Theory Of Biological Systems Research Articles

A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data.

Learning cellular dynamics through reconstruction of the underlying cellular potential energy landscape (aka Waddington landscape) from time-series single-cell RNA sequencing (scRNA-seq) data is a current challenge. Prevailing data-driven computational methods can be hampered by the lack of physical principles to guide learning from complex data, resulting in reduced prediction accuracy and interpretability when applied to infer cell population dynamics. Here, we propose PI-SDE, a physics-informed neural stochastic differential equation (SDE) framework that combines the Hamilton-Jacobi (HJ) equation and neural SDE to learn cellular dynamics. Grounded in potential energy theory of biological systems, PI-SDE integrates the principle of least action by enforcing the HJ equation when reconstructing cellular potential energy function. This approach not only facilitates accurate predictions, but also improves interpretability, especially in the reconstructed potential energy landscape. Through benchmarking on two real scRNA-seq datasets, we demonstrate the importance of incorporating the HJ regularization term in dynamic inference, especially in predicting gene expression at held-out time points. Meanwhile, the learned potential energy landscape provides biologically interpretable insights into the process of cell differentiation. Our framework enhances model performance, while maintaining robustness and stability. PI-SDE software is available at https://github.com/QiJiang-QJ/PI-SDE.

The New Antireductionism: Its Components and Its Significance

Beginning in the 1970s and culminating in the first two decades of the 21st century, there has been a marked shift in the sciences from a predominantly reductionist and mechanistic approach to a broader and more holistic viewpoint. It goes without saying that such a shift in point of view will have significant implications, not only for the sciences but for our concepts of nature and of human beings. The present essay is an attempt to assess the significance of this change in the focus of the sciences and to describe the nature of its components. Originally, it had a far more limited scope, that of comparing two of the parts of the new nonreductionist stance: brain plasticity and biological systems theory. Unfortunately, my understanding of one of these factors (systems theory) turned out to be incorrect, while the section on brain plasticity was incomplete. The result of this dual realization is an essay of far greater scope, taking in both new developments in the sciences far beyond that of plasticity, and reassessing the content and impact of systems theory, which is greater than I had thought. I will begin with a study of systems theory, dealing first with the unexpected mathematics which made its present status possible. Then I will deal with its history, which reaches back over a century. One of the confusions into which we are liable to fall is to fail to distinguish the old systems theory from the new. This is even more likely because the two versions of the theory have many features in common.

Teaching in the time of COVID-19: A biological systems theory approach

In 2020, schools around the United States and globally closed to in-person instruction in response to the COVID-19 pandemic. This study, embedded in ongoing research supported by a United States Department of Education Jacob K. Javits Gifted and Talented Education Award, investigated changes in roles, relationships, and educational activities resulting from the pandemic as perceived by educators in one rural and low SES Appalachian primary school. Using Bronfenbrenner’s (1977; 1979; 2001) Bioecological Theory of Human Development, this study examined instructional modifications (proximal processes) resulting from the pandemic (chronosystem) in the school and home (microsystem context) and the development of teachers, parents, and students (persons) in response to those changes. Survey data were collected pre- and post-pandemic onset. Results of this mixed-methods study indicated teachers perceived the pandemic as influencing what they taught, how they taught, and the roles of and relationships between teachers, parents, and students. Teachers adapted to the changing educational environment developing proficiency in online tools and skills to enhance communication. Parents assumed a more prominent role in their K-2 student’s schooling to ensure students logged in and were active online, paid attention while in class, and completed their assignments at home. These remote learning environments, which naturally distanced teachers from their students, coupled with uncertain parental involvement, challenged teachers in their formative assessments of student knowledge. While some students thrived with increased support from attentive parents—many students, particularly those already at-risk or in homes where internet or parental support were lacking—were adversely affected, thus widening the achievement gap.

Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.

Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~, which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~. Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it.

