JournalTOCs

Acta Biotheoretica
Journal Prestige (SJR): 0.284

Citation Impact (citeScore): 1
Number of Followers: 3

Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1572-8358 - ISSN (Online) 0001-5342
Published by Springer-Verlag

[2469 journals]

Finding or Creating a Living Organism' Past and Future Thought
Experiments in Astrobiology Applied to Artificial Intelligence
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  Abstract: Abstract This is a digest of how various researchers in biology and astrobiology have explored questions of what defines living organisms—definitions based on functions or structures observed in organisms, or on systems terms, or on mathematical conceptions like closure, chirality, quantum mechanics and thermodynamics, or on biosemiotics, or on Darwinian evolution—to clarify the field and make it easier for endeavors in artificial intelligence to make progress. Current ideas are described to promote work between astrobiologists and computer scientists, each concerned with living organisms. A four-parameter framework is presented as a scaffold that is later developed into what machines lack to be considered alive: systems, evolution, energy and consciousness, and includes Jagers operators and the idea of dual closure. A novel definition of consciousness is developed which describes mental objects both with and without communicable properties, and this helps to clarify how consciousness in machines may be studied as an emergent process related to choice functions in systems. A perspective on how quantization, acting on nucleic acids, sets up natural limits to system behavior is offered as a partial address to the problem of biogenesis.
  PubDate: 2022-04-28
Mathematical Analysis of Membrane Transporters Dynamics: A Calcium Fluxes
Case Study
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  Abstract: Abstract A tight control of intracellular [Ca $^{2+}$ ] is essential for the survival and normal function of cells. In this study we investigate key mechanistic steps by which calcium is regulated and calcium oscillations could occur using in silico modeling of membrane transporters. To do so we give a deterministic description of intracellular Ca $^{2+}$ dynamics using nonlinear dynamics in order to understand Ca $^{2+}$ signaling. We first present the ordinary differential equations (ODEs) system for cell calcium kinetics and make a preliminary work on Sobol indices. We then describe and analyze complex transporters action. Besides, we analyze the whole system. We finally perform numerical simulations and compare our results to real data.
  PubDate: 2022-04-28
Nonlocal Reaction–Diffusion Equations in Biomedical Applications
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  Abstract: Abstract Nonlocal reaction–diffusion equations describe various biological and biomedical applications. Their mathematical properties are essentially different in comparison with the local equations, and this difference can lead to important biological implications. This review will present the state of the art in the investigation of nonlocal reaction–diffusion models in biomedical applications. We will consider various models arising in mathematical immunology, neuroscience, cancer modelling, and we will discuss their mathematical properties, nonlinear dynamics, resulting spatiotemporal patterns and biological significance.
  PubDate: 2022-03-17
Qualitative and Dynamical Analysis of a Bionomic Fishery Model with Prey
Refuge
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  Abstract: Abstract Predation and escaping from predation through hiding are two fundamental phenomena in ecology. The most common approach to reducing the chance of predation is to use a refuge. Here, we consider a three species fishery model system with prey refuge induced by a Holling type-II functional response. These three species of fish populations are named prey, middle predator, and top predator. Harvesting is employed in most fishery models to achieve both ecological and commercial benefits. Research proves that non-linear harvesting (Michaelis–Menten type) returns more realistic outcomes. So, we have combined the Michaelis–Menten type of harvesting efforts for all populations. Uniform boundedness conditions for the solutions of the model are discussed. The existence conditions for possible equilibrium points with stability are presented. We explain the dynamical behavior at each equilibrium point through bifurcation analysis. The persistent criteria of the system are examined. Bionomic equilibrium and optimal harvesting control using Pontryagin’s maximum principle are calculated. For validation of the model in the real world, we have implemented this in the freshwater ecosystem of Lake Victoria. Extraction of native fish species and ecological balances are the foremost solicitude of Lake Victoria. We may resolve this concern partially by implementing prey refuge, since it may sustain the ecology of Lake Victoria, and therefore also its economical importance. Lake Victoria is acclaimed worldwide for the trade of fishing. Also, it provides the largest employment in east-central Africa and is beneficial to fishing equipment manufacturers. So, the bionomic equilibrium and harvesting control have significant applications in the fisheries. All the analytical studies are verified by numerical simulations. We have plotted phase portraits, bifurcation diagrams, Lyapunov exponents to explore the dynamics of the proposed model.
