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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  [2468 journals]
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- The Role of Information in Evolutionary Biology
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Abstract: The Modern Synthesis has received criticism for its purported gene-centrism. That criticism relies on a concept of the gene as a unit of instructional information. In this paper I discuss information concepts and endorse one, developed from Floridi, that sees information as a functional relationship between data and context. I use this concept to inspect developmental criticisms of the Modern Synthesis and argue that the instructional gene arose as an idealization practice when evolutionary biologists made comment on development. However, a closer inspection of key claims shows that at least some associated with the Modern Synthesis were in fact adopting the data led definition I favour and made clear arguments for the role of developmental processes beyond genetic input. There was no instructional gene.
PubDate: 2023-05-15
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- Mathematical Model of Synaptic Long-Term Potentiation as a Bistability in
a Chain of Biochemical Reactions with a Positive Feedback-
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Abstract: Nitric oxide (NO) is involved in synaptic long-term potentiation (LTP) by multiple signaling pathways. Here, we show that LTP of synaptic transmission can be explained as a feature of signal transduction—bistable behavior in a chain of biochemical reactions with positive feedback, formed by diffusion of NO to the presynaptic site and facilitating the release of glutamate (Glu). The dynamics of Glu, calcium (Ca2+) and NO is described by a system of nonlinear reaction–diffusion equations with modified Michaelis–Menten (MM) kinetics. Numerical investigation reveals that the chain of biochemical reactions analyzed can exhibit a bistable behavior under physiological conditions when production of Glu is described by MM kinetics and decay of NO is modeled by means of two enzymatic pathways with different kinetic properties. Our finding extends understanding of the role of NO in LTP: a short high-intensity stimulus is “memorized” as a long-lasting elevation of NO concentration. The conclusions obtained by analysis of the chain of biochemical reactions describing LTP can be generalized to other chains of interactions or for creating the logical elements for biological computers.
PubDate: 2023-05-06
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- The Membrane Potential Has a Primary Key Equation
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Abstract: It is common to say that the origin of the membrane potential is attributed to transmembrane ion transport, but it is theoretically possible to explain its generation by the mechanism of ion adsorption. It has been previously suggested that the ion adsorption mechanism even leads to potential formulae identical to the famous Nernst equation or the Goldman-Hodgkin-Katz equation. Our further analysis, presented in this paper, indicates that the potential formula based on the ion adsorption mechanism leads to an equation that is a function of the surface charge density of the material and the surface potential of the material. Furthermore, we have confirmed that the equation holds in all the different experimental systems that we have studied. This equation appears to be a key equation that governs the characteristics of the membrane potential in all systems.
PubDate: 2023-05-06
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- Sulfur is in the Air: Cyanolichen Marriages and Pollution
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Abstract: Cyanolichens are symbiotic organisms involving cyanobacteria and fungi (bipartite) or with the addition of an algal partner (tripartite). Cyanolichens are known for their heightened susceptibility to environmental pollution. We focus here on the impacts on cyanolichens due to rising air pollution; we are especially interested in the role of sulfur dioxide on cyanolichen biology. Cyanolichens due to air pollution including sulfur dioxide exposure, show symptomatic changes including degradation of chlorophyll, lipid membrane peroxidation, decrease in ATP production, changes in respiration rate, and alteration of endogenous auxins and ethylene production, although symptoms are known to vary with species and genotype. Sulfur dioxide has been shown to be damaging to photosynthesis but is relatively benign on nitrogen fixation which proposes as a hypothesis that the algal partner may be more in harm’s way than the cyanobiont. In fact, the Nostoc cyanobiont of sulfur dioxide-susceptible Lobaria pulmonaria carries a magnified set of sulfur (alkane sulfonate) metabolism genes capable of alkane sulfonate transport and assimilation, which were only unraveled by genome sequencing, a technology unavailable in the 1950–2000 epoch, where most physiology- based studies were performed. There is worldwide a growing corpus of evidence that sulfur has an important role to play in biological symbioses including rhizobia-legumes, mycorrhizae-roots and cyanobacteria-host plants. Furthermore, the fungal and algal partners of L. pulmonaria appear not to have the sulfonate transporter genes again providing the roles of ambient-sulfur (alkanesulfonate metabolism etc.) mediated functions primarily to the cyanobacterial partner. In conclusion, we have addressed here the role of the atmospheric pollutant sulfur dioxide to tripartite cyanolichen viability and suggest that the weaker link is likely to be the photosynthetic algal (chlorophyte) partner and not the nitrogen-fixing cyanobiont.