LA ONTOGENIA Y LA EVOLUCIÓN DESDE LA PERSPECTIVA DE LA TEORÍA DE LOS SISTEMAS DE DESARROLLO (TSD)

La teoría de los sistemas de desarrollo (TSD) pretende realizar una síntesis conceptual que vincule el desarrollo ontogenético con la evolución. Sus antecedentes pueden ser encontrados básicamente en los trabajos de Waddington y de Bertalanffy quienes aportaron las bases de la canalización del desarrollo y la teoría de sistemas biológicos, respectivamente. El objetivo de este artículo es realizar un análisis conceptual preliminar de la TSD y reflexionar acerca de los aportes potenciales de la TSD como marco teórico para la biología del desarrollo en particular y la biología evolutiva en general. Para ello, se tendrán en cuenta algunos de los conceptos y propuestas que componen este marco y se trabajará sobre datos secundarios obtenidos de la bibliografía. Se concluye que la TSD: 1-logra argumentar en contra de la visión gen-centrista respecto de las explicaciones que pretenden justificar el desarrollo biológico y evolutivo; 2- argumenta de manera coherente a favor del rol de la epigenética en la ontogenia y la evolución; 3- en relación con lo anterior el rol de la selección natural se restringe a un segundo plano; 4- propone que la dicotomía naturaleza/cultura debe ser superada; y 5- constituye un posible programa de investigación metodológico compuesto de una diversidad de hipótesis y teorías no necesariamente relacionadas que pueden ser corroboradas de manera relativamente independientes del resto de la red teórica.

Хаотическая динамика параметров плазменного звена гемостаза при синдроме критической ишемии нижних конечностей

Active development of medical diagnostic base of instrumental studies demands the introduction of a new methodological support. Now it can be done on the basis of system analysis and synthesis of information to identify the significance of clinical diagnostic criteria for quasi-stationary states of the hemostatic system. Such a task is most successfully solved by the new trend of system analysis and synthesis, management and processing of information in evidence-based medicine: identification of quasi-attractors parameters of the human body state vector in terms of the theory of chaos and self-organization, and compartment-cluster theory of biological systems. According to classical statistics, the most effective treatment we observe in the third group patients, while the second group makes a significant impact too. As a result, the volume of quasi-attractors identify the best results in a change rX and xV obtained from the second group patients, in the third group the data are less evident. According to the data analysis of interattractors distances matrices showed the greatest increase in the distances (Zij) between the chaotic centers of the quasi-attractors in the third group, that shows a more effective conservative treatment in the third group than in group 1 and group 2.

Effect of convective term on temperature distribution in biological tissue

We introduce a phase imprint into the order parameter describing the influence of blood flow on the temperature distribution in the tissue described by the one-dimensional Pennes equation and then engineer the imprinted phase suitably to generate a modified Pennes equation with a gradient term (known in the theory of biological systems as convective term) which is associated with the heat convected by the flowing blood. Using the derived model, we analytically investigate temperature distribution in biological tissues subject to two different spatial heating methods. The applicability of our results is illustrated by one of typical bio-heat transfer problems which is often encountered in therapeutic treatment, cancer hyperthermia, laser surgery, thermal injury evaluation, etc. Analyzing the effect of the convective term on temperature distribution, we found that an optimum heating of a biological system can be obtained through regulating the convective term.

Kinetic theory of situated agents applied to pedestrian flow in a corridor

A situated agent-based model for simulation of pedestrian flow in a corridor is presented. In this model, pedestrians choose their paths freely and make decisions based on local criteria for solving collision conflicts. The crowd consists of multiple walking agents equipped with a function of perception as well as a competitive rule-based strategy that enables pedestrians to reach free access areas. Pedestrians in our model are autonomous entities capable of perceiving and making decisions. They apply socially accepted conventions, such as avoidance rules, as well as individual preferences such as the use of specific exit points, or the execution of eventual comfort turns resulting in spontaneous changes of walking speed. Periodic boundary conditions were considered in order to determine the density-average walking speed, and the density-average activity with respect to specific parameters: comfort angle turn and frequency of angle turn of walking agents. The main contribution of this work is an agent-based model where each pedestrian is represented as an autonomous agent. At the same time the pedestrian crowd dynamics is framed by the kinetic theory of biological systems.

