Acta Biotheoretica

Transitive inference (TI) refers to social cognition that facilitates the discernment of unknown relationships between individuals using known relationships. It is extensively reported that TI evolves in animals living in a large group because TI could assess relative rank without deducing all dyadic relationships, which averts costly fights. The relationships in a large group become so complex that social cognition may not be developed adequately to handle such complexity. If members apply TI to all possible members in the group, TI requires extremely highly developed cognitive abilities especially in a large group...

In this article we analyse the issue of what accounts for developmental potential, i.e., the possible phenotypes a developing organism can manifest during ontogeny. We shall argue in favour of two theses. First, although the developing organism is the unit of development, the complete causal basis for its potential to develop does neither lie entirely in itself as a whole nor in any specific part of itself (such as its genome). Thus, the extra-organismal environment must be counted as one of the three necessary, partial and complementary causal bases for development potential...

In this work we propose the partial Wiener index as one possible measure of branching in phylogenetic evolutionary trees. We establish the connection between the generalized Robinson-Foulds (RF) metric for measuring the similarity of phylogenetic trees and partial Wiener indices by expressing the number of conflicting pairs of edges in the generalized RF metric in terms of partial Wiener indices. To do so we compute the minimum and maximum value of the partial Wiener index [Formula: see text], where [Formula: see text] is a binary rooted tree with root [Formula: see text] and [Formula: see text] leaves...

The paper is devoted to a conceptual model of cell patterning, based on a generalized notion of the epigenetic code of a cell determining its state. We introduce the concept of signaling depending both upon the spatial distance between cells and the distance between their cell states (s-distance); signaling can repel cells in the space of cell states (s-space) or attract them. The influence of different types of repelling signaling on the evolution of cells is considered. Stabilizing signaling, namely a signaling monotonically decreasing with s-distance, causes the restoring of cell states after perturbations; destabilizing signaling, i...

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A modified version of the SEIR model with the effects of vaccination and inter-state movement is proposed to simulate the spread of COVID-19 in Malaysia. A mathematical analysis of the proposed model was performed to derive the basic reproduction number. To enhance the model's forecasting capabilities, the model parameters were estimated using the Nelder-Mead simplex method by fitting the model outputs to the observed data. Our results showed a good fit between the model outputs and available data, where the model was then able to perform short-term predictions...

We propose a framework for the description of the effects of vaccinations on the spreading of an epidemic disease. Different vaccines can be dosed, each providing different immunization times and immunization levels. Differences due to individuals' ages are accounted for through the introduction of either a continuous age structure or a discrete set of age classes. Extensions to gender differences or to distinguish fragile individuals can also be considered. Within this setting, vaccination strategies can be simulated, tested and compared, as is explicitly described through numerical integrations...

We extend the comparatively simple processes of group symmetry-breaking in physical systems to groupoid/equivalence class phase transitions characterizing adiabatically, piecewise stationary, information transmission in prebiotic, biological, and social phenomena: High vs. Low probability paths [Formula: see text] Interior and Exterior Interact [Formula: see text] Multiple Interacting Tunable Workspaces Application to nonstationary processes seems possible via generalizations of the symmetry algebra, for example, to semigroupoids...

In all kinds of implementations of computing, whether technological or biological, some material carrier for the information exists, so in real-world implementations, the propagation speed of information cannot exceed the speed of its carrier. Because of this limitation, one must also consider the transfer time between computing units for any implementation. We need a different mathematical method to consider this limitation: classic mathematics can only describe infinitely fast and small computing system implementations...

In this work, we study and analyze the aggregate death counts of COVID-19 reported by the United States Centers for Disease Control and Prevention (CDC) for the fifty states in the United States. To do this, we derive a stochastic model describing the cumulative number of deaths reported daily by CDC from the first time Covid-19 death is recorded to June 20, 2021 in the United States, and provide a forecast for the death cases. The stochastic model derived in this work performs better than existing deterministic logistic models because it is able to capture irregularities in the sample path of the aggregate death counts...

