Recently it has been shown that the classical “stick and ball” viewpoint of molecules is inconsistent with quantum theory (QT). We suggest an unusual reconciliation: The QT state is not a physical property, but instead reflects our state of knowledge about observable aspects of “reality.” We show how this perspective is nevertheless objective. Applied to molecules, the view permits “structure” to exist only when observable evidence is compatible with this feature. Typically one must replace the a priori model (...) (in particular, the dynamical generator) with one consistent with the evidence. We show that such “structure” is stable in the context of first-order perturbation theory. We also indicate how dynamics can be inferred from scattering data—a process alternative to postulating (field-theoretic) models for “environment.”. (shrink)

The extension of quantum mechanics to a general functional space (“rigged Hilbert space”), which incorporates time-symmetry breaking, is applied to construct extract dynamical models of entropy production and entropy flow. They are illustrated by using a simple conservative Hamiltonian system for multilevel atoms coupled to a time-dependent external force. The external force destroys the monotonicity of the ℋ-function evolution. This leads to a model of the entropy flow that allows a steady nonequilibrium structure of the emitted field around (...) the unstable particles. (shrink)

Research on electroencephalogram (EEG) characteristics associated with major depressive disorder (MDD) has accumulated diverse neurophysiologic findings related to the content, topography, neurochemistry, and functions of EEG oscillations. Significant progress has been made since the first landmark EEG study on affective disorders by Davidson 35 years ago. A systematic account of these data is important and necessary for building a consistent neuropsychophysiologic model of MDD and other affective disorders. Given the extensive data on frequency-dependent functional significance of EEG oscillations, a (...) frequency domain approach may reveal the types of brain functions involved and disturbed in MDD. In this review, we systematize and integrate diverse and often unconnected observations on the content, topography, neurochemistry, and functions of EEG oscillations involved in MDD within the general concept of an EEG oscillatory pattern. (shrink)

In the 1940s and 1950s, nuclear magnetic resonance , one of the most important analytical techniques in chemistry, grew to maturity in the intermediate research field of chemical physics. Chemists and physicists adapted the new technology to the experimental culture of molecular spectroscopy which was based on a pragmatic experimental style. In molecular spectroscopy, the purpose of experiments was the establishment of methods that suited both the physicists' quest for precision and theoretical model building and the chemists' (...) longing for empirical data and understanding of structural formulae and reaction courses. In this process, an experimental style emerged that can be characterized as reliance on self‐built instrumentation, theoretical foundation in quantum mechanics, and proof of utility in the solution of structural and dynamical questions. This article focuses on the early development of NMR at Harvard University, with particular emphasis on the contributions of the first chemist working in the field of NMR, Herbert S. Gutowsky. (shrink)

Ten new graduate speech pathologists recounted their experiences in managing workplace ethical dilemmas in semi-structured interviews. Their stories were analysed for elements that described the nature and management of the ethical dilemmas. Ethical reasoning themes were generated to reflect the participants’ approaches to managing these dilemmas. Finally, a conceptual model, the Dynamic Model of Ethical Reasoning, was developed. This model incorporates the elements of awareness, independent problem solving, supported problem solving, and decision and outcome evaluation. Features (...) of the model demonstrate the complexity of ethical reasoning and the challenges that new graduates encounter when managing ethical dilemmas. The results have implications for preparing new graduates to manage ethical dilemmas in the workplace. (shrink)

The concept of molecular structure is fundamental to the practice and understanding of chemistry, but the meaning of this term has evolved and is still evolving. The Born–Oppenheimer separation of electronic and nuclear motions lies at the heart of most modern quantum chemical models of molecular structure. While this separation introduces a great computational and practical simplification, it is neither essential to the conceptual formulation of molecular structure nor universally valid. Going beyond the Born–Oppenheimer (...) approximation introduces new paradigms, bringing fresh insight into the chemistry of fluxional molecules, proteins, superconductors and macroscopic dielectrics, thus opening up new avenues for exploration. But it requires that our ideas of molecular structure need to evolve beyond simple ball-and-stick-type models. (shrink)

The Continuous Parameter Estimation Model is applied to develop individual genomic-level heritabilities for the latent hierarchical structure and developmental dynamics of Life History (LH) strategy LH strategies relate to the allocations of bioenergetic resources into different domains of fitness. LH has moderate to high population-level heritability in humans, both at the level of the high-order Super-K Factor and the lower-order factors, the K-Factor, Covitality Factor, and General Factor of Personality (GFP). Several important questions remain unexplored. We developed measures (...) of genome-level heritabilities employing an American sample of 316 monozygotic (MZ) and 274 dizygotic (DZ) twin dyads and a Swedish sample of 863 MZ and 475 DZ twin dyads. This novel heritability index measures individual genetic transmissibility, therefore opening new avenues for analyzing complex interactions among heritable traits inaccessible to standard structural equations methods. For these samples: (1) moderate to high heritability of factor loadings of Super-K on its lower-order factors is demonstrated, evidencing biological preparedness, genetic accommodation, and the gene-culture coevolution of biased epigenetic rules of development; (2) moderate to high heritability of the magnitudes of the effect of the higher-order factors upon their loadings on their constituent factors, evidencing genetic constraints upon phenotypic plasticity; and (3) that heritability of the LH factors, of factor loadings, and of the magnitudes of the correlations among factors are weaker among those with slower LH speeds, demonstrating that inter-individual variation in transmissibility is a function of individual socioecological selection pressures. (shrink)

Understanding what is distinctive about the role of models in science requires characterizing broad patterns in how these models evolve in the face of experimental results. That is, we must examine not just model statics—how the model relates to theory, or represents the world, at some point in time—but also model dynamics—how the model both generates new experimental results and is modified in response to them. Visual representations of structure play a central role in the (...) theoretical reasoning of organic chemists. Not surprisingly, these representations have changed in important ways–in response to experimental and theoretical developments– throughout the history of organic chemistry. In many cases it is appropriate to understand the visual representations used by organic chemists as models. The evolution of the structural representations of organic chemists therefore provides a clear example of the dynamics of scientific modeling. In this paper I use a conception of scientific modeling drawn from the work of Mary Hesse to examine how the concept of a molecular conformation was incorporated into the visual representations of structure used by organic chemists. (shrink)

This paper presents a dynamic perspective in which the psychological contract is treated as a structured set of beliefs that are held by individual employees about the mutual obligations of the organization as employer and themselves as employees. This set of beliefs is assumed to produce a state of commitment to the organization in which the employee is willing to accept work roles and tasks offered by the organization, and to carry them out in accordance with certain standards. The (...) dynamic model that is presented can help to explain why the commitment of employees remains relatively stable over time, and why it may suddenly decrease or increase under circumstances that are perceived as critical by the employee. The model assumes that the employee's evaluation of the organization's behavior changes over time, but that the structure of the psychological contract and the associated commitment change only when certain limits are overstepped. This perspective on changes in the psychological contract transforms the concept into a powerful construct that may lead to fruitful research on the dynamics of organization-employee relationships. Implications for future research are discussed. (shrink)

The temporal behaviour of the nonlinear compartmental model we have developed for rat calcium metabolism is discussed with respect to the theoretical properties of the self-oscillating autocatalytic subunit around which the model is constructed. Depending on the approximations made, this subunit is described by a minimal two-variable model, SU2, or by a three-variable one, SU3. The diversity of the theoretical dynamic behaviours possible with SU2 is greatly increased with SU3. But the identification of SU3 parameter values (...) in three different experimental situations reveals that biological constraints efficiently preserve a simple circadian rhythm for bone metabolism. This analysis indicates the significant contribution of the available bone crystal pool to the dynamic organization of this tissue, and hence to extracellular calcium homeostasis. (shrink)

The SARS‐CoV‐2 virus is responsible for the COVID‐19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike protein (...) at the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants. (shrink)

This paper proposes a new robotic fish which avoids the complex mechanical structure and reduces the model complexity comparing to the existing bioinspired robotic fish, giving rise to a semibiomimetic robotic fish. The generalized Lagrange equation is adopted to establish the dynamic model of the robotic fish. The controllability of the system is analyzed, upon which a trajectory tracking control algorithm is designed by using the feedback linearization technique. The simulation results show that the dynamic (...) model adopted in this paper can achieve better control performance. (shrink)

Hierarchical Bayesian models (HBMs) provide an account of Bayesian inference in a hierarchically structured hypothesis space. Scientific theories are plausibly regarded as organized into hierarchies in many cases, with higher levels sometimes called ‘para- digms’ and lower levels encoding more specific or concrete hypotheses. Therefore, HBMs provide a useful model for scientific theory change, showing how higher-level theory change may be driven by the impact of evidence on lower levels. HBMs capture features described in the Kuhnian tradition, particularly the (...) idea that higher-level theories guide learning at lower levels. In addition, they help resolve certain issues for Bayesians, such as scientific preference for simplicity and the problem of new theories. (shrink)

Hierarchical Bayesian models (HBMs) provide an account of Bayesian inference in a hierarchically structured hypothesis space. Scientific theories are plausibly regarded as organized into hierarchies in many cases, with higher levels sometimes called ‘paradigms’ and lower levels encoding more specific or concrete hypotheses. Therefore, HBMs provide a useful model for scientific theory change, showing how higher‐level theory change may be driven by the impact of evidence on lower levels. HBMs capture features described in the Kuhnian tradition, particularly the idea (...) that higher‐level theories guide learning at lower levels. In addition, they help resolve certain issues for Bayesians, such as scientific preference for simplicity and the problem of new theories. *Received July 2009; revised October 2009. †To contact the authors, please write to: Leah Henderson, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 32D‐808, Cambridge, MA 02139; e‐mail: [email protected]. (shrink)

This paper describes DIVA (Dynamic Imagery for Visual Analogy), a computational model of visual imagery based on the scene graph, a powerful representational structure widely used in computer graphics. Scene graphs make possible the visual display of complex objects, including the motions of individual objects. Our model combines a semantic-network memory system with computational procedures based on scene graphs. The model can account for people’s ability to produce visual images of moving objects, in particular the (...) ability to use dynamic visual analogies that compare two systems of objects in motion. (shrink)

Van Gelder (1995) has recently spearheaded a movement to challenge the dominance of connectionist and classicist models in cognitive science. The dynamical conception of cognition is van Gelder's replacement for the computation bound paradigms provided by connectionism and classicism. He relies on the Watt governor to fulfill the role of a dynamicist Turing machine and claims that the Motivational Oscillatory Theory (MOT) provides a sound empirical basis for dynamicism. In other words, the Watt governor is to be the theoretical exemplar (...) of the class of systems necessary for cognition and MOT is an empirical instantiation of that class. However, I shall argue that neither the Watt governor nor MOT successfully fulfill these prescribed roles. This failure, along with van Gelder's peculiar use of the concept of computation and his struggle with representationalism, prevent him from providing a convincing alternative to current cognitive theories. (shrink)

Much of our understanding of human thinking is based on probabilistic models. This innovative book by Jerome R. Busemeyer and Peter D. Bruza argues that, actually, the underlying mathematical structures from quantum theory provide a much better account of human thinking than traditional models. They introduce the foundations for modelling probabilistic-dynamic systems using two aspects of quantum theory. The first, 'contextuality', is a way to understand interference effects found with inferences and decisions under conditions of uncertainty. The second, 'quantum (...) entanglement', allows cognitive phenomena to be modeled in non-reductionist ways. Employing these principles drawn from quantum theory allows us to view human cognition and decision in a totally new light. Introducing the basic principles in an easy-to-follow way, this book does not assume a physics background or a quantum brain and comes complete with a tutorial and fully worked-out applications in important areas of cognition and decision. (shrink)

Van Gelder (1995) has recently spearheaded a movement to challenge the dominance of connectionist and classicist models in cognitive science. The dynamical conception of cognition is van Gelder's replacement for the computation bound paradigms provided by connectionism and classicism. He relies on the Watt governor to fulfill the role of a dynamicist Turing machine and claims that the Motivational Oscillatory Theory (MOT) provides a sound empirical basis for dynamicism. In other words, the Watt governor is to be the theoretical exemplar (...) of the class of systems necessary for cognition and MOT is an empirical instantiation of that class. However, I shall argue that neither the Watt governor nor MOT successfully fulfill these prescribed roles. This failure, along with van Gelder's peculiar use of the concept of computation and his struggle with representationalism, prevent him from providing a convincing alternative to current cognitive theories. (shrink)

The contents and structure of semantic memory have been the focus of much recent research, with major advances in the development of distributional models, which use word co‐occurrence information as a window into the semantics of language. In parallel, connectionist modeling has extended our knowledge of the processes engaged in semantic activation. However, these two lines of investigation have rarely been brought together. Here, we describe a processing model based on distributional semantics in which activation spreads throughout a (...) semantic network, as dictated by the patterns of semantic similarity between words. We show that the activation profile of the network, measured at various time points, can successfully account for response times in lexical and semantic decision tasks, as well as for subjective concreteness and imageability ratings. We also show that the dynamics of the network is predictive of performance in relational semantic tasks, such as similarity/relatedness rating. Our results indicate that bringing together distributional semantic networks and spreading of activation provides a good fit to both automatic lexical processing (as indexed by lexical and semantic decisions) as well as more deliberate processing (as indexed by ratings), above and beyond what has been reported for previous models that take into account only similarity resulting from network structure. (shrink)

This text addresses the problems of complex systems in understanding natural phenomena and the behaviour of systems related to human activity, from a science and humanities perspective. It discusses molecular behaviour and structures, and offers examples of ecological and environmental modelling.

