Complex, multigenic biological traits are shaped by the emergent interaction of proteins being the main functional units at the molecular scale. Based on a phenomenological approach, algorithms for quantifying two different aspects of emergence were introduced (Wegner and Hao in Progr Biophys Mol Biol 161:54–61, 2021) describing: (i) pairwise reciprocal interactions of proteins mutually modifying their

Despite several research on HIV/AIDS, it is still incumbent to investigate more effective control measures to mitigate its infection level. Therefore, we introduce an HIV/AIDS-resistant model with behavior change and study its basic properties. In order to determine the most sensitive parameters that are responsible for disease transmission with respect to the basic reproduction number and those responsible

Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either

Natural selection of specific protobiomonomers during abiogenic development of the prototype genetic code is hindered by the diversity of structural, spatial, and rotational isomers that have identical elemental composition and molecular mass (M), but can vary significantly in their physicochemical characteristics, such as the melting temperature Tm, the Tm:M ratio, and the solubility in water, due

The concept of causal specificity is drawing considerable attention from philosophers of biology. It became the rationale for rejecting (and occasionally, accepting) a thesis of causal parity of developmental factors. This literature assumes that attributing specificity to causal relations is at least in principle a straightforward (if not systematic) task. However, the parity debate in philosophy

To mitigate the spread of schistosomiasis, a deterministic human-bovine mathematical model of its transmission dynamics accounting for contaminated water reservoirs, including treatment of bovines and humans and mollusciciding is formulated and theoretically analyzed. The disease-free equilibrium is locally and globally asymptotically stable whenever the basic reproduction number \(R_0<1\), while global

Radial growth has long been a subject of interest in tree biology research. Recent studies have brought a significant change in the understanding of some basic processes characteristic to the vascular cambium, a meristem that produces secondary vascular tissues (phloem and xylem) in woody plants. A new hypothesis regarding the mechanism of intrusive growth of the cambial initials, which has been ratified

The proliferation of mitochondrial DNA (mtDNA) with deletion mutations has been linked to aging and age related neurodegenerative conditions. In this study we model the effect of mtDNA half-life on mtDNA competition and selection. It has been proposed that mutation deletions (\(\text {mtDNA}_{del}\)) have a replicative advantage over wild-type (\(\text {mtDNA}_{wild}\)) and that this is detrimental

A correction to this paper has been published: https://doi.org/10.1007/s10441-021-09414-2

Ion channels are transport proteins present in the lipid bilayers of biological membranes. They are involved in many physiological processes, such as the generation of nerve impulses, hormonal secretion, and heartbeat. Conformational changes in the ion channel-forming protein allow the opening or closing of pores to control the ionic flux through the cell membranes. The opening and closing of the ion

We propose a mathematical model for a class of predator–prey systems more complex than the usual one, involving a commensalism effect consisting in an influence of the predator on the sustainability of the prey. This effect induces interesting new features, including bi-stability (two attractors with disjoint attraction basins). The question of the possibility of reaching a certain attractor starting

Three competing ‘methods’ have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific

Tuberculosis has continued to retain its title as “the captain among these men of death”. This is evident as it is the leading cause of death globally from a single infectious agent. TB as it is fondly called has become a major threat to the achievement of the sustainable development goals (SDG) and hence require inputs from different research disciplines. This work presents a mathematical model of

Lithopanspermia is a theory proposing a natural exchange of organisms between solar system bodies as a result of asteroidal or cometary impactors. Research has examined not only the physics of the stages themselves but also the survival probabilities for life in each stage. However, although life is the primary factor of interest in lithopanspermia, this life is mainly treated as a passive cargo. Life

This review essays provides an analysis of the context and content of Trevor Pearce’s Pragmatism’s Evolution. The work highlights the bond between organisms and their environments.

As our understanding of biological evolution continues to deepen, tension still surrounds the relationship between competition and cooperation in the evolution of the biosphere, with rival viewpoints often associated with the Red Queen and Black Queen hypotheses respectively. This essay seeks to reconcile these viewpoints by integrating observations of some general trends in biosphere evolution with

An individual-based approach is used to describe population dynamics. Two kinds of models have been constructed with different distributions illustrating individual variability. In both models, the growth rate of an individual and its final body weight at the end of the growth period, which determines the number of offspring, are functions of the amount of resources assimilated by an individual. In

A nonlinear differential equation model is proposed to study the dynamics of HIV/AIDS and its effects on workforce productivity. The disease-free equilibrium point of the model is shown to be locally asymptotically stable when the associated basic reproduction number \(\mathcal{{R}}_{0}\) is less than unity. The model is also shown to exhibit multiple endemic states for some parameter values when