  PubDate: 2022-02-04
  DOI: 10.1007/s10441-022-09435-5
The Hybrid Incidence Susceptible-Transmissible-Removed Model for Pandemics
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  Abstract: Abstract The susceptible-transmissible-removed (STR) model is a deterministic compartment model, based on the susceptible-infected-removed (SIR) prototype. The STR replaces 2 SIR assumptions. SIR assumes that the emigration rate (due to death or recovery) is directly proportional to the infected compartment’s size. The STR replaces this assumption with the biologically appropriate assumption that the emigration rate is the same as the immigration rate one infected period ago. This results in a unique delay differential equation epidemic model with the delay equal to the infected period. Hamer’s mass action law for epidemiology is modified to resemble its chemistry precursor—the law of mass action. Constructing the model for an isolated population that exists on a surface bounded by the extent of the population’s movements permits compartment density to replace compartment size. The STR reduces to a SIR model in a timescale that negates the delay—the transmissible timescale. This establishes that the SIR model applies to an isolated population in the disease’s transmissible timescale. Cyclical social interactions will define a rhythmic timescale. It is demonstrated that the geometric mean maps transmissible timescale properties to their rhythmic timescale equivalents. This mapping defines the hybrid incidence (HI). The model validation demonstrates that the HI-STR can be constructed directly from the disease’s transmission dynamics. The basic reproduction number ( ${\mathcal{R}}_0$ ) is an epidemic impact property. The HI-STR model predicts that ${\mathcal{R}}_0 \propto \root \mathfrak{B} \of {\rho_n}$ where $\rho_n$ is the population density, and ${\mathfrak{B}}$ is the ratio of time increments in the transmissible- and rhythmic timescales. The model is validated by experimentally verifying the relationship. ${\mathcal{R}}_0$ ’s dependence on $\rho_n$ is demonstrated for droplet-spread SARS in Asian cities, aerosol-spread measles in Europe and non-airborne Ebola in Africa.
  PubDate: 2022-01-29
  DOI: 10.1007/s10441-021-09431-1
A Mathematical Model of the Transmission Dynamics of Bovine
Schistosomiasis with Contaminated Environment
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  Abstract: Abstract Schistosomiasis, a vector-borne chronically debilitating infectious disease, is a serious public health concern for humans and animals in the affected tropical and sub-tropical regions. We formulate and theoretically analyze a deterministic mathematical model with snail and bovine hosts. The basic reproduction number $R_0$ is computed and used to investigate the local stability of the model’s steady states. Global stability of the endemic equilibrium is carried out by constructing a suitable Lyapunov function. Sensitivity analysis shows that the basic reproduction number is most sensitive to the model parameters related to the contaminated environment, namely: shedding rate of cercariae by snails, cercariae to miracidia survival probability, snails-miracidia effective contact rate and natural death rate of miracidia and cercariae. Numerical results show that when no intervention measures are implemented, there is an increase of the infected classes, and a rapid decline of the number of susceptible and exposed bovines and snails. Effects of the variation of some of the key sensitive model parameters on the schistosomiasis dynamics as well as on the initial disease transmission threshold parameter $R_0$ are graphically depicted.
  PubDate: 2022-01-12
  DOI: 10.1007/s10441-021-09434-y
Modeling the Waves of Covid-19
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  Abstract: Abstract The challenges with modeling the spread of Covid-19 are its power-type growth during the middle stages of the waves with the exponents depending on time, and that the saturation of the waves is mainly due to the protective measures and other restriction mechanisms working in the same direction. The two-phase solution we propose for modeling the total number of detected cases of Covid-19 describes the actual curves for many its waves and in many countries almost with the accuracy of physics laws. Bessel functions play the key role in our approach. The differential equations we obtain are of universal type and can be used in behavioral psychology, invasion ecology (transient processes), etc. The initial transmission rate and the intensity of the restriction mechanisms are the key parameters. This theory provides a convincing explanation of the surprising uniformity of the Covid-19 waves in many places, and can be used for forecasting the epidemic spread. For instance, the early projections for the 3rd wave in the USA appeared sufficiently exact. The Delta-waves (2021) in India, South Africa, UK, and the Netherlands are discussed at the end.