PubDate: 2023-05-06
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- From Minerals to Simplest Living Matter: Life Origination Hydrate Theory
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Abstract: Long since, people tried to solve the mystery of the way that led to the appearance and propagation of living entities. However, no harmonious understanding of this mystery existed, because neither the scientifically grounded source minerals nor the ambient conditions were proposed and because it was groundlessly taken that the process of living matter origination is endothermal. The Life Origination Hydrate Theory (LOH-Theory) first suggests the chemical way capable of leading from the specified abundant natural minerals to origination of multitudes of multitudes of simplest living entities and gives an original explanation for the phenomena of chirality and racemization delay. The LOH-Theory covers the period up to origination of the genetic code. The LOH-Theory is grounded on the following three discoveries based on the available information and on the results of our experimental works performed using original instrumentation and computer simulations. (1) There is the only one triad of natural minerals applicable for exothermal thermodynamically possible chemical syntheses of simplest living-matter components. (2) N-base, ribose, and phosphdiester radicals and nucleic acids as whole are size-compatible with structural gas-hydrate cavities. (3) The gas-hydrate structure arises around amido-groups in cooled undisturbed systems consisting of water and highly-concentrated functional polymers with amido-groups.The natural conditions and historic periods favorable for simplest living matter origination are revealed. The LOH-Theory is supported by results of observations, biophysical and biochemical experiments, and wide application of original three-dimensional and two-dimensional computer simulations of biochemical structures within gas-hydrate matrix. The instrumentation and procedures for experimental verification of the LOH-Theory are suggested. If future experiments are successful, they, possibly, could be the first step on the way to industrial synthesis of food from minerals, i.e., to execution of the work that is performed by plants. Graphical
PubDate: 2023-03-28
DOI: 10.1007/s10441-023-09463-9
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- Random with Respect to Fitness or External Selection' An Important but
Often Overlooked Distinction-
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Abstract: Mutations are often described as being “random with respect to fitness.” Here we show that the experiments used to establish randomness with respect to fitness are only capable of showing that mutations are random with respect to current external selection. Current debates about whether or not mutations are directed may be at least partially resolved by making use of this distinction. Additionally, this distinction has important mathematical, experimental, and inferential implications.
PubDate: 2023-03-18
DOI: 10.1007/s10441-023-09464-8
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- A Gender-Selective Harvesting Strategy: Weak Allee Effects and a
Non-hyperbolic Extinction Boundary-
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Abstract: Recently a gender-selective harvesting strategy has been proposed for possible control of aquatic invasive species, wherein females of the invasive species are harvested, whilst stocking the males (abbreviated as FHMS strategy) (Lyu et al. in Nat Resour Model 33(2):e12252, 2020). We consider the FHMS strategy with a weak Allee effect, and show that its extinction boundary need not be hyperbolic. To the best of our knowledge, this is the first example of a non-hyperbolic extinction boundary in two-compartment mating models structured by sex. The model possesses a rich dynamical structure, with several local co-dimension one bifurcations occurring. We also show the occurrence of a global homoclinic bifurcation, which has applicability for large scale strategic bio-control.
PubDate: 2023-03-18
DOI: 10.1007/s10441-023-09462-w
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- Fast Track Treatment of Hypothyroidism with Levothyroxine: Reaching
Homeostasis within Four Weeks-
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Abstract: With the current clinical method for the treatment of hypothyroidism the target for the optimum individual values for free thyroxine concentrations [FT4] and thyrotropine concentrations [TSH] of the specific patient are unknown. This situation leads to unnecessary long experimental medication administration that can take a period of sometimes one year. In this article a method will be described where hypothyroid patients are characterized with weekly measured FT4 and TSH concentrations during the first three weeks of synthetic thyroxine or levothyroxine (L-T4) treatment to predict their optimum [FT4] and belonging [TSH] endpoint for a euthyroid homeostatic state. The treatment with levothyroxine will start for all patients with a reference dose of 100 µg, which can be adjusted by the treating physician to a more safe and appropriate dose for the individual which is monitored with weekly thyroid function tests to observe the progress. After three weeks all characteristics of the patient can be inferred from the measured data. The final titration target together with the individual thyroxine half life can be calculated. With the known characteristics and the L-T4 titration target the clinician or treating physician has an instrument to reduce the experimental treatment burden for the patient from one year to a maximum of four weeks.