The scope of this paper can be clarified by means of a well-known phenomenon that is usually called ‘industrial melanism’: the fact that the melanic form of the peppered moth became dominant in industrial areas in England in the second half of the nineteenth century. Such changes in relative phenotype frequencies are important explananda for population biologists. Apart from trying to explain such

In this work, a co-infection model for human papillomavirus (HPV) and Chlamydia trachomatis with cost-effectiveness optimal control analysis is developed and analyzed. The disease-free equilibrium of the co-infection model is shown not to be globally asymptotically stable, when the associated reproduction number is less unity. It is proven that the model undergoes the phenomenon of backward bifurcation

Bacteria are divided primarily into monoderms (with one cell membrane, and usually Gram-positive, due to a thick peptidoglycan layer) and diderms (with two cell membranes, and mostly Gram-negative, due to a thin peptidoglycan layer sandwiched between the two membranes). Photosynthetic species are spread among the taxonomic groups, some having type I reaction centers (RCI in monoderm phylum Firmicutes;

Evolution in modern life requires high replication fidelity to allow for natural selection. A simulation model utilizing simulated phenotype data on cellular probability of survival was developed to determine how self-replication fidelity could evolve in early life. The results indicate that initial survivability and replication fidelity both contribute to overall fitness as measured by growth rates

Does natural selection favor veridical percepts-those that accurately (if not exhaustively) depict objective reality? Perceptual and cognitive scientists standardly claim that it does. Here we formalize this claim using the tools of evolutionary game theory and Bayesian decision theory. We state and prove the "Fitness-Beats-Truth (FBT) Theorem" which shows that the claim is false: If one starts with

The static properties of leaves with parallel venation from terrestrial orchids of the genus Epipactis were modelled as coupled elastic rods using the geometrically exact Cosserat theory and the resulting boundary-value problem was solved numerically using a method from Shampine, Muir and Xu. The response of the leaf structure to the applied force was obtained from preliminary measurements. These measurements

The emphasis on the organization of entities and their activities and interactions has been labeled one of the most distinct contributions of mechanistic philosophy. In this paper I discuss the manner in which the organization of entities and their activities and interactions participates in bringing about phenomena. I present a well-known example from molecular biology-the functioning of the genetic

In this paper, we adopt a physiological perspective in order to produce an intelligible overview of biological transmission in all its diversity. This allows us to put forward the analysis of transmission mechanisms, with the aim of complementing the usual focus on transmitted factors. We underline the importance of the structural, dynamical, and functional features of transmission mechanisms throughout

The risk of cigarette smoking plays a pivotal role in increasing the incidence rates of lung cancer. This paper sheds new light on modeling the impact of cigarette smoking on lung cancer evolution, especially genetic instability and the number of gene mutations in the genome of stem cells. To handle this issue, we have set up stochastic multi-stage models to fit the data set of the probabilities of

Thresholds for disease extinction provide essential information for the prevention and control of diseases. In this paper, a stochastic epidemic model, a continuous-time Markov chain, for the transmission dynamics of West Nile virus in birds is developed based on the assumptions of its analogous deterministic model. The branching process is applied to derive the extinction threshold for the stochastic

We investigate the epistemological consequences of a positive polymerase chain reaction SARS-CoV test for two relevant hypotheses: (i) V is the hypothesis that an individual has been infected with SARS-CoV-2; (ii) C is the hypothesis that SARS-CoV-2 is the cause of flu-like symptoms in a given patient. We ask two fundamental epistemological questions regarding each hypothesis: First, how much confirmation

Herpes simplex virus type 2 (HSV-2) is the most prevalent sexually transmitted infection in the world, despite the availability of effective anti-viral treatments. A mathematical model to explore the association between gender and HSV-2 treatment adherence is developed. Threshold parameters are determined and stabilities analyzed. Sensitivity analysis of the reproduction number and the numerical simulations

Acoustic signals serving intraspecific communication by predators are perceived by potential prey as warning signals. We analysed the acoustic characteristics of howling of wolves and found a striking similarity to the warning sounds of technical sirens. We hypothesize that the effectivity of sirens as warning signals has been enhanced by natural sensory predisposition of humans to get alerted by howling

Both physiological and evolutionary criteria of biological individuality are underpinned by the idea that an individual is a functionally integrated whole. However, a precise account of functional integration has not been provided so far, and current notions are not developed in the details, especially in the case of composite systems. To address this issue, this paper focuses on the organisational

The theory of chemical symbiosis (TCS) suggests that biological systems started with the collaboration of two polymeric molecules existing in early Earth: nucleic acids and peptides. Chemical symbiosis emerged when RNA-like nucleic acid polymers happened to fold into 3D structures capable to bind amino acids together, forming a proto peptidyl-transferase center. This folding catalyzed the formation