Approaches to Chronic Disease and Chronic Care

The increasing prevalence and cost of chronic diseases and care indicate that comprehensive changes and paradigm shifts are needed in how healthcare systems approach and care for the chronically ill. Biological systems theory has been suggested as a model to explain human differences within surrounding systems that could translate into biological mechanisms, and is consistent with the chronic care model. Biological systems theory defines five levels of environmental contexts within the social milieu of an individual: the microsystem, comprising the direct interactions and intimate relationships of an individual’s everyday life; the mesosystem, relating to interactions between the components of the microsystem; the exosystem, comprising the wider social and community setting; the macrosystem, consisting of cultural value, ethnic identity, beliefs, laws, and customs; and the chronosystem, comprising the patterns of events throughout the lifecourse. Interventions incorporating biological systems theory have shown some success in pediatric populations. Bioecological systems theory presents an out-of-the-box discipline approach for potential application or contribution to chronic care that is consistent with the chronic care model.

The Biopsychosocial Model and Philosophic Pragmatism: Is George Engel a Pragmatist?

Abstract: George Engel designed his biopsychosocial model to be a broad framework for medicine and psychiatry. Although the model met with great initial success, it now needs conceptual attention to make it relevant for future generations. Engel articulated the model as a version of biological systems theory, but his work is better interpreted as the beginnings of a richly nuanced philosophy of medicine. We can make this reinterpretation by connecting Engel’s work with the tradition of American pragmatism. Engel initiates inquiry like a pragmatist, he understands theory and philosophy like a pragmatist, he justifies beliefs like a pragmatist, and he understands the world like a pragmatist. By drawing out these similarities, medical and psychiatric scholars can revitalize the biopsychosocial model, and they can open medicine and psychiatry to a rich philosophic heritage and a flourishing interdisciplinary tradition.

A framework for gene expression analysis

Global gene expression measurements as obtained, for example, in microarray experiments can provide important clues to the underlying transcriptional control mechanisms and network structure of a biological cell. In the absence of a detailed understanding of this gene regulation, current attempts at classification of expression data rely on clustering and pattern recognition techniques employing ad-hoc similarity criteria. To improve this situation, a better understanding of the expected relationships between expression profiles of genes associated by biological function is required. It is shown that perturbation expansions familiar from biological systems theory make precise predictions for the types of relationships to be expected for expression profiles of biologically associated genes, even if the underlying biological factors responsible for this association are not known. Classification criteria are derived, most of which are not usually employed in clustering algorithms. The approach is illustrated by using the AtGenExpress Arabidopsis thaliana developmental expression map.

The sociological critique of evolutionary psychology: Beyond mass modularity

This paper addresses evolutionary psychology's (EP's) mass modularity account of human intelligence. First, EP is located within 'naturalization of society' discourses. Secondly, the nature and weakness of mass modularity theory is examined. In the third part of the paper, the genetic reductionism of EP is challenged with reference to developmental systems theory (DST). However, in the fourth part, the danger of importing one biological theory to defuse the colonial ambitions of another is highlighted through an examination of sociological systems theory and its relationship with biological systems theory. Nevertheless, DST has stimulated valuable insights in theoretical sociology/anthropology. Modularity is also common in computer models of intelligence as algorithmic computation. EP draws parallels with computer modelling to claim confirmation of its own account. The fifth part of this article challenges the validity of this parallel, drawing upon Harry Collins's sociology of what humans and computers can do. Collins's work highlights the non-modular cultural 'rules' that today's computers cannot follow. In the light of these theoretical and empirical developments I conclude that contemporary sociology offers a valuable and systematic counter to discourses of genetic reductionism and the discourses of technological determination upon which they are parasitic.

Coping with Stressors on the Home Front

This article seeks to correct the paucity of attention to the psychological impact on families of having a member engaged in war. The initial section focuses on the impact of the Persian Gulf War on military families, drawing upon family stress and coping and Miller's biological systems theory to help categorize and account for the stressors affecting these families at various strategic points in the Persian Gulf War: deployment, during the war, homecoming and reintegration, and long‐term reactions. The middle section focuses on the stress reactions and the factors that tend to mediate these reactions, such as effective methods of coping. Among the most significant yet widely overlooked reactions is secondary traumatization. The final section—based on both the extant research and the theoretical orientation articulated in section one—focuses on intervention. Among those interventions listed are programs that were successful during the Persian Gulf War. Implications for research and policy are noted.

FAMILY THERAPY AND IDEOLOGY*

Contemporary family therapy is examined in terms of its ideological content. The adoption of cybernetics and biological systems theory to the family has led to the erroneous belief that familytherapy is exclusively concerned with natural systems, is process oriented, content relative, and above ideology. This article argues that the family and the enterprise of family therapy are social systems and under the influence of the ideology particular to a given society. The strategic family therapy treatment of a family with a drug‐addicted member serves as an example to clarify the ideological themes of contemporary family therapy. These themes are: (a) family reductionism and blaming; (b) the relabeling of personal injustice into communicational terminology; (c) the assumption that the nuclear family is optimal; (d) the conceptualization of therapy as a commodity; and (e) the model of human relatedness and intimacy supported by family therapy.

Observation and biological systems.

A number of apparently different lines of inquiry into fundamental biological processes point to the central role played by the notion of observation in the theory of biological systems. Not only do we use the results of our own observations to obtain the system descriptions which are the starting-points for an understanding of biological processes, but it is a basic postulate of physics that the interactions between biological systems themselves can be regarded as observations. On this basis, it is clear that we cannot properly understand biological interactions unless the observables we employ for system description are the same as those involved in the interactions we are describing. To do this requires a general theory of observables and system description, establishing the relationship between different modes of description. A sketch of such a theory is developed in the present paper, using only two postulates: (a) that all interactions are determined by the values of observables of a system evaluated on specific states, and (b) that real-valued observables suffice. As an application, a specific test is proposed whereby it can be determined whether the observables employed to describe interacting systems are sufficient to specify the observables involved in the interaction itself.

Remarks on Mathematical Signal Processing by the Brain During Rhythmic Neurophysiological Stimulation

In order to study information transfer in physiological systems, one method is used very frequently. This method consists in the determination of systems frequency characteristics on application of sinusoidal stimulation signals. Unfortunately a biological systems theory does not exist yet and the application of the methods of general systems theory to biological systems is limited and not always satisfactory. Generally biological systems are frequency-dependent nonlinear systems and a big number of biological systems, especially the brain system exhibit spontaneous rhythmic activities which makes the problem much more complicated.The aim of this study is to try to find some approaches which will offer new possibilities for interpretation in the analysis of brain systems (or biological systems in general).

A relational theory of biological systems II

The general Theory of Categories is applied to the study of the (M, R)-systems previously defined. A set of axioms is provided which characterize “abstract (M, R)-systems”, defined in terms of the Theory of Categories. It is shown that the replication of the repair components of these systems may be accounted for in a natural way within this framework, thereby obviating the need for anad hoc postulation of a replication mechanism. A time-lag structure is introduced into these abstract (M, R)-systems. In order to apply this structure to a discussion of the “morphology” of these systems, it is necessary to make certain assumptions which relate the morphology to the time lags. By so doing, a system of abstract biology is in effect constructed. In particular, a formulation of a general Principle of Optimal Design is proposed for these systems. It is shown under what conditions the repair mechanism of the system will be localized into a spherical region, suggestive of the nuclear arrangements in cells. The possibility of placing an abstract (M, R)-system into optimal form in more than one way is then investigated, and a necessary and sufficient condition for this occurrence is obtained. Some further implications of the above assumptions are then discussed.

The representation of biological systems from the standpoint of the theory of categories

A mathematical framework for a rigorous theory of general systems is constructed, using the notions of the theory of Categories and Functors introduced by Eilenberg and MacLane (1945,Trans. Am. Math. Soc.,58, 231–94). A short discussion of the basic ideas is given, and their possible application to the theory of biological systems is discussed. On the basis of these considerations, a number of results are proved, including the possibility of selecting a unique representative (a “canonical form”) from a family of mathematical objects, all of which represent the same system. As an example, the representation of the neural net and the finite automaton is constructed in terms of our general theory.

A relational theory of biological systems

A relational theory of biological systems