PubDate: 2023-03-07
DOI: 10.1007/s10441-023-09461-x
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- Mathematical Model of COVID-19 Pandemic with Double Dose Vaccination
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Abstract: This paper is concerned with the formulation and analysis of an epidemic model of COVID-19 governed by an eight-dimensional system of ordinary differential equations, by taking into account the first dose and the second dose of vaccinated individuals in the population. The developed model is analyzed and the threshold quantity known as the control reproduction number \(\mathcal {R}_{0}\) is obtained. We investigate the equilibrium stability of the system, and the COVID-free equilibrium is said to be locally asymptotically stable when the control reproduction number is less than unity, and unstable otherwise. Using the least-squares method, the model is calibrated based on the cumulative number of COVID-19 reported cases and available information about the mass vaccine administration in Malaysia between the 24th of February 2021 and February 2022. Following the model fitting and estimation of the parameter values, a global sensitivity analysis was performed by using the Partial Rank Correlation Coefficient (PRCC) to determine the most influential parameters on the threshold quantities. The result shows that the effective transmission rate \((\alpha )\) , the rate of first vaccine dose \((\phi )\) , the second dose vaccination rate \((\sigma )\) and the recovery rate due to the second dose of vaccination \((\eta )\) are the most influential of all the model parameters. We further investigate the impact of these parameters by performing a numerical simulation on the developed COVID-19 model. The result of the study shows that adhering to the preventive measures has a huge impact on reducing the spread of the disease in the population. Particularly, an increase in both the first and second dose vaccination rates reduces the number of infected individuals, thus reducing the disease burden in the population.
PubDate: 2023-03-06
DOI: 10.1007/s10441-023-09460-y
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- Heuristics Facilitates the Evolution of Transitive Inference and Social
Hierarchy in a Large Group-
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Abstract: 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. Instead of developing cognitive abilities significantly, animals may apply simplified TI we call reference TI in this study as heuristic approaches. The reference TI allows members to recognize and remember social interactions only among a set of reference members rather than all potential members. Our study assumes that information processes in the reference TI comprises (1) the number of reference members based on which individuals infer transitively, (2) the number of reference members shared by the same strategists, and (3) memory capacity. We examined how information processes evolve in a large group using evolutionary simulations in the hawk–dove game. Information processes with almost any numbers of reference members could evolve in a large group as long as the numbers of shared reference member are high because information from the others’ experiences is shared. TI dominates immediate inference, which assesses relative rank on direct interactions, because TI could establish social hierarchy more rapidly applying information from others’ experiences.
PubDate: 2023-03-03
DOI: 10.1007/s10441-023-09459-5
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- A Very Nice Meal with an Unsatisfying Appetizer
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Abstract: As an Italian from the South, I have been socialized to care a lot about cooking. Quality of the food is a fundamental starting point for a successful result; in addition, you need expertise in food preparation and the capacity to balance dishes together in a single meal, from appetizer to dessert. I find Isabella Sarto-Jackson’s book The Making and Breaking of Mind a very nice meal with good-quality food prepared with expert hands, but the dish balance is a bit unsatisfying. I find dishes not always coherently combined with the general style of the meal, starting with the appetizer. A good appetizer would tell you what you should expect from the overall meal and would make you crave for tasting the rest. Instead, the book’s introduction and the first chapter seem to promise something different and does not give you a satisfactory idea of what you will read later. This is a pity, because overall the meal is quite nice, and most of the dishes delicious.
PubDate: 2023-03-03
DOI: 10.1007/s10441-023-09458-6
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- The Multi-Causal Basis of Developmental Potential Construction
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Abstract: 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. Secondly, we shall defend a constructivist view of the developmental process. If the genome, the developing organism and the extra-organismal environment are to be counted as proper elements of the causal basis for an organism’s developmental potential, the latter is not a given. Rather, it is the result of an interaction-based construction, a process sometimes generating genuine developmental novelty. We will thus argue for an interactionist multi-causal basis view of developmental potential construction. We contend that our view provides a biologically tenable and metaphysically coherent account of developmental dynamics.
PubDate: 2023-01-30
DOI: 10.1007/s10441-023-09456-8
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- The Connection of the Generalized Robinson–Foulds Metric with
Partial Wiener Indices-
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Abstract: 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 \(W\left(T,r, n\right)\) , where \(T\) is a binary rooted tree with root \(r\) and \(n\) leaves. Moreover, under the Yule probabilistic model, we show how to compute the expected value of \(W\left(T,r, n\right)\) . As a direct consequence, we give exact formulas for the upper bound and the expected number of conflicting pairs. By doing so we provide a better theoretical understanding of the computational complexity of the generalized RF metric.
PubDate: 2023-01-25
DOI: 10.1007/s10441-023-09457-7
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- Model of Morphogenesis with Repelling Signaling
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Abstract: 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.e., the one in which the signaling monotonically increases with s-distance, causes the appearance of pairs of cells with alternating cell states (one close to the state conventionally called “head”, and another close to the “tail” state). Non-monotonic (in s-space) signaling splits the cells into groups. The model shows that different types of signaling may provide different types of cellular patterns. General principles for applying this model to complex cellular structures are discussed.
PubDate: 2022-12-20
DOI: 10.1007/s10441-022-09454-2
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- Correction to: Stem Cells and the Microenvironment: Reciprocity with
Asymmetry in Regenerative Medicine-
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PubDate: 2022-12-09
DOI: 10.1007/s10441-022-09455-1
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- Modelling the Effect of Vaccination Program and Inter-state Travel in the
Spread of COVID-19 in Malaysia-
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Abstract: 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. In line with the rapid vaccination program, our model predicted that the COVID-19 cases in the country would decrease by the end of August. Furthermore, our findings indicated that relaxing travel restrictions from a highly vaccinated region to a low vaccinated region would result in an epidemic outbreak.
PubDate: 2022-11-17
DOI: 10.1007/s10441-022-09453-3
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- Infectious Disease Spreading Fought by Multiple Vaccines Having a
Prescribed Time Effect-
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Abstract: 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.
PubDate: 2022-11-15
DOI: 10.1007/s10441-022-09452-4
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- Major Transitions as Groupoid Symmetry-Breaking in Nonergodic Prebiotic,
Biological and Social Information Systems-
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Abstract: 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 \(\rightarrow\) Interior and Exterior Interact \(\rightarrow\) Multiple Interacting Tunable Workspaces Application to nonstationary processes seems possible via generalizations of the symmetry algebra, for example, to semigroupoids. The dynamic probability models explored here can be transformed into statistical tools for the analysis of real-time and other data across a spectrum of important disciplines confronted by biological and other forms of cognition and their dysfunctions.
PubDate: 2022-10-29
DOI: 10.1007/s10441-022-09451-5
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- On the Role of Speed in Technological and Biological Information Transfer
for Computations-
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Abstract: 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. The difference between mathematical handling methods leads to different descriptions of the computing features of the systems. The proposed handling also explains why biological implementations can have lifelong learning and technological ones cannot. Our conclusion about learning matches published experimental evidence, both in biological and technological computing.
PubDate: 2022-10-26
DOI: 10.1007/s10441-022-09450-6
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- Stochastic Modeling and Forecasting of Covid-19 Deaths: Analysis for the
Fifty States in the United States-
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Abstract: 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. The probability distribution of the aggregate death counts is derived, analyzed, and used to estimate the count’s per capita initial growth rate, carrying capacity, and the expected value for each given day as at the time this research is conducted. Using this distribution, we estimate the expected first passage time when the aggregate death count is slowing down. Our result shows that the expected aggregate death count is slowing down in all states as at the time this analysis is conducted (June 2021). A formula for predicting the end of Covid-19 deaths is derived. The daily expected death count for each states is plotted as a function of time. The probability density function for the current day, together with the forecast and its confidence interval for the next four days, and the root mean square error for our simulation results are estimated.
PubDate: 2022-09-16
DOI: 10.1007/s10441-022-09449-z
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