Causal pluralism can be defended not only in respect to causal concepts and methodological guidelines, but also at the finer-grained level of causal inference from a particular source of evidence for causation. An argument for this last variety of pluralism is made based on an analysis of causal inference from randomized experiments (RCTs). Here, the causal interpretation of a statistically significant association can be established via multiple paths of reasoning, each relying on different assumptions and providing distinct elements of information in favour of a causal interpretation...

Much of the current research in regenerative medicine concentrates on stem-cell therapy that exploits the regenerative capacities of stem cells when injected into different types of human tissues. Although new therapeutic paths have been opened up by induced pluripotent cells and human mesenchymal cells, the rate of success is still low and mainly due to the difficulties of managing cell proliferation and differentiation, giving rise to non-controlled stem cell differentiation that ultimately leads to cancer...

The interplay between the virus, infected cells and immune responses to SARS-CoV-2 is still under debate. By extending the basic model of viral dynamics, we propose here a formal approach to describe neutralisation versus weak (or non-)neutralisation scenarios and compare them with the possible effects of antibody-dependent enhancement (ADE). The theoretical model is consistent with the data available in the literature; we show that both weakly neutralising antibodies and ADE can result in final viral clearance or disease progression, but that the immunodynamics are different in each case...

Radopholus Similis (R. Similis) or burrowing nematode, is one of the most damaging and widespread nematodes attacking bananas, causing toppling or blackhead disease. A mathematical model for the population dynamics of R. Similis is considered, with the aim of investigating the impact of climatic factors on the growth of R. Similis. In this paper, based on the life cycle of R. Similis, we first propose a mathematical model to study and control the population dynamics of this banana pest. We show also how control terms based on biological and chemical controls can be integrated to reduce the population of R...

Here, an epidemiological model considering pro and anti-vaccination groups is proposed and analyzed. In this model, susceptible individuals can migrate between these two groups due to the influence of false and true news about safety and efficacy of vaccines. From this model, written as a set of three ordinary differential equations, analytical expressions for the disease-free steady state, the endemic steady state, and the basic reproduction number are derived. It is analytically shown that low vaccination rate and no influx to the pro-vaccination group have similar impacts on the long-term amount of infected individuals...

Mechanistic models are built using knowledge as the primary information source, with well-established biological and physical laws determining the causal relationships within the model. Once the causal structure of the model is determined, parameters must be defined in order to accurately reproduce relevant data. Determining parameters and their values is particularly challenging in the case of models of pathophysiology, for which data for calibration is sparse. Multiple data sources might be required, and data may not be in a uniform or desirable format...

Ecologists are challenged by the need to bridge and synthesize different approaches and theories to obtain a coherent understanding of ecosystems in a changing world. Both food web theory and regime shift theory shine light on mechanisms that confer stability to ecosystems, but from different angles. Empirical food web models are developed to analyze how equilibria in real multi-trophic ecosystems are shaped by species interactions, and often include linear functional response terms for simple estimation of interaction strengths from observations...

We propose a novel model to explain the mechanisms underlying dominance hierarchical structures. Guided by a predetermined social convention, agents with limited cognitive abilities optimize their strategies in a Hawk-Dove game. We find that several commonly observed hierarchical structures in nature such as linear hierarchy and despotism, emerge as the total fitness-maximizing social structures given different levels of cognitive abilities.

The COVID-19 pandemic has resulted in more than 524 million cases and 6 million deaths worldwide. Various drug interventions targeting multiple stages of COVID-19 pathogenesis can significantly reduce infection-related mortality. The current within-host mathematical modeling study addresses the optimal drug regimen and efficacy of combination therapies in the treatment of COVID-19. The drugs/interventions considered include Arbidol, Remdesivir, Interferon (INF) and Lopinavir/Ritonavir. It is concluded that these drugs, when administered singly or in combination, reduce the number of infected cells and viral load...

Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits...