Mathematical Biology Research Articles

Integrating Diversity, Equity, and Inclusion into Preclinical, Clinical, and Public Health Mathematical Models.

Mathematical modelling applied to preclinical, clinical, and public health research is critical for our understanding of a multitude of biological principles. Biology is fundamentally heterogeneous, and mathematical modelling must meet the challenge of variability head on to ensure the principles of diversity, equity, and inclusion (DEI) are integrated into quantitative analyses. Here we provide a follow-up perspective on the DEI plenary session held at the 2023 Society for Mathematical Biology Annual Meeting to discuss key issues for the increased integration of DEI in mathematical modelling in biology.

Study of traveling soliton and fronts phenomena in fractional Kolmogorov-Petrovskii-Piskunov equation

Abstract The present research work presents the modified Extended Direct Algebraic Method (m-EDAM) to construct and analyze propagating soliton solutions for fractional Kolmogorov-Petrovskii-Piskunov Equation (FKPPE) which incorporates Caputo's fractional derivatives. The FKPPE has significance in various disciplines such as population growth, reaction-diffusion mechanisms, and mathematical biology. By leveraging the series form solution, the proposed m-EDAM determines plethora of travelling soliton solutions through the transformation of FKPPE into Nonlinear Ordinary Differential Equation (NODE). These soliton solutions shed light on propagation processes in the framework of the FKPPE model. Our study also offers some graphical representations that facilitate the characterization and investigation of propagation processes of the obtained soliton solutions which include kink, shock soliton solutions. Our work advances our understanding of complicated phenomena across multiple academic disciplines by fusing insights from mathematical biology and reaction-diffusion mechanisms.

Advice to a Young Mathematical Biologist

This paper offers advice to early-mid career researchers in Mathematical Biology from ten past and current Presidents of the Society for Mathematical Biology. The topics covered include deciding if a career in academia is right for you; finding and working with a mentor; building collaborations and working with those from other disciplines; formulating a research question; writing a paper; reviewing papers; networking; writing fellowship or grant proposals; applying for faculty positions; and preparing and giving lectures. While written with mathematical biologists in mind, it is hoped that this paper will be of use to early and mid career researchers across the mathematical, physical and life sciences, as they embark on careers in these disciplines.

Fitness surfaces and local thermal adaptation in Drosophila along a latitudinal gradient.

Local adaptation is commonly cited to explain species distribution, but how fitness varies along continuous geographical gradients is not well understood. Here, we combine thermal biology and life-history theory to demonstrate that Drosophila populations along a 2500 km latitudinal cline are adapted to local conditions. We measured how heat tolerance and viability rate across eight populations varied with temperature in the laboratory and then simulated their expected cumulative Darwinian fitness employing high-resolution temperature data from their eight collection sites. Simulations indicate a trade-off between annual survival and cumulative viability, as both mortality and the recruitment of new flies are predicted to increase in warmer regions. Importantly, populations are locally adapted and exhibit the optimal combination of both traits to maximize fitness where they live. In conclusion, our method is able to reconstruct fitness surfaces employing empirical life-history estimates and reconstructs peaks representing locally adapted populations, allowing us to study geographic adaptation in silico.

Comparative transcriptomics revealed the ecological trap effect of linearly polarized light on Oratosquilla oratoria

Although polarized light can assist many animals in performing special visual tasks, current polarized light pollution (PLP) caused by urban construction has been shown to induce maladaptive behaviors of PL-sensitive animals and change ecological interactions. However, the underlying mechanisms remain unclear. Our previous work hypothesized that linearly polarized light (LPL) is an ecological trap for Oratosquilla oratoria, a common Stomatopoda species in the China Sea. Here we explored the underlying negative effects of artificially LPL on O. oratoria based on comparative transcriptomics. We identified 3616 differentially expressed genes (DEGs) in O. oratoria compound eyes continuous exposed to natural light (NL) and LPL scenarios. In comparison with the NL scenario, a total of 1972 up- and 1644 down- regulated genes were obtained from the O. oratoria compound eyes under LPL scenario, respectively. Furthermore, we performed functional annotation of those DEGs described above and identified 65 DEGs related to phototransduction, reproduction, immunity, and synapse. Based on the functional information, we suspected that continuous LPL exposure could block the light transmission, disrupt the reproductive process, and lead to the progressive failure of the immune response of O. oratoria. In conclusion, this study is the first to systematically describe the negative effects of artificial LPL exposure on O. oratoria at the genetic level, and it can improve the biological conservation theory behind PLP.