  PubDate: 2021-12-27
  DOI: 10.1007/s10441-021-09428-w
Average and Standard Deviation of the Error Function for Random Genetic
Codes with Standard Stop Codons
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  Abstract: Abstract The origin of the genetic code has been attributed in part to an accidental assignment of codons to amino acids. Although several lines of evidence indicate the subsequent expansion and improvement of the genetic code, the hypothesis of Francis Crick concerning a frozen accident occurring at the early stage of genetic code evolution is still widely accepted. Considering Crick’s hypothesis, mathematical descriptions of hypothetical scenarios involving a huge number of possible coexisting random genetic codes could be very important to explain the origin and evolution of a selected genetic code. This work aims to contribute in this regard, that is, it provides a theoretical framework in which statistical parameters of error functions are calculated. Given a genetic code and an amino acid property, the functional code robustness is estimated by means of a known error function. In this work, using analytical calculations, general expressions for the average and standard deviation of the error function distributions of completely random codes with standard stop codons were obtained. As a possible biological application of these results, any set of amino acids and any pure or mixed amino acid properties can be used in the calculations, such that, in case of having to select a set of amino acids to create a genetic code, possible advantages of natural selection of the genetic codes could be discussed.
  PubDate: 2021-12-17
  DOI: 10.1007/s10441-021-09427-x
A Partition Theorem for a Randomly Selected Large Population
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  Abstract: Abstract A theorem on the partitioning of a randomly selected large population into stationary and non-stationary components by using a property of the stationary population identity is stated and proved. The methods of partitioning demonstrated are original and these are helpful in real-world situations where age-wise data is available. Applications of this theorem for practical purposes are summarized at the end.
  PubDate: 2021-12-16
  DOI: 10.1007/s10441-021-09433-z
Achieving Minimum-Time Biological Conservation and Pest Management for
Additional Food provided Predator–Prey Systems involving Inhibitory
Effect: A Qualitative Investigation
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  Abstract: Abstract Theoretical and experimental studies on prey–predator systems where predator is supplied with alternate sources of food have received significant attention over the years due to their relevance in achieving biological conservation and biological control. Some of the outcomes of these studies suggest that with appropriate quality and quantity of additional food, the system can be steered towards any desired state eventually with time. One of the limitations of previous studies is that the desired state is reached asymptotically, which makes the outcomes not easily applicable in practical scenarios. To overcome this limitation, in this work, we formulate and study optimal control problems to achieve the desired outcomes in minimum (finite) time. We consider two different models of additional food provided prey–predator systems involving Holling type IV functional response (with inhibitory effect of prey). In the first scenario, additional food is incorporated implicitly into the predator’s functional response with a possibility of achieving biological conservation through co-existence of species and biological control by maintaining prey at a level that is least harmful to the system. In the second, the effect of additional food is incorporated explicitly into the predator’s compartment with the goal of pest management by maintaining prey density at a very minimal damaging level. For both cases, appropriate optimal control strategies are derived and the theoretical findings are illustrated by numerical simulations. We also discuss the ecological significance of the theoretical findings for both models.
  PubDate: 2021-12-14
  DOI: 10.1007/s10441-021-09430-2
Host Manipulation Mechanisms of SARS-CoV-2
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  Abstract: Abstract Viruses are the simplest of pathogens, but possess sophisticated molecular mechanisms to manipulate host behavior, frequently utilizing molecular mimicry. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to bind to the host receptor neuropilin-1 in order to gain entry into the cell. To do this, the virus utilizes its spike protein polybasic cleavage site (PCS), which mimics the CendR motif of neuropilin-1’s endogenous ligands. In addition to facilitating cell entry, binding to neuropilin-1 has analgesic effects. We discuss the potential impact of neuropilin-1 binding by SARS-CoV-2 in ameliorating sickness behavior of the host, and identify a convergent evolutionary strategy of PCS cleavage and subsequent neuropilin binding in other human viruses. In addition, we discuss the evolutionary leap of the ancestor of SARS-COV-2, which involved acquisition of the PCS thus faciliting binding to the neuropilin-1 receptor. Acquisition of the PCS by the ancestor of SARS-CoV-2 appears to have led to pleiotropic beneficial effects including enhancement of cell entry via binding to ACE2, facilitation of cell entry via binding to neuropilin-1, promotion of analgesia, and potentially the formation of decoy epitopes via enhanced shedding of the S1 subunit. Lastly, other potential neuromanipulation strategies employed by SARS-CoV-2 are discussed, including interferon suppression and the resulting reduction in sickness behavior, enhanced transmission through neurally mediated cough induction, and reduction in sense of smell.
  PubDate: 2021-12-13
  DOI: 10.1007/s10441-021-09425-z
The Concept of Evenness/Unevenness: Less Evenness or More Unevenness'
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  Abstract: Abstract While evenness is understood to be maximal if all types (species, genotypes, alleles, etc.) are represented equally (via abundance, biomass, area, etc.), its opposite, maximal unevenness, either remains conceptually in the dark or is conceived as the type distribution that minimizes the applied evenness index. The latter approach, however, frequently leads to conceptual inconsistency due to the fact that the minimizing distribution is not specifiable or is monomorphic. The state of monomorphism, however, is indeterminate in terms of its evenness/unevenness characteristics. Indeed, the semantic indeterminacy also shows up in the observation that monomorphism represents a state of pronounced discontinuity for the established evenness indices. This serious conceptual inconsistency is latent in the widely held idea that evenness is an independent component of diversity. As a consequence, the established evenness indices largely appear as indicators of relative polymorphism rather than as indicators of evenness. In order to arrive at consistent measures of evenness/unevenness, it seems indispensable to determine which states are of maximal unevenness and then to assess the position of a given type distribution between states of maximal evenness and maximal unevenness. Since semantically, unevenness implies inequality among type representations, its maximum is reached if all type representations are equally different. For given number of types, this situation is realized if type representations, when ranked in descending order, show equal differences between adjacent types. We term such distributions “stepladders” as opposed to “plateaus” for uniform distributions. Two approaches to new evenness measures are proposed that reflect different perspectives on the positioning of type distributions between the closest stepladders and the closest plateaus. Their two extremes indicate states of complete evenness and complete unevenness, and the midpoint is postulated to represent the turning point between prevailing evenness and prevailing unevenness. The measures are graphically illustrated by evenness surfaces plotted above frequency simplices for three types, and by transects through evenness surfaces for more types. The approach can be generalized to include variable differences between types (as required in analyses of functional evenness) by simply replacing types with pairs of different types. Pairs, as the new types, can be represented by their abundances, for example, and these can be modified in various ways by the differences between the two types that form the pair. Pair representations thus consist of both the difference between the paired types and their frequency. Omission of pair frequencies leads to conceptual ambiguity. Given this specification of pair representations, their evenness/unevenness can be evaluated using the same indices developed for simple types. Pair evenness then turns out to quantify dispersion evenness.
  PubDate: 2021-12-10
  DOI: 10.1007/s10441-021-09429-9
The $$a$$ a -Wave of the Electroretinogram and Iron-Induced Oxidative
Stress: A Model
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  Abstract: Abstract In photoreceptors of a dark adapted eye, the inward flux of sodium and calcium ions in the outer segment is balanced by the outward flux of potassium ions. But in the presence of light the creation of cyclic guanosine monophosphate in the outer segment decreases. Due to low concentration of cG (cyclic GMP) the channels in the outer segment open relatively less and thus the influx of calcium ion decreases, leading finally to hyperpolarization of the photoreceptors. We have analyzed theoretically the effect of oxidizing iron ions on the photoreceptors. In order to explain the effects of iron-induced oxidative stress, the different molecules and ions involved in phototransduction are quantified leading to a differential equation for calculating the electroretinogram a-wave voltage. The theoretical results are compared with published experimental data. In the presence of light, the iron ions could push outward the similarly charged calcium ions resulting in a small increase in the amount of inward calcium flux. Again, the presence of iron ions generates Reactive Oxygen Species, and ROS could attract the calcium ions which also increases the calcium flux. This will result in a reduction in the amplitude and slope of the a-wave voltage in the electroretinogram. These results are parametrized in terms of calcium ion concentrations. As the amplitude of the a-wave shows how much electrical signal is produced, its reduction indicates reduction in the visual signal. Thus, the increase in iron ions could explain the reduction in the electrical signal due to iron-induced oxidative stress.
  PubDate: 2021-12-06
  DOI: 10.1007/s10441-021-09426-y
The Indeterminacy Bottleneck: Implications for Habitable Worlds
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  Abstract: Abstract It is often assumed that the transition between chemical evolution and biological evolution undergoes a smooth process; that once life has arisen, it will automatically ‘flood’ a solar system body. However, there is no a priori reason to assume that a link between them is a given. The fact that both chemical evolution and biological evolution meet in a single point can be critical. Thus, one may ask: can a world’s environment be favourable for chemical evolution but not for biological evolution, or vice versa' This is an important question worth exploration because certain worlds in the solar system in the past seemed to possess the possibility of chemical evolution, while several worlds in the present seem to exhibit such a possibility. Have such solar system bodies thus been, or are, ‘flooded’ by life' Did they possess the opportunity for biological evolution' The answer depends on the very nature of certain conditions under which evolution occurs, which may indicate that a link between chemical evolution and biological evolution is not automatically realised on a habitable solar system body. Thus, these conditions imply that in the emergence and distribution of cellular life, there exists an indeterminacy bottleneck at which chemical evolution and biological evolution meet through a single cell, whose descendants goes ‘information explosive’, ‘entropy implosive’ and ‘habitat expansive’, which determine whether life moves on to new environments. The consequence is that a world's environment can indeed be favourable for biological evolution, but not for chemical evolution. Thus, even if chemical evolution leads to the emergence of a microbial organism in a world, then it is not a given that such a first life form will be subjected to distribution to other environments; and not a given that its existence will continue in the environment it originated in. Thus, the bottleneck may be one of the decisive factors in the differences between habitable and inhabited worlds.
