis. But is it true that the response to sepsis is dysregulated? This review surveys the history of sepsis trials and found that evidence for dysregulation does not exist in many of the physiologic mechanisms of sepsis. It is time to consider the alternative hypothesis, that sepsis traits are often functional, and do more harm than good. This review discusses the implications of this perspective for the future of sepsis research

Membrane remodeling and phospholipid biosynthesis are normally tightly regulated to maintain the shape and function of cells. Indeed, different physiological mechanisms ensure a precise coordination between de novo phospholipid biosynthesis and modulation of membrane morphology. Interestingly, the overproduction of certain membrane proteins hijack these regulation networks, leading to the formation of impressive intracellular membrane structures in both prokaryotic and eukaryotic cells. The proteins triggering membrane proliferation share two major common features: 1) they promote the formation of highly curved membrane domains and 2) they lead to an enrichment in anionic, cone-shaped phospholipids (cardiolipin or phosphatidic acid) in the newly formed membranes. Taking into account the available examples of membrane proliferation upon protein overproduction, together with the latest biochemical, biophysical and structural data, we explore the relationship between protein synthesis and membrane biogenesis. We propose a mechanism for the formation of these non-physiological intracellular membranes that shares similarities with natural inner membrane structures found in α-proteobacteria, mitochondria and some viruses-infected cells, pointing towards a conserved feature through evolution. We hope that the information discussed in this review will give a better grasp of the biophysical mechanisms behind physiological and induced intracellular membrane proliferation, inspiring new biotechnological applications.

Hungateiclostridium thermocellum ATCC 27405 is a promising bacterium with a robust ability to degrade lignocellulosic biomass complexes, including crystalline cellulose components, through a multienzyme cellulosomal system. In contrast, it exhibits poor growth on simple monosaccharides such as fructose and glucose. This phenomenon raises many important questions concerning its glycolytic pathways and sugar transport systems. Until now, the detailed mechanisms of H. thermocellum adaptation to growth on monosaccharides have been poorly explored. In this study, adaptive laboratory evolution was applied to train the bacterium on monosaccharides, and genome resequencing was used to detect the genes that had mutated during adaptation. RNA-seq data of the 1st-generation culture growing on either fructose or glucose revealed that several glycolytic genes in the EMP pathway were expressed at lower levels in these cells than in cellobiose-grown cells. After 8 generations of culture on fructose and glucose, the evolved H. thermocellum strains grew faster and yielded greater biomass than the nonadapted strains. Genomic screening also revealed several mutation events in the genomes of the evolved strains, especially in genes responsible for sugar transport and central carbon metabolism. Consequently, these genes could be applied as targets for further metabolic engineering to improve this bacterium for bioindustrial usage.

In this paper, the lamellar structural evolution and microvoids variations of β-iPP during the processing of two different stretching methods, sequential biaxial stretching and simultaneous biaxial stretching, were investigated in detail. It was found that different stretching methods led to significantly different lamellae deformation modes, and the microporous membranes obtained from the simultaneous biaxial stretching exhibited better mechanical properties. For the sequential biaxial stretching, abundant coarse fibers originated from the tight accumulation of the lamellae parallel to the longitudinal stretching direction, whereas the lamellae perpendicular to the stretching direction were easily deformed and separated. Those coarse fibers were difficult to be separated to form micropores during the subsequent transverse stretching process, resulting in a poor micropores distribution. However, for the simultaneous biaxial stretching, the β crystal had the same deformation mode, that is, the lamellae distributed in different directions were all destroyed, forming abundant microvoids and little coarse fibers formation.

The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis.

In the present work, the charged dark matters of B1, B2 and B3 bastons are explained as the right-handed partners of the left-handed neutrinos. The new Higgs mechanism of SU(2)_DM×SU(2)_Weak×SU(2)_Strong including electromagnetic and gravitational forces is applied. And the rest masses of the elementary particles depend on their charge configurations. The left-handed neutrinos have only the lepton charges (LC) and the right-handed dark matters have only the electric charges (EC). This explains the fact that the rest masses of the left-handed neutrinos are so small, and the rest masses of the right-handed dark matters are relatively very large. The proposed rest mass (26.12 eV/c²) of the B1 dark matter is indirectly confirmed from the supernova 1987A data. The missing neutrinos are newly explained by using the dark matters and lepton charge force. The neutrino excess anomaly of the MinibooNE data is explained by the B1 dark matter scattering within the Cherenkov detectors. The quark mixing and neutrino mixing are not required in the present model. It is shown that our matter universe and its partner antimatter universe can be created from the big bang in the point of view of time -, charge -, space -, and quantum state – symmetric universe evolution.

This work presents some characteristics of MoNet, a computerized platform for the modeling and visualization of complex systems. Emphasis is on the ideas that allowed the successful progressive development of this modeling platform, which goes along with the implementation of applications to the modeling of several studied systems. The platform has the capacity to represent different aspects of systems modeled at different observation scales. This tool offers advantages in the sense of favoring the perception of the phenomenon of the emergence of information, associated with changes of scale. Some criteria used for the construction of this modeling platform are included. The power of current computers has made practical representing graphic resources such as shapes, line thickness, overlaying-text tags, colors and transparencies, in the graphical modeling of systems made up of many elements. By visualizing diagrams conveniently designed to highlight contrasts, these modeling platforms allow the recognition of patterns that drive our understanding of systems and their structure. Graphs that reflect the benefits of the tool regarding the visualization of systems at different scales of observation are presented to illustrate the application of the platform.

Centromeres are among the fastest evolving genomic regions in a diverse array of organisms. The evolutionary process driving this rapid evolution has not been unambiguously established. Here I integrate diverse information to motivate a model in which centromeres evolve rapidly because of their intrinsic molecular phenotype: they tightly bind centromeric proteins throughout the cell cycle. DNA-bound proteins have been shown to cause stalling and collapse of DNA replication forks in many genomic regions, including centromeres. Collapsed replication forks generate one-sided double strand breaks (DSBs) that are repaired by the Break-Induced Repair (BIR) pathway. Here I show why this repair is expected to generate tandem repeat structure and three key features at centromeres: i) increased nucleotide substitution mutation rates, ii) out-of- register re-initiation of replication that leads to indels spanning one or more repeat units, and iii) elevated rates of large and small transpositions within centromeres and between genomic regions. These phenotypes lead to: i) a rapid rate of nucleotide substitutions within a clade of centromeric sequences, ii) continual turnover of monomers within centromeres that fosters molecular-drift and molecular-drive, and iii) recurrent quantum leaps in centromere sequence due to the formation of mosaic monomers and new sequences transposed into non-homologous centromeres. These features are plausibly the major reason centromeres evolve so rapidly. I also speculate on how the DNA sequence of centromeres might perpetually coevolve with the protein sequence of histone CENH3 –the major epigenetic mark of centromeres.

Supervised machine learning (SML) is a powerful method for predicting a small number of well-defined output groups (e.g., potential buyers of a certain product) by taking as input a large number of known well-defined measurements (e.g., past purchases, income, ethnicity, gender, credit record, age, favorite color, favorite chewing gum). SML is predicated upon the existence of a training dataset in which the correspondence between the input and output is known to be true. SML has had enormous success in the world of commerce, and this success may have prompted a few scientists to employ it in the study of molecular and genome evolution. Here, we list the properties of SML that make it an unsuitable tool in certain evolutionary studies. In particular, we argue that SML cannot be used in an evolutionary exploratory context for the simple reason that training datasets that are known to be a priori true do not exist. As a case study, we use an SML study in which it was concluded that most human genomes evolve by positive selection through soft selective sweeps (Schrider and Kern 2017). We show that in the absence of legitimate training datasets, Schrider and Kern (2017) used (1) simulations that employ many manipulatable variables and (2) a system of cherry-picking data that would put to shame most modern evangelical exegeses of the Bible. These two factors, in addition to the lack of methodological detail and negative controls, lead us to conclude that all evolutionary inferences derived from so-called SML algorithms (e.g., S-HIC) should be taken with a huge shovel of salt.

This paper constitutes a first advance in the paleoenvironmental study of a small group of peatland ecosystems, of reduced size, located in the interior of the Iberian Peninsula (Puebla de Don Rodrigo, Ciudad Real, Spain). It represents a singular enclave, because these ecosystems are home to the southern-most peatlands in Europe, located at the lowest altitude in Spain, and are unique to the region of Castilla-La Mancha. They form ecosystems similar to the peat bogs of northern Europe, but in a Mediterranean climate. The analysis is followed of sample collection and data collection from documentary, textual, and cartographic sources drawn up since the 16th century up until the present day. The scientific analyses that were performed and the documentation that was consulted point to the hypothesis that these peatlands are the result of a long process of historical modification of the landscape in which anthropogenic activity has played a leading role, triggering a series of processes on the hillslopes that are culminating in the exhumation of the waterlogged areas, thereby establishing a recent genesis of these ecosystems.

The companion paper (Rice 2020) found that the centromeric repeats of the Western European house mouse (Mus musculus domesticus) have unusual structure: i) despite moderate pairwise sequence divergence (average = 5.9%), no monomer sequence was common and many hundreds of monomer sequences were observed, ii) local sequence divergence among neighboring monomers was nearly as high as genome-wide divergence, and iii) matching sequences were rare between side-by-side monomers. Here I integrate information from many published studies to formulate a hypothesis for the evolution of this structure. Non-matching sequences of neighboring centromeric monomers is hypothesized to be selectively favored in the context of molecular drive because it reduces the rate of monomer deletion during repair of double strand breaks (DSBs) via the Single Strand Annealing (SSA) pathway. The foundation for the hypothesis is the observation that centromeres of most populations of M. m. domestics reside close to the telomere, i.e., all their chromosomes are telocentrics. This proximity influences repair of centromeric DSBs because it places at least part of the centromere within the Telomere-Affected Repair Region (TARR; a location with increased concentrations of the shelterin-complex proteins that bind telomeres, especially TRF2). Shelterin proteins increase the level of 5’→3’ end resection at DSBs and thereby: i) decrease the frequency of repair via the c- NHEJ pathway, and ii) increase the frequency of homology-directed repair (HD-repair) –including the SSA repair pathway. It is hypothesized that certain ‘trigger’ events (e.g., sub-telomeric deletions) occur in local populations that increase the influence of TARR on the centromere. This increase elevates the occurrence of SSA repair of centromeric DSBs to a level that causes centromeres to begin to gradually shrink. Chronic shrinkage leads to coevolution between centromere size and karyotype number. Once centromeres shrink to a size below a critical minimum (that causes substantially reduced kinetochore size), fusions between non- homologous telocentrics with undersized centromeres produces metacentrics with an expanded centromere size (and a corresponding ‘quantum-jump’ in kinetochore size). These metacentrics: i) accumulate to fixation because they are favored by centromere drive, and ii) are released from the influence of TARR and thereby gradually recover larger centromere size. Fission of metacentrics with enlarged centromeres can next plausibly regenerate pairs of telocentrics with sufficiently large centromeres (which recruit normal-sized kinetochores) to be favored by centromere drive and accumulate to fixation. This fixation completes a cycle of coevolution within genomes that oscillate between two extremes: i) high karyotype number (2N = 40; all telocentrics) with larger centromeres, and ii) low karyotype number (2N << 40; mainly metacentrics) with initially small centromeres that gradually increase in size.

Heavy metals are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory concentration reaching up to 3.5 mM Cu(II), 21 mM Zn(II), 1.2 mM Cd(II), and 10.0 mM As(III). Genomes of the four strains were sequenced by Illumina. Sequence analyses revealed the presence of a high abundance of heavy metal resistance (HMR) determinants. One of the strain, M. rubeus P2, carried genes encoding 6 putative P1B-1-ATPase, 5 putative P1B-3-ATPase and 4 putative Zn(II)/Cd(II) P1B-4 type ATPase, and 16 putative RND-type metal transporter systems. Moreover, the four genomes carry a high abundance of genes coding for putative metal binding chaperones. Analysis of the close vicinity of these HMR determinants uncovered the presence of clusters of genes potentially associated with mobile genetic elements. These loci include genes coding for tyrosine recombinases (integrases) and subunits of mating pore (type 4 secretion system) respectively allowing integration/excision and conjugative transfer of numerous genomic islands. Further in silico analyses revealed that their genetic organization and gene products resemble the Bacteroides integrative and conjugative element CTnDOT. These results highlight the pivotal role of genomic islands in the acquisition and dissemination of adaptive traits, allowing for rapid adaption of bacteria and colonization of hostile environments.

Life on Earth evolved to accommodate the biochemical and biophysical boundary conditions of the planet millions of years ago. The former includes nutrients, water, and ability to synthesize other needed chemicals. The latter include the 1 g gravity of the planet, radiation, and the geomagnetic field (GMF)of the planet. How complex life forms have accommodated the GMF is not known in detail considering that Homo sapiens evolved a neuro system and a cardiovascular system that develops electromagnetic fields as part of their functioning. In addition, many proteins and physiologic processes utilize Fe ions, an ion that exhibits magnetic properties. Thus, complex organisms such as current humans generate magnetic fields, contain significant quantities of the Fe ion, and also respond to exogenous-supplied static and electromagnetic fields. Whether humans can store information in self-generated magnetic fields remains to be determined. Given the current body of literature, it remains somewhat unclear how Homo sapiens use exogenous magnetic fields to regulate function, and what can happen if the boundary condition of the GMF of Earth is no longer exerting an effect. Proposed deep space flights to destinations such as Mars will provide some insights as space flight could not have been anticipated by evolution. The results of such space flight “experiments” will provide new insights in the role of magnetic fields on human functioning. The outcomes may also have implications for those on Earth as magnetic field influences may play a role in developmental conditions such as autism and senescence-associated conditions such as dementia when integration of the biological and biophysical aspects of humans of humans are required for effective functioning. This review will discuss the involvement of magnetic fields on various normal and disturbed processes in humans while on Earth and then further discuss potential outcomes when the GMF is no longer available to impact host systems. Thus, the GMF of the Earth has been present throughout evolution but details of its role in human functions still remain to be elucidated.

This paper analyses the evolution of the internal damage in two types of steel that show different fracture behaviours, with one of them being the initial material used for manufacturing prestressing steel wires, which shows a flat fracture surface perpendicular to the loading direction, and the other one being a standard steel used in reinforced concrete structures, which shows the typical cup-cone surface. 3mm-diameter cylindrical specimens are tested with a tensile test carried out in several loading stages and, after each of them, unloaded and analysed with X-ray tomography, which allows detection of internal damage throughout the tensile test. In the steel used for reinforcement, damage is developed progressively in the whole specimen, as predicted by Gurson-type models, while in the steel used for manufacturing prestressing steel-wire damage is developed only in the very last part of the test. In addition to the experimental study, a numerical analysis is carried out by means of the finite element method by using a Gurson model to reproduce the material behaviour.

Closed timelike curves (CTCs), non-intuitive theoretical solutions of general relativity field equations can be modelled in quantum mechanics in a way, known as Deutsch-CTCs, to circumvent one of their most paradoxical implications, namely, the so-called grandfather paradox. An outstanding theoretical result of this model is the demonstration that in the presence of a Deutsch-CTC a classical computer would be computationally equivalent to a quantum computer. In the present study, the possible implications of such a striking result for the foundations of quantum mechanics and the connections between classicality and quantumness are explored. To this purpose, a model for fundamental particles that interact in physical space exchanging carriers of momentum and energy is considered. Every particle is then supplemented with an information space in which a probabilistic classical Turing machine is stored. It is analysed whether, through the action of Darwinian evolution, both a classical algorithm coding the rules of quantum mechanics and an anticipation module might plausibly be developed on the information space from initial random behaviour. The simulation of a CTC on the information space of the particle by means of the anticipation module would imply that fundamental particles, which do not possess direct intrinsic quantum features from first principles in this information-theoretic Darwinian approach, could however generate quantum emergent behaviour in real time as a consequence of Darwinian evolution acting on information-theoretic physical systems.

Multicellularity evolved repeatedly in the history of life, but how it unfolded varies greatly between different lineages. Dictyostelid social amoebas offer a good system to study the evolution of multicellular complexity, with a well-resolved phylogeny and molecular genetic tools being available. We compare the life cycles of the Dictyostelids with closely related amoebozoans to show that complex life cycles were already present in the unicellular common ancestor of Dictyostelids. We propose frost resistance as an early driver of multicellular evolution in Dictyostelids and show that the cell signalling pathways for differentiating spore and stalk cells evolved from that for encystation. The stalk cell differentiation program was further modified, possibly through gene duplication, to evolve a new cell type, cup cells, in Group 4 Dictyostelids. Studies in various multicellular organisms including Dictyostelids, volvocine algae, and metazoans suggest as a common principle in the evolution of multicellular complexity that unicellular regulatory programs for adapting to environmental change serve as “proto-cell types” for subsequent evolution of multicellular organisms. Later, new cell types could further evolve by duplicating and diversifying the “proto-cell type” gene regulatory networks.

Although the majority of mobile phone (MP) users do not attribute adverse effects on health or well-being to MP-emitted radiofrequency (RF) electromagnetic fields (EMFs), the exponential increase in the number of RF devices necessitates continuing research aimed at the objective investigation of such concerns. In this work, we investigate the effects of acute exposure from Long Term Evolution (LTE) MP EMFs on thermal pain threshold in healthy young adults. We use a protocol that was validated in a previous study in a capsaicin-induced hyperalgesia model, and was also successfully used to show that exposure from an RF source mimicking a Universal Mobile Telecommunications System (UMTS) MP led to mildly stronger desensitization to repeated noxious thermal stimulation relative to the sham condition. Using the same experimental design, we did not find any effects of LTE exposure on thermal pain threshold. The present results are in accordance with previous evidence suggesting that effects are likely to be placebo/nocebo effects and are unrelated to the brief acute LTE EMF exposure itself. The fact that this is dissimilar to our previous results on UMTS exposure implies that RF modulations might differentially affect pain perception, and points to the necessity of further research in the topic.