Review of “Hereditary: The Persistence of Biological Theories of Crime”

Review of “Hereditary: The Persistence of Biological Theories of Crime”

Shared Protentions in Multi-Agent Active Inference

In this paper, we unite concepts from Husserlian phenomenology, the active inference framework in theoretical biology, and category theory in mathematics to develop a comprehensive framework for understanding social action premised on shared goals. We begin with an overview of Husserlian phenomenology, focusing on aspects of inner time-consciousness, namely, retention, primal impression, and protention. We then review active inference as a formal approach to modeling agent behavior based on variational (approximate Bayesian) inference. Expanding upon Husserl’s model of time consciousness, we consider collective goal-directed behavior, emphasizing shared protentions among agents and their connection to the shared generative models of active inference. This integrated framework aims to formalize shared goals in terms of shared protentions, and thereby shed light on the emergence of group intentionality. Building on this foundation, we incorporate mathematical tools from category theory, in particular, sheaf and topos theory, to furnish a mathematical image of individual and group interactions within a stochastic environment. Specifically, we employ morphisms between polynomial representations of individual agent models, allowing predictions not only of their own behaviors but also those of other agents and environmental responses. Sheaf and topos theory facilitates the construction of coherent agent worldviews and provides a way of representing consensus or shared understanding. We explore the emergence of shared protentions, bridging the phenomenology of temporal structure, multi-agent active inference systems, and category theory. Shared protentions are highlighted as pivotal for coordination and achieving common objectives. We conclude by acknowledging the intricacies stemming from stochastic systems and uncertainties in realizing shared goals.

The Immunomodulatory Effects of Herbal Supplements in Poultry

Purpose: The general purpose of the study was to explore the immunomodulatory effects of herbal supplements in poultry.
 Methodology: The study adopted a desktop research methodology. Desk research refers to secondary data or that which can be collected without fieldwork. Desk research is basically involved in collecting data from existing resources hence it is often considered a low cost technique as compared to field research, as the main cost is involved in executive’s time, telephone charges and directories. Thus, the study relied on already published studies, reports and statistics. This secondary data was easily accessed through the online journals and library.
 Findings: The findings reveal that there exists a contextual and methodological gap relating to immunomodulatory effects of herbal supplements in poultry. Preliminary empirical review revealed that herbal extracts enhanced immune parameters, such as lymphocyte proliferation and cytokine production, suggesting their potential to improve poultry health and disease resistance. The diverse mechanisms of action of phytochemicals underscored the complexity of herbal supplements' effects on poultry immunity, while considerations such as formulation and environmental factors influenced their efficacy. Overall, while further research is warranted to optimize formulations and deepen our understanding of mechanisms, herbal supplements show considerable promise as alternatives to conventional additives in poultry production, offering holistic and sustainable approaches to enhancing poultry health and welfare.
 Unique Contribution to Theory, Practice and Policy: The Systems Biology theory, Ecological Systems theory and Ethnopharmacology theory may be used to anchor future studies on immunomodulatory effects of herbal supplements in poultry. The study provided recommendations that contributed to theory, practice, and policy in poultry production and animal health. The findings advanced theoretical knowledge by elucidating the complex interactions between phytochemicals and the avian immune system. In practice, recommendations supported the incorporation of herbal supplements into poultry diets to promote immune health and disease resistance, benefiting poultry producers, veterinarians, and feed manufacturers. Moreover, policy recommendations advocated for regulatory frameworks supporting the use of herbal supplements and education initiatives aimed at enhancing stakeholder awareness and understanding. Collaboration between academia, industry, and government agencies was recommended to further research and innovation, while international cooperation facilitated knowledge exchange and harmonization of standards.
 Keywords: Immunomodulatory, Herbal Supplements, Poultry, Phytochemicals, Immune Function, Sustainable, Regulation, Collaboration, International Cooperation

Scientific, Technological and Innovative Development and Cooperation of the Countries of Greater Eurasia

The article provides information about the 6th International research-to-practice conference “Greater Eurasia: National and Civilizational Aspects of Development and Cooperation”. We primarily focus on reports related to determining the place and role of science and education in modernization, innovative and technological development and cooperation between the EAEU countries and other states of Greater Eurasia, including the goals and objectives of modernizing the scientific complex of these countries, priorities of research, the role of the academic community in the formation of a strategic management system, global trends in scientific and technological development, new forms of interaction between science and education, mechanisms for stimulating the development of science and evaluating results of research activities. A significant part of the overview discusses reports on the issues of artificial intelligence. The reporters consider the prospects for using AI in mathematical research, fundamental physics, biology, crystallography and inorganic chemistry, natural language processing, medicine, education, etc. They also characterize the relationship between natural and artificial intelligence, as well as the state of legal regulation of AI at the international level and in the national legislation of the Russian Federation.

Evolution of Institutions or Institutional Change?

The purpose of the article is to analyze the practices of using the expression "evolution of institutions" in the study of institutions to denote the processes and mechanisms of their emergence and change. Very often this means that the authors consider these processes and their mechanisms to be similar to those that operate within the framework of Darwinian biological evolution. Since the emergence and changes of institutions have been studied and investigated outside the evolutionary approach for a long time, the question arises as to what new scientific knowledge about these processes has allowed and allows the evolutionary approach to be obtained? To answer this question, the article considers, firstly, the results of a non-evolutionary study of institutional dynamics, and secondly, the results of various versions of its evolutionary research, including an approach based on the concept of cultural evolution. The analysis showed that evolutionary approaches to the emergence of institutions affect only one of the three established mechanisms of these processes, and evolutionary concepts of institutional change have a number of inaccuracies and inaccuracies. These results give grounds to conclude that in the field of studying institutions, the evolutionary approach has not led (yet?) to develop new knowledge about their origin and change, which could not be obtained outside of this approach. The theories of institutional dynamics available today provide reliable grounds for theoretical and empirical study of the processes of their emergence and change without using analogies with biological and cultural evolutionary theories.

NIAID/SMB Workshop on Multiscale Modeling of Infectious and Immune-Mediated Diseases

On July 19th, 2023, the National Institute of Allergy and Infectious Diseases co-organized a workshop with the Society of Mathematical Biology, with the authors of this paper as the organizing committee. The workshop, “Bridging multiscale modeling and practical clinical applications in infectious diseases” sought to create an environment for mathematical modelers, statisticians, and infectious disease researchers and clinicians to exchange ideas and perspectives.

The Microbiome-Gut-Brain Axis, Nutrition and Parkinson’s Disease

Parkinson’s disease (PD) is a chronic progressive neurodegenerative disorder characterised by both motor and non-motor symptoms. While most PD medications currently available can improve motor symptoms, there is currently no treatment available to halt or slow down the progression of the disease. Recently, there has been increasing focus on environmental factors in the pathophysiology of PD and their possible neuroprotective effects. According to Braak’s hypothesis, an unknown pathogen in the gastrointestinal tract may initiate the production of pathogenic α synuclein, which would subsequently spread to the central nervous system. The microbiome-gut-brain axis may be implicated in this process, whereas nutrition can be one of the modifiable regulatory variables. A variety of foods and nutrients have been suggested as either risk or protective factors based on biological theories. Although epidemiological and experimental studies in animal models have shown their neuroprotective properties, their effectiveness was not confirmed in clinical trials. However, daily food intake comprises many nutrients that can interact and produce either a synergistic or antagonistic effect on the human body. Therefore, dietary patterns that include a certain set of nutrients have recently gained increased interest as potential modifiers of disease progression and alleviators of symptoms. This article reviews the current literature on the role of different nutritional factors and diets in the pathogenesis of PD and their possible neuroprotective and symptomatic effects.

Life and fate of Ervin Bauer (1890–1938), the eminent scholar and foundational theoretical biologist

Ervin Bauer (1890–1938) was the first to build a general molecular-based biological theory. He defined the basic principles of theoretical biology from a thermodynamic perspective, focusing on the capacity of biological systems to produce and support the state of sustainable non-equilibrium. His central work “Theoretical Biology” (1935) was written long before modern advances in molecular biology, genetics, and information theory. Ervin Bauer and his wife Stefánia were executed in Stalin's Great Terror. This paper presents a brief introduction to Ervin Bauer's life and includes his short biography.

Rate-induced tipping can trigger plankton blooms

AbstractPlankton blooms are complex nonlinear phenomena whose occurrence can be described by the two-timescale (fast-slow) phytoplankton-zooplankton model introduced by Truscott and Brindley (Bulletin of Mathematical Biology 56(5):981–998, 1994). In their work, they observed that a sufficiently fast rise of the water temperature causes a critical transition from a low phytoplankton concentration to a single outburst: a so-called plankton bloom. However, the dynamical mechanism responsible for the observed transition has not been identified to the present day. Using techniques from geometric singular perturbation theory, we uncover the formerly overlooked rate-sensitive quasithreshold which is given by special trajectories called canards. The transition from low to high concentrations occurs when this rate-sensitive quasithreshold moves past the current state of the plankton system at some narrow critical range of warming rates. In this way, we identify rate-induced tipping as the underlying dynamical mechanism of largely unpredictable plankton blooms such as red tides, or more general, harmful algal blooms. Our findings explain the previously reported transitions to a single plankton bloom, and allow us to predict a new type of transition to a sequence of blooms for higher rates of warming. This could provide a possible mechanism of the observed increased frequency of harmful algal blooms.

The epoch-making importance of Ervin Bauer's theoretical biology

Ervin Bauer was the only biologist who recognized that the best way to develop theoretical biology on an equal footing with theoretical physics was to follow the method that has ensured the great successes of modern theoretical physics: the general method of science. Following this method, he succeeded to find the universal principle of biology. From this principle he managed to derive all the basic equations of biology, that of metabolism, reproduction, growth, responsiveness and successfully explained all the fundamental phenomena of life. In this paper, I introduce Bauer's theoretical biology and discuss whether he understood it within the framework of the modern physical worldview, or in a broader framework. I point out that the theoretical biology of Ervin Bauer is the first to go beyond the physical worldview, to establish a deeper, biological worldview, and thus to represent a major advance in our understanding of the nature of life, with a significance even greater than that of the Copernican turn. Clarifying the difference between the living and the non-living, it is important to consider the difference between machines and living organisms. It is well known that machines are the manifestations of a dual control; globally, their behavior is controlled by their given structure, while locally, their behavior is governed by the physical laws. Based on Bauer's theoretical biology, it is pointed out that living organisms manifest a three-level causality; the ‘additional’, biological level corresponds to the autonomous, time-dependent control of their structures.

Complex systems in ecology: a guided tour with large Lotka–Volterra models and random matrices

Ecosystems represent archetypal complex dynamical systems, often modelled by coupled differential equations of the form d x i d t = x i ϕ i ( x 1 , … , x N ) , where N represents the number of species and x i , the abundance of species i . Among these families of coupled differential equations, Lotka–Volterra (LV) equations, corresponding to ϕ i ( x 1 , … , x N ) = r i − x i + ( Γ x ) i , play a privileged role, as the LV model represents an acceptable trade-off between complexity and tractability. Here, r i is the intrinsic growth of species i and Γ stands for the interaction matrix: Γ i j represents the effect of species j over species i . For large N , estimating matrix Γ is often an overwhelming task and an alternative is to draw Γ at random, parameterizing its statistical distribution by a limited number of model features. Dealing with large random matrices, we naturally rely on random matrix theory (RMT). The aim of this review article is to present an overview of the work at the junction of theoretical ecology and large RMT. It is intended to an interdisciplinary audience spanning theoretical ecology, complex systems, statistical physics and mathematical biology.

Predation risk-mediated indirect effects promote submerged plant growth: Implications for lake restoration

Biological manipulation, involving fish stockings, is commonly used to counteract the deterioration of submerged vegetation in eutrophic lakes. Nevertheless, the non-consumptive effects (NCEs) of stocked carnivorous fish are often overlooked. Using a controlled experimental system, we investigated the NCEs of a native carnivorous fish, snakehead (Channa argus), on two key biological factors, herbivore-dominated grass carp (Ctenopharyngodon idella) and disturbance-dominated loach (Misgurnus anguillicaudatus), influencing submerged plants growth. Additionally, we conducted a meta-analysis on predation risk and primary productivity. The results reveal that predation risk induces oxidative stress damage and affects grass carp growth. Non-significant changes in cortisol and glucose may be linked to predation risk prediction. Simultaneously, predation risk reduces fish feeding and disturbance behavior, relieving pressure on submerged plants to be grazed and disturbed, thereby supporting plant development. The presence of submerged plants, in turn, enhances loach activity and influences water body characteristics through negative feedback. Furthermore, the meta-analysis results indicate the facilitative effect of predation risk on primary producers. Our findings contribute to the understanding of biological manipulation theory. We demonstrate that the predation risk associated with introducing carnivorous fish can promote the growth of submerged plants through behaviorally mediated indirect effects. This highlights the potential utility of predation risk in lake restoration efforts.

URBAN CONTEXT ANALYSIS ACCORDING TO THE CONCEPT OF SPENCER'S BIOLOGICAL THEORY USING GIS: BALAD CITY CASE STUDY

Concepts of evolution theory (by Herbert Spencer) were analyzed using a Geographic Information System according to living notions in the context of an urban city. The idea of the theory was applied to the society within the context of Balad city to find out whether the concepts of contrast, integration, specialization, and exclusivity on which the theory is based have an impact on the services in the city and an effect on the structure of the social elements and the stages of its development. The research problem centered on the shortcomings of the theory in predicting and explaining the morphological and functional structure of the city, while the main objective is to analyze the concepts of biological theory according to the requirements of the context of the study area. The analysis results of the living context notions present in the city were compared with the urban housing standards using GIS to determine the extent to which the context conforms to the concept of Spencer's theory. The research found the inability of the biological side of the theory to explain the population concentration in residential neighborhoods, as well as the lack of reliance on the concepts of contrast and integration in predicting the reasons for the growth and expansion of the city, and that the city neighborhoods showed a variance in their services without showing integration and exclusivity in these services, that is, the lack of integration organic between the biological parts of the city.

ISLAM AND EVOLUTION: A BRIEF REVIEW OF QURANIC CONCEPT AND CONTEMPORARY THOUGHTS

Of all the biological theories, the speculation of human evolution considerably poses a noteworthy challenge to the Islamic standpoint because it directly threatens the central position of mankind in this universe.  According to the Qur’anic point of view, the miracle of the creation of man directly belongs to Allah almighty’s intention and His deliberate will. That’s why Human Evolution has turned out to be a hot discussion amongst believers and non-believers, as it can’t be rejected or accepted in one stroke. The Muslim thinkers appeared to be typically hostile and suspicious of human evolution, meanwhile, the evolutionists area unit is busy to prove that homology (similarities amongst species) shows common ancestry of different species. Anyhow, bioscience has rejected this theory as it contains contradictory statements due to some faulty assumptions like it can’t answer a straightforward question: “How did life come into existence on this planet, namely Earth?” But Sacred writing (Qur’an) has created an unambiguous and absolute conception in this regard. The purpose of this qualitative research mainly has two folds. The first is to spotlight the conception of the evolution of man in step with primary sources of Islamic shari`ah (Qur’an and Hadith), and the second is to analyze the theology of the researchers, philosophers, and scholars based on human evolution. However, the theory of evolution is not ideologically appreciated by Islamic groups. In fact, it is considered nothing but a material-based thought. Somebody ought to be very careful to make a final statement concerning human evolution without a deep analysis of Islam and bioscience.

Triadic signatures of global human mobility networks.

Global refugee and migrant flows form complex networks with serious consequences for both sending and receiving countries as well as those in between. While several basic network properties of these networks have been documented, their finer structural character remains under-studied. One such structure is the triad significance profile (TSP). In this study, the TSPs of global refugee and migrant flow networks are assessed. Results indicate that the migrant flow network's size and TSP remain stable over the years; its TSP shares patterns with social networks such as trade networks. In contrast, the refugee network has been more dynamic and structurally unstable; its TSP shares patterns with networks in the information-processing superfamily, which includes many biological networks. Our findings demonstrate commonality between migrant and social networks as well as between refugee and biological networks, pointing to possible interdisciplinary collaboration-e.g., application of biological network theories to refugee network dynamics-, potentially furthering theoretical development with respect to both network theory and theories on human mobility.