776 results match your criteria Acta Biotheoretica[Journal]

Memory in Ion Channel Kinetics.

Acta Biotheor 2021 May 27. Epub 2021 May 27.

Department of Animal Morphology and Physiology, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil.

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. Read More

View Article and Full-Text PDF

On Predation-Commensalism Processes as Models of Bi-stability and Constructive Role of Systemic Extinctions.

Acta Biotheor 2021 May 13. Epub 2021 May 13.

Sorbonne Université, UPMC Univ Paris 06, and CNRS, UMR 7598, Laboratoire Jacques-louis Lions, 75005, Paris, France.

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 from initial conditions with a small population of predators, which presents an interest from the vewpoint of the onset of the predator in evolution, is addressed. Read More

View Article and Full-Text PDF

Phylogenetic Inference and the Misplaced Premise of Substitution Rates.

Kirk Fitzhugh

Acta Biotheor 2021 May 6. Epub 2021 May 6.

Natural History Museum of Los Angeles County, 900 Exposition Blvd, Los Angeles, CA, 90007, USA.

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 inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential actions leading to explanatory hypotheses. Read More

View Article and Full-Text PDF

A Mathematical Model of the Tuberculosis Epidemic.

Acta Biotheor 2021 Apr 20. Epub 2021 Apr 20.

University of KwaZulu-Natal, Durban, South Africa.

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. Read More

View Article and Full-Text PDF

Evolutionary Processes Transpiring in the Stages of Lithopanspermia.

Ian von Hegner

Acta Biotheor 2021 Apr 10. Epub 2021 Apr 10.

Aarhus University, Ny Munkegade 116, DK-8000, Aarhus, Denmark.

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. Read More

View Article and Full-Text PDF

Cooperative Equilibrium in Biosphere Evolution: Reconciling Competition and Cooperation in Evolutionary Ecology.

John Herring

Acta Biotheor 2021 Feb 17. Epub 2021 Feb 17.

Purdue University West Lafayette, 610 Purdue Mall, West Lafayette, IN, 47907, USA.

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 concepts from game theory. It is here argued that biodiversity and ecological cooperation are intimately related, and that both tend to cyclically increase over biological history; this is likely due to the greater relative stability of cooperation over competition as a means of long-term conflict resolution within ecosystems. Read More

View Article and Full-Text PDF
February 2021

Can a More Variable Species Win Interspecific Competition?

Acta Biotheor 2021 Feb 12. Epub 2021 Feb 12.

Cardinal Stefan Wyszyński University, Wóycickiego 1/3, 01-938, Warsaw, Poland.

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. Read More

View Article and Full-Text PDF
February 2021

Mathematical Analysis of an Industrial HIV/AIDS Model that Incorporates Carefree Attitude Towards Sex.

Acta Biotheor 2021 Jan 27. Epub 2021 Jan 27.

Department of Science and Mathematics Education, School of Science and Technology Education, CK Tedam University of Technology and Applied Sciences, Navrongo, Ghana.

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 [Formula: see text] is less than unity. The model is also shown to exhibit multiple endemic states for some parameter values when [Formula: see text] and [Formula: see text]. Read More

View Article and Full-Text PDF
January 2021

The Structure of Causal Explanations in Population Biology.

Acta Biotheor 2021 Jan 14. Epub 2021 Jan 14.

Universiteit Gent, Ghent, Belgium.

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 changes over time, population biologists also often try to explain differences between populations, e. Read More

View Article and Full-Text PDF
January 2021

Optimal Control and Cost-Effectiveness Analysis of an HPV-Chlamydia trachomatis Co-infection Model.

Acta Biotheor 2021 Jan 3. Epub 2021 Jan 3.

Department of Mathematics, Federal University of Technology, Owerri, Nigeria.

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 when the associated reproduction number is less than unity. Read More

View Article and Full-Text PDF
January 2021

Photosynthetic Systems Suggest an Evolutionary Pathway to Diderms.

Scott O Rogers

Acta Biotheor 2020 Dec 7. Epub 2020 Dec 7.

Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.

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; and diderm phyla Acidobacteria and Chlorobi), others with type II reaction centers (RCII in monoderm phylum Chloroflexi; and diderm taxa Gemmatimonadetes, and alpha-, beta-, and gamma-Proteobacteria), and some containing both (RCI and RCII, only in diderm phylum Cyanobacteria). In most bacterial phylograms, photosystem types and diderm taxa are polyphyletic. Read More

View Article and Full-Text PDF
December 2020

The Continuity Principle and the Evolution of Replication Fidelity.

Seymour Garte

Acta Biotheor 2020 Nov 29. Epub 2020 Nov 29.

Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ, 08854-8020, USA.

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 of the cell population. Read More

View Article and Full-Text PDF
November 2020

Fitness Beats Truth in the Evolution of Perception.

Acta Biotheor 2020 Nov 24. Epub 2020 Nov 24.

, Caunes Minervois, France.

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 assumption that perception involves inference to states of the objective world, then the FBT Theorem shows that a strategy that simply seeks to maximize expected-fitness payoff, with no attempt to estimate the "true" world state, does consistently better. Read More

View Article and Full-Text PDF
November 2020

Mechanical Properties of Long Leaves: Experiment and Theory.

Acta Biotheor 2021 Jun 31;69(2):151-172. Epub 2020 Oct 31.

Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.

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 allowed the Young's modulus of the Epipactis leaves to be determined. Read More

View Article and Full-Text PDF

The Metaphysics of Causation in Biological Mechanisms: A Case of the Genetic Switch in Lambda Phage.

Zvonimir Anić

Acta Biotheor 2020 Oct 27. Epub 2020 Oct 27.

Institute of Philosophy, Ulica grada Vukovara 54, 10000, Zagreb, Croatia.

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 switch in phage lambda-and discuss Marco J. Read More

View Article and Full-Text PDF
October 2020

Inheritance as Evolved and Evolving Physiological Processes.

Acta Biotheor 2020 Oct 21. Epub 2020 Oct 21.

IHPST-Université Paris 1 Panthéon-Sorbonne & CNRS, 13 rue du Four, 75006, Paris, France.

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 organisms' life cycles in order to answer to the question of what is passed on across generations, how and why. Read More

View Article and Full-Text PDF
October 2020

Different Mechanisms of Cigarette Smoking-Induced Lung Cancer.

Acta Biotheor 2021 Mar 26;69(1):37-52. Epub 2020 Sep 26.

School of Mathematics and Statistics, Central China Normal University, Wuhan, 430079, P. R. China.

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 current and former smokers from the Nurses' Health Study cohort of females (NHS) and the Health Professionals Follow up Study cohort of men (HPFS). Read More

View Article and Full-Text PDF

Probability of Disease Extinction or Outbreak in a Stochastic Epidemic Model for West Nile Virus Dynamics in Birds.

Acta Biotheor 2021 Jun 5;69(2):91-116. Epub 2020 Sep 5.

Mathematical Sciences Department, University of Malawi, Chancellor College, P. O. Box 280, Zomba, Malawi.

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 model and conditions for disease extinction or persistence. Read More

View Article and Full-Text PDF

The Epistemology of a Positive SARS-CoV-2 Test.

Acta Biotheor 2020 Sep 4. Epub 2020 Sep 4.

Department of History & Philosophy, Montana State University, Bozeman, MT, USA.

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 does a positive test lend to each hypothesis? Second, how much evidence does a positive test provide for each hypothesis against its negation? We respond to each question within a formal Bayesian framework. We construe degree of confirmation as the difference between the posterior probability of the hypothesis and its prior, and the strength of evidence for a hypothesis against its alternative in terms of their likelihood ratio. Read More

View Article and Full-Text PDF
September 2020

Computational and Theoretical Analysis of the Association Between Gender and HSV-2 Treatment Adherence.

Acta Biotheor 2021 Jun 3;69(2):117-149. Epub 2020 Sep 3.

Department of Mathematics, University of Zimbabwe, Box MP 167, Mount Pleasant, Harare, Zimbabwe.

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. Read More

View Article and Full-Text PDF

Wolf Howling and Emergency Sirens: A Hypothesis of Natural and Technical Convergence of Aposematic Signals.

Acta Biotheor 2021 Mar 2;69(1):53-65. Epub 2020 Sep 2.

Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 129, 165 21, Prague 6, Czech Republic.

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 of wolves, with which they have a long history of coexistence. Read More

View Article and Full-Text PDF

Functional Integration and Individuality in Prokaryotic Collective Organisations.

Acta Biotheor 2020 Aug 20. Epub 2020 Aug 20.

IAS-Research Centre for Life, Mind and Society, Department of Logic and Philosophy of Science, University of the Basque Country (UPV/EHU), Avenida de Tolosa 70, 20018, Donostia-San Sebastian, Spain.

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 dimension of two representative associations of prokaryotes: biofilms and the endosymbiosis between prokaryotes. Read More

View Article and Full-Text PDF

The Theory of Chemical Symbiosis: A Margulian View for the Emergence of Biological Systems (Origin of Life).

Acta Biotheor 2021 Mar 11;69(1):67-78. Epub 2020 Aug 11.

Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brasil.

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 of quasi-random small peptides, some of them capable to bind this ribozyme structure back and starting to form an initial layer that would produce the larger subunit of the ribosome by accretion. Read More

View Article and Full-Text PDF

Fractured Symmetries: Information and Control Theory Perspectives on Mitochondrial Dysfunction.

Rodrick Wallace

Acta Biotheor 2020 Jul 28. Epub 2020 Jul 28.

The New York State Psychiatric Institute, New York, USA.

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 a foundation for the development of statistical tools useful in clinical and public health address of those disorders. Read More

View Article and Full-Text PDF

A Note Against the Use of "Belonging To" Properties in Multilevel Selection Theory.

Ciprian Jeler

Acta Biotheor 2020 Jul 13. Epub 2020 Jul 13.

Institute for Interdisciplinary Research, Social Sciences and Humanities Research Department, "Alexandru Ioan Cuza" University of Iaşi, Iaşi, Romania.

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. Read More

View Article and Full-Text PDF

Assessing the Effects of Holling Type-II Treatment Rate on HIV-TB Co-infection.

Acta Biotheor 2021 Mar 16;69(1):1-35. Epub 2020 Jun 16.

Postdoctoral Researcher at ELTE, Institute for Theoretical Physics, Eotvos University, Budapest, Hungary.

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. Read More

View Article and Full-Text PDF

Correction to: Mathematical Basis of Predicting Dominant Function in Protein Sequences by a Generic HMM-ANN Algorithm.

Siddhartha Kundu

Acta Biotheor 2020 09;68(3):393

Department of Biochemistry, Dr. Baba Saheb Ambedkar Medical College and Hospital, Government of NCT of Delhi, Sector - 6, Rohini, Delhi, 110085, India.

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

View Article and Full-Text PDF
September 2020

How Could This Happen? : Narrowing Down the Contagion of COVID-19 and Preventing Acute Respiratory Distress Syndrome (ARDS).

Acta Biotheor 2020 Dec 25;68(4):441-452. Epub 2020 Apr 25.

Biological Publishing A&O and Immunology Department, Erasmus MC, Rotterdam, The Netherlands.

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 understanding the present pandemic outbreak. However, important questions remain unanswered about the underlying mechanism causing the very high case fatality ratios (CFR) and mechanisms regarding severe reactions like ARDS, fatal cardiac and renal failures, associated with a number of important comorbidity factors. Read More

View Article and Full-Text PDF
December 2020

What's Wrong with Evolutionary Causation?

Jan Baedke

Acta Biotheor 2021 Mar 13;69(1):79-89. Epub 2020 Apr 13.

Department of Philosophy I, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany.

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 Uller's and Kevin Laland's volume Evolutionary Causation as well as recent reviews of it as a starting point to reflect on the causal role of agency, individuality, and the environment in evolution. Read More

View Article and Full-Text PDF

The Goodwin Oscillator and its Legacy.

Acta Biotheor 2020 Mar 25. Epub 2020 Mar 25.

Centre for Organelle Research, University of Stavanger, Richard Johnsens gate 4, 4021, Stavanger, Norway.

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 aiming at identifying minimal mechanisms to generate limit cycle oscillations and deciphering design principles of biological oscillators. Read More

View Article and Full-Text PDF