The spread of viral pathogens both between and within hosts is inherently a spatial process. While the spatial aspects of viral spread at the epidemiological level have been increasingly well characterized, the spatial aspects of viral spread within infected hosts are still understudied. Recent experimental studies, however, have started to shed more light on the mechanisms and spatial dynamics of viral spread within hosts. Here, we review these experimental studies as well as the limited number of computational modeling efforts that have begun to integrate spatial considerations for understanding within-host viral spread. We limit our review to influenza virus to highlight key mechanisms affecting spatial aspects of viral spread for pathogens of the respiratory tract. There is considerable empirical evidence for highly spatial within-host spread of influenza virus, yet few computational modeling studies that shed light on possible factors that structure the dynamics of this spatial spread. In existing modeling studies, there is also a striking absence of theoretical expectations of how spatial dynamics may impact the dynamics of viral populations. To mitigate this, we turn to the extensive ecological and evolutionary literature to provide informed theoretical expectations for what viral and host factors may impact the spatial patterns of within-host viral dynamics and for how spatial spread will affect the genetic composition of within-host viral populations. We end by discussing current knowledge gaps related to the spatial component of within-host influenza virus spread and the potential for within-host spatial considerations to inform the development of disease control strategies.

This study analyzed the structural changes of semicrystalline polylactide (PLA) in the form of spun-bonded mulching nonwoven, during outdoor composting. The investigation was carried out at the microstructural, supramolecular and molecular levels using scanning electron microscopy (SEM), wide-angle X-ray diffraction (WAXD) and the viscosity method, respectively. The results showed the varying degree of influence of the climatic condition, prepared compost mixtures and time on the molecular, supramolecular and micromorphological structure of PLA spun-bonded mulching nonwoven and its degradation rate. The obtained experimental results revealed how the popular outdoor composting method, realized under two different European climatic conditions (in Poland and in Bulgary), affects the degradation of PLA nonwoven, designed for agriculture use.

Cryonotothenioidea is the main group of fishes that thrive in the extremely cold Antarctic environment, thanks to the acquisition of peculiar morphological, physiological and molecular adaptations. We have previously disclosed that IgM, the main immunoglobulin isotype in teleosts, display typical cold-adapted features. Recently, we have analyzed the gene encoding the heavy chain constant region (CH) of the IgT isotype from the Antarctic teleost Trematomus bernacchii (family Nototheniidae), characterized by the near-complete deletion of the CH2 domain. Here, we aimed to track the loss of the CH2 domain along notothenioid phylogeny and to identify its ancestral origins. To this end, we obtained the IgT gene sequences from several species belonging to the Antarctic families Nototheniidae, Bathydraconidae and Artedidraconidae. All species display a CH2 remnant of variable size, encoded by a short Cτ2 exon, which retains functional splicing sites and therefore is included in the mature transcript. We also considered representative species from the three non-Antarctic families: Eleginopsioidea (Eleginops maclovinus), Pseudaphritioidea (Pseudaphritis urvillii) and Bovichtidae (Bovichtus diacanthus and Cottoperca gobio). Even though only E. maclovinus, the sister taxa of Cryonotothenioidea, shared the partial loss of Cτ2, the other non-Antarctic notothenioid species displayed early molecular signatures of this event. These results shed light on the evolutionary path that underlies the origins of this remarkable gene structural modification.

Water splitting technology is an efficient approach to generate hydrogen (H2) energy, which can well address the problems of environmental deterioration and energy shortage, as well as establishment of a clean and sustainable hydrogen economy powered by renewable energy sources due to the green reaction of H2 with O2. While the efficiency of H2 production by water splitting technology is intimately related with the reactions on electrode. Nowadays, the efficient electrocatalysts in water splitting reactions are the precious metal-based materials, i.e., Pt/C, RuO2 and IrO2. Ni (Co, Fe)-based layered double hydroxides (LDH) 2D materials are the typical non-precious metal-based materials in water splitting with advantages of low cost, excellent electrocatalytic performance and simple preparation methods, which exhibits a great potential for the substitution for precious metal-based materials. This review summarizes the recent progress of Ni (Co, Fe)-based LDH 2D materials for water splitting, which mainly focuses on discussing and analyzing the different strategies to modify LDH materials towards high electrocatalytic performance. We also discuss the recent achievements including their electronic structure, electrocatalytic performance, catalytic center, preparation process and catalytic mechanism. Furthermore, the characterization progress in revealing electronic structure and catalytic mechanism of LDH is highlighted in this review. Finally, we put forward some future perspectives related to design and explore advanced LDH catalysts in water splitting.

RNA interference (RNAi) is one of the main mechanisms for disease resistance and small RNA production in plants. The main proteins involved in RNAi include Dicer-like (DCL), RNA-dependent RNA polymerase (RDR), double-stranded RNA-binding (DRB), and Argonaute (AGO). Juglandaceae contains a variety of important woody plants, and walnuts are one of the four major woody plant groups and one of the four major dried fruits in the world. To clarify the evolution and functional differentiation of RNAi-related proteins in the walnut (Juglans regia) genome, this study integrated various web resources from gene family acquisition to structural analysis and transcriptome data to correlate walnuts and their congeners. The walnut genome has 5 DCL, 13 RDR, 15 DRB and 15 AGO genes, similar genes encoding conserved protein structural domains and conserved motifs with similar subcellular localization. Walnut AGO proteins are classified into three classes and seven subclasses. The DCL is divided into four categories, while RDR is mainly divided into four categories, and DRB can be divided into six categories. The exception is that the copy number of walnut RDR1 is 9, in which seven RDR1 are distributed in clusters on chromosome 16. Purifying selection drove the formation of walnut genes, but protein classes were subjected to varying degrees of purifying selection. Additionally, these results showed some similarity in other plants of the walnut family. Moreover, different RNAi-related genes of walnut produced abundant selective expression in response to different tissues and stresses. In this study, DCL, RDR, DRB and AGO gene families were identified and analysed in the genome of the walnut family for the first time and preliminarily examined the evolution, structure and expression characteristics of these families to provide a preliminary basis for the evolution of the walnut RNAi pathway and breeding research.

