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

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 \(R_0\), which determines the herd immunity threshold or the critical proportion of

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

In the original publication of the article, the y axis labels present in Figs. 1a and 2a are incorrect. The correct Figs. 1a and 2a are provided here.

Phylogenetic systematics (e.g., cladistics) is one of the most important analytical frameworks of modern Biology. It seems to be common knowledge that within phylogenetics, ‘groups’ must be defined based solely on the synapomorphies or on the “derived” characters that unite two or more taxa in a clade or monophyletic group. Thus, the idea of synapomorphy seems to be of fundamental influence and importance

The ecological impact of alien species is a function of the area colonised. Impact assessments of alien species are thus incomplete unless they take the spatial component of invasion processes into account. This paper describes a measure, termed expansion speed, that quantifies the speed with which a species increases its spatial presence in an assessment area. It is based on the area of occupancy

Recent years have seen the growing promise of cultural evolutionary theory as a new approach to bringing human behaviour fully within the broader evolutionary synthesis. This review of two recent seminal works on this topic argues that cultural evolution now holds the potential to bring together fields as disparate as neuroscience and social anthropology within a unified explanatory and ontological

The Evolution of the Sensitive Soul is a landmark attempt to make progress on the problem of animal consciousness. Ginsburg and Jablonka propose a general cognitive marker of the presence of consciousness: Unlimited Associative Learning. They use this marker to defend a generous view about the distribution of consciousness in the natural world, on which a capacity for conscious experience is common

Individuation and organization in complex living multi-level ecosystem occurs as dynamical processes from early ontogeny. The notion of living “holon” displaying dynamic self-assertion and integration is used here to explain the ecosystems dynamic processes. The update of the living holon state according to the continuous change of the dynamic system allows for its viability. This is interpreted as

We critique the organizational account of biological functions by showing how its basis in the closure of constraints fails to be objective. While the account treats constraints as objective features of physical systems, the number and relationship of potential constraints are subject to potentially arbitrary redescription by investigators. For example, we show that self-maintaining systems such as

The objective of the current study was to propose a sensitivity analysis of a 3D left ventricle model in order to assess the influence of parameters on myocardial mechanical dispersion. A finite element model of LV electro-mechanical activity was proposed and a screening method was used to evaluate the sensitivity of model parameters on the standard deviation of time to peak strain. Results highlight

The latitudinal gradient in species richness is perhaps the most fundamental pattern of biodiversity, yet a satisfactory explanation for its existence remains elusive. A geometric “mid-domain effect” is often cited as having potential to help explain the latitudinal gradient in species richness, but the logic underpinning this hypothesis is apparently built on two incorrect assumptions: (1) that a

In this paper, we revisit a host–parasite system with multiple parasite strains and superinfection proposed by Nowak and May (Proc R Soc Lond B 255(1342):81–89, 1994), and study its global dynamics when we relax the two strict conditions assumed therein. As for system with two parasite strains, we derive that the basic reproduction number \(R_0\) is the threshold condition for parasite extinction and

Simulation of complex biological systems with agent-based models is becoming more relevant with the increase in Graphics Processing Unit (GPU) power. In those simulations, up to millions of virtual cells are individually computed, involving daunting processing times. An important part of computational models is the algorithm that manages how agents perceive their surroundings. This can be particularly