  PubDate: 2021-12-04
  DOI: 10.1007/s10441-021-09432-0
Correction to: Biology and Pragmatism: The Organism-Environment Bond
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  Abstract: A correction to this paper has been published: https://doi.org/10.1007/s10441-021-09414-2
  PubDate: 2021-12-01
  DOI: 10.1007/s10441-021-09414-2
Biology and Pragmatism: The Organism-Environment Bond
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  Abstract: Abstract This review essay 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.
  PubDate: 2021-12-01
  DOI: 10.1007/s10441-021-09410-6
On Predation–Commensalism Processes as Models of Bi-stability and
Constructive Role of Systemic Extinctions
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  Abstract: Abstract 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. We propose two possibilities: the classical one involving adapted conditions in the far past and a new (up to our knowledge) one using biodiversity, specifically the presence of another predator which operates as a starter, being displaced in the sequel.
  PubDate: 2021-12-01
  DOI: 10.1007/s10441-021-09413-3
How Do Trees Grow in Girth' Controversy on the Role of Cellular Events
in the Vascular Cambium
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  Abstract: Abstract 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 by studies of the arrangement of cambial cells, negates the influence of this apical cell growth on the expansion of the cambial circumference. Instead, it suggests that the tip of the elongating cambial initial intrudes between the tangential (periclinal) walls, rather than the radial (anticlinal) walls, of the initial(s) and its(their) derivative(s) lying ahead of the elongating cell tip. The new concept also explains the hitherto obscure mechanism of the cell event called ‘elimination of initials’. This article evaluates these new concepts of the cambial cell dynamics and offers a new interpretation for some curious events occurring in the cambial meristem in relation to the radial growth in woody plants.
  PubDate: 2021-12-01
  DOI: 10.1007/s10441-021-09418-y
Factors in Protobiomonomer Selection for the Origin of the Standard
Genetic Code
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  Abstract: Abstract 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 to different positions of atoms in the molecule. These parameters differ between cis- and trans-isomers of dicarboxylic acids, spatial monosaccharide isomers, and structural isomers of α-, β-, and γ-amino acids. The stable planar heterocyclic molecules of the major nucleobases comprise four (C, H, N, O) or three (C, H, N) elements and contain a single –C=C bond and two nitrogen atoms in each heterocycle involved in C–N and C=N bonds. They exist as isomeric resonance hybrids of single and double bonds and as a mixture of tautomer forms due to the presence of –C=O and/or –NH2 side groups. They are thermostable, insoluble in water, and exhibit solid-state stability, which is of central importance for DNA molecules as carriers of genetic information. In M–Tm diagrams, proteinogenic amino acids and the corresponding codons are distributed fairly regularly relative to the distinct clusters of purine and pyrimidine bases, reflecting the correspondence between codons and amino acids that was established in different periods of genetic code development. The body of data on the evolution of the genetic code system indicates that the elemental composition and molecular structure of protobiomonomers, and their M, Tm, photostability, and aqueous solubility determined their selection in the emergence of the standard genetic code.
  PubDate: 2021-12-01
  DOI: 10.1007/s10441-021-09420-4
A Human-Bovine Schistosomiasis Mathematical Model with Treatment and
Mollusciciding
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  Abstract: Abstract 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 stability of the endemic equilibrium is investigated by constructing a suitable Lyapunov function. To support the analytical results, parameter values from published literature are used for numerical simulations and where applicable, uncertainty analysis on the non-dimensional system parameters is performed using the Latin Hypercube Sampling and Partial Rank Correlation Coefficient techniques. Sensitivity analysis to determine the relative importance of model parameters to disease transmission shows that the environment-related parameters namely, $\varepsilon _s$ (snails shedding rate of cercariae), $p_s$ (probability that cercariae shed by snails survive), c (fraction of the contaminated environment sprayed by molluscicides) and $\mu _c$ (mortality rate of cercariae) are the most significant to mitigate the spread of schistosomiasis. Mollusciciding, which directly impacts the contaminated environment as a single control strategy is more effective compared to treatment. However, concurrently applying mollusciciding and treatment will yield a better outcome.
  PubDate: 2021-12-01
  DOI: 10.1007/s10441-021-09416-0