The prevailing interpretations of physics are based on deeply entrenched assumptions, rooted in classical mechanics. Logical implications include: the denial of entropy and irreversible change as fundamental properties of state; the inability to explain random quantum measurements and nonlocality without unjustifiable assumptions and untestable metaphysical implications; and the inability to explain or even define the evolution of complexity. The dissipative conceptual model (DCM) is based on empirically justified assumptions. It generalizes mechanics’ definition of state by acknowledging the contextual relationship between a physical system and its positive-temperature ambient background, and it defines the DCM entropy as a fundamental contextual property of physical states. The irreversible production of entropy establishes the thermodynamic arrow of time and a system’s process of dissipation as fundamental. The DCM defines a system’s utilization by the measurable rate of internal work on its components and as an objective measure of stability for a dissipative process. The spontaneous transition of dissipative processes to higher utilization and stability defines two evolutionary paths. The evolution of life proceeded by both competition for resources and cooperation to evolve and sustain higher functional complexity. The DCM accommodates classical and quantum mechanics and thermodynamics as idealized non-contextual special cases.

No single evolutionary event has been identified as the cause for the final emergence of our species. I propose that a mutation on CD155 receptor gene occurred to establish a symbiosis with poliovirus, which exerted its beneficial impact via RNA dependent non-genetic transgenerational inheritance, which caused a qualitative enhancement of cognitive functions. I posit that this mutation occurred in what we call, Anatomically Modern Humans, our immediate ancestor species and that the disruption of this symbiosis causes autism spectrum disorder. Positive selection of CD155 to the extent of becoming a species defining characteristic, the chronology of autism spectrum disorder prevalence increase and continued increase, the multigenerational nature of RNA inheritance, the universal infection of humans by poliovirus and a very low associated mortality rate, and several other factors support this hypothesis. Specific genetic, epidemiological and sperm miRNA content studies are suggested to test this hypothesis.

In this paper we present an argument in favor of the possibility of an artificial intelligence above human intelligence. AI technology has shown a stepwise increase in its capacity and complexity. The last step took place several years ago, due to increased progress in deep neural network technology. Each such step goes hand in hand with our understanding of ourselves, understanding human cognition. Indeed, AI was always about the question of understanding human nature. AI percolates into our lives, step by step, changing our environment. We believe the next few steps in AI technology, and in our understanding of human behavior, will bring about a much more powerful machines, flexible enough to resemble human behavior. In this context, there are two research fields: Artificial Social Intelligence (ASI) and General Artificial Intelligence (AGI). On the ground of ASI and AGI we present an evolutionary argument which uses research in artificial life simulations, showing an increase in complexity due to an emergent property coming out of lower complexity constituents. The whole process is driven by an evolutionary force. What could such an evolutionary force be? We suggest a social communicative driving force. We end the discussion demonstrating a way to overcome our fears of singularity, harnessing value alignment.

Cancers have been interpreted either as somatic evolution of cheater cells that escape replication regulation or alternatively as non-healing wounds. Both the interpretations have substantial support as well as glaring anomalies but the two have not been put together to make a coherent synthesis. We argue here that mechanisms and pathways to escape the normal regulation of cell proliferation do not need to evolve de novo. Mechanisms to override the normal regulation have already evolved for wound healing and tissue regeneration. Almost all of the hallmarks of cancer are also seen in the wound healing process. This suggests that cancer develops not by any de novo gain of function but by exaptation of pre-evolved wound healing functions. Somatic evolution that makes the wound healing triggers constitutive is not mutation limited but selection limited and the selective forces are dependent on the tissue microenvironment. Some mechanisms for such selection have been suggested. Many more need to be investigated. A series of mechanisms have evolved to minimize the risk of cancers which may fail in an altered lifestyle context. We support our synthesis with multiple lines of evidence and also make differential testable predictions. This evolutionary perspective suggests novel lines of research and also has translatable implications for cancer prevention.

Cetacean Morbillivirus, the most relevant pathogen impacting the health and conservation of cetaceans worldwide, has shown in recent years an increased tendency to cross “interspecies barriers”, thereby giving rise to disease and mortality outbreaks in free-ranging dolphins and whales. The present article deals with the evolutionary “trajectories” of this viral pathogen, likely originating from Rinderpest Virus, along with its “journey” from land to sea (and viceversa), mimicking that of cetaceans' terrestrial ancestors.

Double-spiral galaxies are common in the Universe. It is known that the logarithmic double spiral is a Maximum Entropy geometry and represents spiral galaxies well. It is also known that the virial mass of such a galaxy can be approximately determined from the entropy of its central supermassive black hole. But over time the black hole must accrete mass, and therefore the overall galactic entropy must increase. From the associated entropic Euler-Lagrange equation (forming the basis of the Principle of Least Exertion, and also enabling the application of Nöther’s theorem) we show that the galactic entropy production is a conserved quantity, and we derive an appropriate expression for the relativistic entropic Hamiltonian of an idealised spiral galaxy. We generalise Onsager’s celebrated expression for entropy production and demonstrate that galactic entropy production has two parts, one many orders of magnitude larger than the other, and where the smaller is comparable to the Hawking radiation of the central supermassive black hole. We conclude that galaxies cannot be isolated, since even idealised spiral galaxies have non-zero entropy production.

Although cooperative social networks are considered key to human evolution, emphasis has most often been placed on the functions of male cooperative networks. As a result, gender differences in social networks are under-studied and remain incompletely theorized. Variation in kinship systems may be leveraged to test and generate hypotheses that explain the causes and effects of variation in gendered social networks. Specifically, by linking socio-ecological drivers to variation in kinship systems, human behavioral ecology provides a framework to anticipate and explain divergent patterns in gendered social networks within different kinship ecologies. In this paper, we test the ‘universal gender differences’ hypothesis positing gender-specific network structures against the ‘gender reversal’ hypothesis that women’s social networks in matriliny will more closely resemble those of men’s in patriliny. We compare these hypotheses using tools from social network analyses and data on men’s and women’s social networks in matrilineal and patrilineal Mosuo communities. In support of the gender reversal hypothesis, we find that women’s networks in matriliny are more similar to men’s in patriliny. Specifically, women in matriliny have higher edge density than do men, and women have higher measures of degree centralization than do men in matriliny whereas patrilineal men have higher measures of centrality than do women. Additionally, we find that geographic proximity and relatedness together predict women’s friendships in patriliny whereas relatedness predominates in matriliny. Finally, we find that friendship predicts ties in other domains of cooperation and social support. These results support the idea that the socio-ecological factors that result in different kinship systems also impact the ways that men and women operate within these systems, underscoring the importance of human flexibility in family making, and challenging the predominant narrative of universal gender differences.

Bioluminescence – i.e., the emission of visible light by living organisms - is defined as a biochemical reaction involving, at least, a luciferin substrate, an oxygen derivative, and a specialised luciferase enzyme. In some cases, the enzyme and the substrate are durably associated and form a photoprotein. While this terminology is educatively useful to explain bioluminescence, it gives a false idea that all luminous organisms are using identical or homologous molecular tools to achieve light emission. As usually observed in biology, reality is more complex. To date, 11 different luciferins have indeed been discovered, and several non-homologous luciferases lato sensu have been identified which, all together, confirms that bioluminescence emerged independently multiple times during the evolution of living organisms. While some phylogenetically related organisms may use non-homologous luciferases (e.g., at least four convergent luciferases are found in Pancrustacea), it has also been observed that phylogenetically distant organisms may use homologous luciferases (e.g., parallel evolution observed in some cnidarians, tunicates and echinoderms that are sharing a homologous luciferase-based system). The evolution of luciferases then appears puzzling. The present review takes stock of the diversity of known “bioluminescent proteins”, their evolution and potential evolutionary origins. A total of 134 luciferase and photoprotein sequences have been investigated (from 75 species and 11 phyla), and our analyses identified 12 distinct types – defined as a group of homologous bioluminescent proteins. The literature review indicated that genes coding for luciferases and photoproteins have potentially emerged as new genes or have been co-opted from ancestral non-luciferase/photoprotein genes. In this latter case, the homologous gene’s co-options may occur independently in phylogenetically distant organisms.

Nowadays, the human population is facing the third and may be the worst pandemic caused by human coronaviruses (CoVs). The virus was first reported in Wuhan, China on 31 December 2019 and spread within short time to almost all countries of the world. Genome analysis of the early virus isolates has revealed high similarity with SARS-CoV and hence the new virus was officially named SARS-CoV-2. Since CoVs have the largest genome among all RNA viruses, they can adapt many point mutation and recombination events; particularly in spike gene, that enable these viruses to rapidly change and evolve in nature. CoVs are known to cross the species boundaries by using different cellular receptors. SARS-CoV-2 is believed to originate in bats and transmitted to human being through an ill-defined intermediate host. In the current review, different aspects of SARS-CoV-2 biology and pathogenicity are discussed including virus genetics and evolution, spike protein and its role in evolution and adaptation to novel hosts, and virus transmission and persistence in nature. In addition, the immune response developed during SARS-CoV-2 infection is demonstrated with special reference to the interplay between immune cells and their role in disease progression. We believe that SARS-CoV-2 outbreak will not be the last and spillover of CoVs from bats will continue. Therefore, establishing intervention approaches to reduce the likelihood of future CoVs spillover from the natural reservoirs is a priority.

We know that living matter must behave in accordance with the universal laws of physics and chemistry. However, these laws are insufficient to explain the specific characteristics of the vital phenomenon and, therefore, we need new principles, intrinsic to biology, which are the basis for developing a theoretical framework for understanding life. Here I propose what I call the seven commandments of life (the Vital Order, the Principle of Inexorability, the Central Dogma, the Tyranny of Time, the Evolutionary Imperative, the Conservative Rule, the Cooperating Thrust) as a set of principles that help us explain the vital phenomenon from an evolutionary perspective. In a metaphorical way, we can consider life like an endless race in which living beings are the runners, who are changing as the race goes on (the evolutionary process), and the commandments the rules.

Many studies deal synthesis of carbon because of its versatility but lack the arresting of understanding at convincing and compelling levels. A binding energy shape-like parabola is linked to state of handing over electron to state of taking over electron at each opposite side of the atom maintaining the equilibrium of resulting new state of the carbon atom. Through this mechanism of transferring electrons for the gas state carbon atom, it converts into graphitic state, nanotube state, fullerene state, diamond state, lonsdaleite state and graphene state carbon atom. Forces of relevant poles remain neutral at instant of transferring electrons to attain specific state of their carbon atom. Structure evolutions in graphitic, nanotube and fullerene state carbon atoms are remained one-dimensional, two-dimensional and four-dimensional, respectively, where energy shape-like parabola is also involved along the relevant quadrant executing electron-dynamics to engage neutral behavior of exerting relevant poles forces. A graphite structure when develops under attained dynamics of atoms and their binding is under a bit difference of involved opposite pole forces, it develops in two-dimensional also. Evolution of structure in diamond, lonsdaleite and graphene state carbon atoms is under involving potential energy of electrons dealing double clamping of energy knot where relevant poles forces exerted in the orientationally controlled manner. Growth of diamond is south to ground, but binding of atoms is ground to south, so, it is a tetra-electrons ground to south topological structure. Lonsdaleite is a bi-electrons ground to just-south topological structure. Growth of graphene is just-north to ground, but binding of atoms is ground to just-north, so, it is a tetra-electrons ground to just-north topological structure. Glassy carbon is related to a layered-topological structure where successive tri-layers of gas, graphitic and lonsdaleite state atoms bind in the repetition manner. In glassy carbon, pairs of orientated electrons of gas and lonsdaleite state carbon atoms deal double clamping of energy knot by entering from the rear-side and front-side, respectively, to bind to intermediate layers of graphitic state atoms. Different carbon atoms develop amorphous structures when they bind under frustrating amalgamation. Hardness of carbon-based materials is also sketched in the light of different force-energy behaviors of different state carbon atoms. Here, structure evolution in each carbon state atom explores its own science.

Many positive sense RNA viruses, especially those infecting plants, are known to experience stringent, stochastic population bottlenecks inside the cells they invade, but exactly how and why these populations become bottlenecked are unclear. A model proposed ten years ago advocates that such bottlenecks are evolutionarily favored because they cause the isolation of individual viral variants in separate cells. Such isolation in turn allows the viral variants to manifest the phenotypic differences they encode. Recently published observations lend mechanistic support to this model, and prompt us to refine the model with novel molecular details. The refined model, designated Bottleneck, Isolate, Amplify, Select (BIAS), postulates that these viruses impose population bottlenecks on themselves by encoding bottleneck-enforcing proteins (BNEPs) that function in a concentration-dependent manner. In cells simultaneously invaded by numerous virions of the same virus, BNEPs reach the bottleneck-ready concentration sufficiently early to arrest nearly all internalized viral genomes. As a result, very few (as few as one) viral genomes stochastically escape to initiate reproduction. Repetition of this process in successively infected cells isolate viral genomes with different mutations in separate cells. This isolation prevents mutant viruses encoding defective viral proteins from hitchhiking on sister genome-encoded products, leading to the swift purging of such mutants. Importantly, genome isolation also ensures viral genomes harboring beneficial mutations accrue the cognate benefit exclusively to themselves, leading to the fixation of such beneficial mutations. Further interrogation of the BIAS hypothesis promises to deepen our understanding of virus evolution, and inspire new solutions to virus disease mitigation.

Transposable elements (TEs) are mobile genetic elements capable of rapidly altering the genome through their movements. The importance of TE activity has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs results in the growing number of bioinformatics software to identify insertion events. However, the application of existing TE finding tools is limited by either narrow-focused design of the package, too many dependencies on other tools, or prior knowledge required as input files that may not be readily available to all users. Here, we report a simple pipeline, TEfinder, developed for the detection of new TE insertions with minimal software dependencies using four inputs that can be easily generated with popular variant calling pipelines. The external software requirements are BEDTools, SAMtools, and Picard. Necessary inputs include TEs present in the reference genome, binary paired-end alignment, reference genome index, and a list of TE names. We tested TEfinder pipeline among several evolving populations of Fusarium oxysporum generated through a short-term adaptation study. Our results demonstrate that this easy-to-use tool can effectively detect new TE insertion events, making it accessible and practical for TE analysis.

The physics–biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the physical coupling between the synthesis of nucleic acids and the synthesis of amino acid polymers. Owing to this physical coupling, amino acid polymers (or proto-phenotypes) maintained the physicochemical parameter equilibria (proto-homeostasis) in the immediate environment of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical stresses, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome generating an internal environment whose physicochemical parameters guarantee homeostasis and genome integrity has a higher probability to be reproduced without variation and therefore to reproduce the same phenotype in offspring. Otherwise, the genome is modified by the imbalances of the internal physicochemical parameters it generates, until new emerging biological activities maintain homeostasis. In sum, evolution depends on feedforward and feedback loops between genome and phenotype, since the internal physicochemical conditions that a genome generates in response to environmental fluctuations in turn either guarantee the stability or direct the variation of the genome.

Genetic activation of the class I PI3K pathway is very common in cancer. This mostly results from oncogenic mutations in PIK3CA, the gene encoding the ubiquitously expressed PI3Kα catalytic subunit, or from inactivation of the PTEN tumour suppressor, a lipid phosphatase which opposes class I PI3K signalling. The clinical impact of PI3K inhibitors in solid tumours, aimed at dampening cancer-cell-intrinsic PI3K activity, has thus far been limited. Challenges include poor drug tolerance, incomplete pathway inhibition and pre-existing or inhibitor-induced resistance. The principle of pharmacologically targeting cancer-cell-intrinsic PI3K activity also assumes that all cancer-promoting effects of PI3K activation are reversible, which might not be the case. Emerging evidence suggests that genetic PI3K pathway activation can induce and/or allow cells to tolerate chromosomal instability, which – even if occurring in a low fraction of the cell population – might help to facilitate and/or drive tumour evolution. While it is clear that such genomic events cannot be reverted pharmacologically, a role for PI3K in the regulation of chromosomal instability could be exploited by using PI3K pathway inhibitors to prevent those genomic events from happening and/or reduce the pace at which they are occurring, thereby dampening cancer development or progression. Such an impact might be most effective in tumours with clonal PI3K activation and achievable at lower drug doses than the maximum-tolerated doses of PI3K inhibitors currently used in the clinic.

Addressing global environmental problem, water splitting to produce hydrogen fuel by solar energy is getting so much attention. In the water splitting, the essential problem to solve is the development of efficient　catalysts for oxygen production. In this paper, having the prospect for a practical application of photocatalysts to artificial photosynthesis, molecular mechanisms in the current literature are briefly reviewed. At first, recent progress in the function of Mn cluster at the natural photosystem II is briefly described. The kinds of devices in which oxygen evolution reaction (OER) catalysts are used were designated; water electrolyzers, photoelectrodes, and photocatalysts. Some methods for analyzing molecular mechanism in OER catalysis, emphasized by FTIR method, are shown briefly. After describing common OER mechanisms, the molecular mechanisms are discussed for TiO2 and BiVO4 photoelectrodes with our novel data, followed by presenting of co-catalysts IrO2, RuO2, NiO2, and other metal oxides for OER catalysts. Recent reports describing OER catalysts of perovskites, layered double hydroxides (LDH), metal-organic frameworks (MOF), single atom catalysts, as well as metal complexes are reviewed. Finally, by comparing with natural photosystem, the requiring factors to improve the activity of the catalysts for artificial photosynthesis will be discussed.

Malignant tumors behave dynamically as cell communities governed by ecological principles. Massive sequencing tools are unveiling the true dimension of the heterogeneity of these communities along their evolution in most human neoplasms, clear cell renal cell carcinomas (CCRCC) included. Although initially thought to be purely stochastic processes, very recent genomic analyses have shown that temporal tumor evolution in CCRCC may follow some deterministic pathways that give rise to different clones and sub-clones randomly spatially distributed across the tumor. This fact makes each case unique, unrepeatable and unpredictable. Precise and complete molecular information is crucial for patients with cancer since it may help in establishing a personalized therapy. Intratumor heterogeneity (ITH) detection relies on the correctness of tumor sampling and this is part of the pathologist’s daily work. International protocols for tumor sampling are insufficient today. They were conceived decades ago, when ITH was not an issue, and have remained unchanged until now. Noteworthy, an alternative and more efficient sampling method for detecting ITH has been developed recently. This new method, called multisite tumor sampling (MSTS), is specifically addressed to large tumors that are impossible to be totally sampled, and represent an opportunity to improve ITH detection without extra costs.

The simple sequence repeats (SSRs) are small 1-6bp tandem repeat elements present across diverse genomes and involved in gene regulation and evolution. Presently we analyzed SSRs in genomes of 98 species of family Polyomaviridae across four genera. The genome size ranged from 3962bp (BM87) to 7369bp (BM85) but maximum genomes were in the range of 5 to 5.5 kb. The GC% had an average of 42% and ranged between 34.69 (BM95) to 52.35 (BM81). A total of 3036 SSRs and 223 cSSRs were extracted using IMEx with incident frequency from 18 to 56 and 0 to 7 respectively. The most prevalent mono-nucleotide repeat motif was “T” (48.95%) followed by “A” (33.48%). “AT/TA” was the most prevalent dinucleotide motif closely followed by “CT/TC”. The distribution was expectedly more in coding region with 77.6% SSRs of which nearly half were in Large T Antigen (LTA) gene. Notably, most viruses with humans, apes and related species as host exhibited exclusivity of mono-nucleotide repeats in AT region, a proposed predictive marker for determination of humans as host in virus in course of its evolution. Each genome has a unique SSR signature which is pivotal for viral evolution particularly in terms of host divergence.

Reptilians or reptoids are staple characters of Hollywood cinema, science fiction literature, ufology and conspiracy theories. Despite its popularity, the reptoid has been dismissed by the scientific community as a figment of the imagination; born out of a speculation, paranoia and wanton anthropocentricism. In this paper, however, the Life Sequence Conjecture is advanced as a supportive framework for the notion of reptilian extraterrestrials. This paper is not an argument in support of the existence of extraterrestrials. Rather, it proposes that if extraterrestrials do exist, then a reptilian morphology is not untenable.

PD-1/PD-L1 axis is one key therapeutic target against tumor cell immune escape. Structurally essential to the PD-1/PD-L1-linked immune escape is the binding interface of the PD-1/PD-L1 complex structure. Incorporating currently available PD-1/PD-L1-related experimental structures, this article unveils two sets of experimentally observed inter-molecular electrostatic interactions which stabilize the binding interface of the PD-1/PD-L1 complex structure. For the first time, this article proposes an evolutionary structural hypothesis that, as a result of natural selection, PD-1 is able to genetically mutate itself to structurally disrupt the PD-1/PD-L1 axis towards the restoration of T cell-mediated anti-tumor immunity.

It remains poorly understood how the life history strategies and transmission ecologies of viruses of plants, arthropods, and vertebrates are interrelated. The present analysis hinges on the virus transmission success. Virus transmission reflects where in the host-body viruses are retained or replicating. Plants, arthropods, and vertebrates share a protective outer-layer, a circulatory system, and reproductive organs. The latter enables vertical virus transmission and associates with virus-host mutualism. Two broadly opposing virus life history strategies are considered. Acute viruses tend to be replicative and are swiftly transmitted to the next host. Instead, persistent viruses keep virus replicating costs and host damage to a minimum. The intertwined life histories and transmission ecologies are accordingly pieced together, based on the virus mono- or instead dual-host tropism, the location of virus retention or replication on or in the host-body, the presence of cyclical or mechanical transmission by arthropods, and of horizontal and vertical host-to-host transmission modes. It is shown that in the arthropod and in the vertebrate animal host, virus circulation in the hemocoel or blood circulation goes hand-in-hand with vertical transmission. Instead, plant phloem viruses do not transmit via seed. The latter is the rule for the plant-only viruses. The risk management implications are discussed in brief.

This article challenges the notion of the randomness of mutations in eukaryotic cells by unveiling stress-induced human non-random genome editing mechanisms. To account for the existence of such mechanisms, I have developed molecular concepts of the cell environment and cell environmental stressors and, making use of a large quantity of published data, hypothesized the origin of some crucial biological leaps along the evolutionary path of life on Earth under the pressure of natural selection, in particular, 1) virus-cell mating as a primordial form of sexual recombination and symbiosis; 2) Lamarckian CRISPR-Cas systems; 3) eukaryotic gene development; 4) antiviral activity of retrotransposon-guided mutagenic enzymes and finally; 5) the exaptation of antiviral mutagenic mechanisms to stress-induced genome editing mechanisms directed at “hypertranscribed” endogenous genes. Genes transcribed at their maximum rate (hypertranscribed), yet still unable to meet new chronic environmental demands generated by “pollution”, are inadequate and generate more and more intronic retrotransposon transcripts. In this scenario, RNA-guided mutagenic enzymes (e.g. AID/APOBECs), which have been shown to bind to retrotransposon RNA-repetitive sequences, would be surgically targeted by intronic retrotransposons on opened chromatin regions of the same “hypertranscribed” genes. RNA-guided mutagenic enzymes may therefore “Lamarkianly” generate single nucleotide polymorphisms (SNP) and copy number variations (CNV), as well as transposon transposition and chromosomal translocations in the restricted areas of hyperfunctional and inadequate genes, leaving intact the rest of the genome. CNV and SNP of hypertranscribed genes may allow cells to surgically explore a new fitness scenario, which increases their adaptability to stressful environmental conditions. Like the mechanisms of immunoglobulin somatic hypermutation, non-random genome editing mechanisms may generate several cell mutants, and those codifying for the most environmentally-adequate proteins would have a survival advantage and would therefore be Darwinianly selected. Non-random genome editing mechanisms represent a link between environmental changes and biological novelty and plasticity, and provide a molecular basis to reconcile gene-centered and “ecological” views of evolution.