Mitochondrial dysfunction underlies a vast array of chronic disorders across the life span. The asymptotic limit theorems of information and control theories, supplemented by symmetry-breaking phase transition arguments adapted from physical theory, give deep insight into canonical mechanisms of cognition and regulation associated with such dysfunction. The probability models studied here can provide

In this short paper, I argue against what I call the “belonging to” interpretation of group selection in scenarios in which a group’s fitness is defined as the per capita reproductive output of the individuals of the group. According to this interpretation, group selection acts on “belonging to” properties of individuals, i.e. on relational or contextual properties that all the individuals of a group

In this paper, a HIV-TB co-infection model is explored which incorporates a non-linear treatment rate for TB. We begin with presenting a HIV-TB co-infection model and analyze both HIV and TB sub-models separately. The basic reproduction numbers corresponding to HIV-only, TB-only and the HIV-TB full model are computed. The disease-free equilibrium point of the HIV sub-model is shown to be locally as

An amendment to this paper has been published and can be accessed via the original article.

In this rapid commentary, a mini-review is given of the present state-of-knowledge regarding the etiology and epidemiology of the new coronavirus 2019-nCoV and the risks for developing Acute respiratory distress syndrome (ARDS). The available knowledge on the viral genomics, molecular biology and pathogenicity of viruses of the Coronaviridae family and other Nidovirales, forms a helpful template for

This review essay reflects on recent discussions in evolutionary biology and philosophy of science on the central causes of evolution and the structure of causal explanations in evolutionary theory. In this debate, it has been argued that our view of evolutionary causation should be rethought by including more seriously developmental causes and causes of the individual acting organism. I use Tobias

Evolutionary theorists often talk as if natural selection were choosing the most adapted traits, or if organisms were deciding to do the most adaptive strategy. Moreover, the payoff of those decisions often depend on what others are doing, and since Hamilton ( 1964 ), biologists possess conceptual tools such as kin selection and inclusive fitness to make sense of outcomes of evolution in these contexts

In the 1960’s Brian Goodwin published a couple of mathematical models showing how feedback inhibition can lead to oscillations and discussed possible implications of this behaviour for the physiology of the cell. He also presented key ideas about the rich dynamics that may result from the coupling between such biochemical oscillators. Goodwin’s work motivated a series of theoretical investigations

The authors have retracted this article [1] because they found a fundamental mistake in the methodology that is not correctable at this time. This mistake is found in the methodology and the derivation of the model with Tukey and Huber’s losses. Because of the error, the findings in the article are not reliable. All authors agree to this retraction.

In this review of Milan Ćirković's The Great Silence: Science and Philosophy of Fermi's Paradox, we attempt to reconstruct the logic of Fermi's paradox as understood by the author, and we critically examine the reasoning that leads to the paradox. We show that there is no plausible solution to Fermi's paradox that can satisfy all of Ćirković's proposed desiderata, which in turn suggests that the author's

This study was funded by Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Grant Number 402619/2016-1) and Fundacao para a Ciencia e a Tecnologia (Grant Number DL57/2016/CP1479/CT0064).

An additional compartment of vaccinated individuals is considered in a SIS stochastic epidemic model with infection reintroduction. The quantification of the spread of the disease is modeled by a continuous time Markov chain. A well-known measure of the initial transmission potential is the basic reproduction number $$R_0$$ R 0 , which determines the herd immunity threshold or the critical proportion

The asymptotic limit theorems of information and control theories permit exploration of a surprising number of temperature-like measures and symmetry-breaking dynamics associated with cognition. Each of several markedly different perspectives produces a distinct temperature-analog, capturing a rich and highly-punctuated behavioral landscape across the complex, hierarchical cognitive phenomena that

Correct interpretation of the data from integral laboratory tests, including Thrombin Generation Test (TGT), requires biochemistry-based mathematical models of blood coagulation. The purpose of this study is to describe the experimental TGT data from healthy donors and hemophilia A (HA) and B (HB) patients. We derive a simplified ODE model and apply it to analyze the TGT data from healthy donors and

Provision of additional food supplements for the purpose of biological conservation has been widely researched both theoretically and experimentally. The study of these biosystems is usually done using predator-prey models. In this paper, we consider an additional food provided predator-prey system in the presence of the inhibitory effect of the prey. This model is analyzed in the control parameter

This manuscript considers the transmission dynamics of lymphatic filariasis with some intervention strategies in place. Unlike previously developed models, our model takes into account both the exposed and infected classes in both the human and mosquito populations, respectively. We also consider vaccinated, treated and recovered humans in the presented model. The global dynamics of the proposed model

The propensity account of fitness intends to solve the classical tautologicity issue by identifying fitness with a disposition, the ability to survive and reproduce. As proponents recognized early on, this account requires operational independence from actual reproductive success to avoid circularity and vacuousness charges. They suggested that operational independence is achieved by measuring fitness