Information is a basic structure of the world, while computation is a process of the dynamic change of information. This book provides a cutting-edge view of world's leading authorities in fields where information and computation play a central role. It sketches the contours of the future landscape for the development of our understanding of information and computation, their mutual relationship and the role in cognition, informatics, biology, artificial intelligence, and information technology. -/- This book is an utterly enjoyable (...) and engaging read which gives readers an opportunity to understand and relate phenomena seemingly unrelated in a completely new light — especially the connections between information, computation, cognition and life. -/- Contents: Cybersemiotics and the Question of Knowledge (Søren Brier) Information Dynamics in a Categorical Setting (Mark Burgin) Mathematics as a Biological Process (G J Chaitin) Information, Causation and Computation (John Collier) From Descartes to Turing: The Computational Content of Supervenience (S Barry Cooper) A Dialogue Concerning Two World Systems: Info-Computational vs Mechanistic (Gordana Dodig-Crnkovic & Vincent C Müller) Does Computing Embrace Self-Organization? (Wolfgang Hofkirchner) Analysis of Information and Computation in Physics Explains Cognitive Paradigms: From Full Cognition to Laplace Determinism to Statistical Determinism to Modern Approach (Vladik Kreinovich, Roberto Araiza & Juan Ferret) Bodies — Both Informed and Transformed Embodied Computation and Information Processing (Bruce J MacLennan) Computation on Information, Meaning and Representations: An Evolutionary Approach (Christophe Menant) Interior Grounding, Reflection, and Self-Consciousness (Marvin Minsky) A Molecular Dynamic Network: Minimal Properties and Evolutionary Implications (Walter Riofrio) Super-recursive Features of Evolutionary Processes and the Models for Computational Evolution (Darko Roglic) Towards a Modeling View of Computing (Oron Shagrir) What's Information, for an Organism or Intelligent Machine? How can a Machine or Organism Mean? (Aaron Sloman) Inconsistent Knowledge as a Natural Phenomenon: The Ranking of Reasonable Inferences as a Computational Approach to Naturally Inconsistent (Legal) Theories (Kees (CNJ) de Vey Mestdagh & Jaap Henk (JH) Hoepman) On the Algorithmic Nature of the World (Hector Zenil & Jean-Paul Delahaye) . (shrink)

The Hamiltonian structure of General Relativity (GR), for both metric and tetrad gravity in a definite continuous family of space-times, is fully exploited in order to show that: i) the "Hole Argument" can be bypassed by means of a specific "physical individuation" of point-events of the space-time manifold M^4 in terms of the "autonomous degrees of freedom" of the vacuum gravitational field (Dirac observables), while the "Leibniz equivalence" is reduced to differences in the "non-inertial appearances" (connected to gauge variables) (...) of the same phenomena. ii) the chrono-geometric structure of a solution of Einstein equations for given, gauge-fixed, initial data (a "3-geometry" satisfying the relevant constraints on the Cauchy surface), can be interpreted as an "unfolding" in mathematical global time of a sequence of "achronal 3-spaces" characterized by "dynamically determined conventions" about distant simultaneity. This result stands out as an important conceptual difference with respect to the standard chrono-geometrical view of Special Relativity (SR) and allows, in a specific sense, for an "endurantist" interpretations of ordinary physical objects in GR. (shrink)

Spatial predator-prey models have been studied by researchers for many years, because the exact distributions of the population can be well illustrated via pattern formation. In this paper, amplitude equations of a spatial Holling–Tanner predator-prey model are studied via multiple scale analysis. First, by amplitude equations, we obtain the corresponding intervals in which different kinds of patterns will be onset. Additionally, we get the conclusion that pattern transitions of the predator are induced by the increasing rate of conversion into (...) predator biomass. Specifically, pattern transitions of the predator between distinct Turing pattern structures vary in an orderly manner: from spotted patterns to stripe patterns, and finally to black-eye patterns. Moreover, it is discovered that pattern transitions of prey can be induced by cross-diffusion; that is, patterns of prey transmit from spotted patterns to stripe patterns and finally to a mixture of spot and stripe patterns. Meanwhile, it is found that both effects of cross-diffusion and interaction between the prey and predator can lead to the complicated phenomenon of dynamics in the system of biology. (shrink)

If societies, like institutions, are built to endure, then the bond that exists between generations must be considered. Constructing a framework to establish a philosophy of future generations, Tiziana Andina explores the factors that make it possible for a society to reproduce over time. Andina's study of the diachronic structure of societies considers the never-ending passage of generations, as each new generation comes to form a part of the new social fabric and political model. Her model draws (...) on the anthropologies offered by classical political philosophies such as Hobbes and Macchiavelli and the philosophies of power as discussed by Nietzsche. She confronts the ethics and function of this fundamental relationship, examines the role of transgenerationality in the formation and endurance of Western democracies and recognizes an often overlooked problem: each new generation must form part of social and political arrangements designed for them by the generations that came before. (shrink)

An in-situ transmission electron microscopy straining technique has been used to investigate the dynamics of dislocation-defect interactions in ion-irradiated copper and the subsequent formation of defect-free channels. Defect removal frequently required interaction with multiple dislocations, although screw dislocations were more efficient at annihilating defects than edge dislocations were. The defect pinning strength was determined from the dislocation curvature prior to breakaway and exhibited values ranging from 15 to 175 MPa. Pre-existing dislocations percolated through the defect field but did not show (...) long-range motion, indicating that they are not responsible for creating the defect-free channels and have a limited contribution to the total plasticity. Defect-free channels were associated with the movement of many dislocations, which originated from grain boundaries or regions of high stress concentration such as at a crack tip. These experimental results are compared with atomistic simulations of the interaction of partial dislocations with defects in copper and a dispersed-barrier-hardening crystal plasticity model to correlate the observations to bulk mechanical properties. (shrink)

A classification of models of reduction into three categories — theory reductionism, explanatory reductionism, and constitutive reductionism — is presented. It is shown that this classification helps clarify the relations between various explications of reduction that have been offered in the past, especially if a distinction is maintained between the various epistemological and ontological issues that arise. A relatively new model of explanatory reduction, one that emphasizes that reduction is the explanation of a whole in terms of its parts (...) is also presented in detail. Finally, the classification is used to clarify the debate over reductionism in molecular biology. It is argued there that while no model from the category of theory reduction might be applicable in that case, models of explanatory reduction might yet capture the structure of the relevant explanations. (shrink)

According to the traditional Bayesian view of credence, its structure is that of precise probability, its objects are descriptive propositions about the empirical world, and its dynamics are given by conditionalization. Each of the three essays that make up this thesis deals with a different variation on this traditional picture. The first variation replaces precise probability with sets of probabilities. The resulting imprecise Bayesianism is sometimes motivated on the grounds that our beliefs should not be more precise than the (...) evidence calls for. One known problem for this evidentially motivated imprecise view is that in certain cases, our imprecise credence in a particular proposition will remain the same no matter how much evidence we receive. In the first essay I argue that the problem is much more general than has been appreciated so far, and that it’s difficult to avoid without compromising the initial evidentialist motivation. The second variation replaces descriptive claims with moral claims as the objects of credence. I consider three standard arguments for probabilism with respect to descriptive uncertainty—representation theorem arguments, Dutch book arguments, and accuracy arguments—in order to examine whether such arguments can also be used to establish probabilism with respect to moral uncertainty. In the second essay, I argue that by and large they can, with some caveats. First, I don’t examine whether these arguments can be given sound non-cognitivist readings, and any conclusions therefore only hold conditional on cognitivism. Second, decision-theoretic representation theorems are found to be less convincing in the moral case, because there they implausibly commit us to thinking that intertheoretic comparisons of value are always possible. Third and finally, certain considerations may lead one to think that imprecise probabilism provides a more plausible model of moral epistemology. The third variation considers whether, in addition to conditionalization, agents may also change their minds by becoming aware of propositions they had not previously entertained, and therefore not previously assigned any probability. More specifically, I argue that if we wish to make room for reflective equilibrium in a probabilistic moral epistemology, we must allow for awareness growth. In the third essay, I sketch the outline of such a Bayesian account of reflective equilibrium. Given that this account gives a central place to awareness growth, and that the rationality constraints on belief change by awareness growth are much weaker than those on belief change by conditionalization, it follows that the rationality constraints on the credences of agents who are seeking reflective equilibrium are correspondingly weaker. (shrink)

Empirical results suggest that defocusing attention results in primary process or associative thought, conducive to finding unusual connections, while focusing attention results in secondary process or analytic thought, conducive to rule-based operations. Creativity appears to involve both. It is widely believed that it is possible to escape mental fixation by spontaneously and temporarily engaging in a more divergent or associative mode of thought. The resulting insight may be refined in a more analytic mode of thought. The question addressed here is: (...) how does the architecture of memory support these two modes of thought, and what is happening at the neural level when one shifts between them? Recent advances in neuroscience shed light on this. It was demonstrated that activated cell assemblies are composed of multiple ‘neural cliques’, groups of neurons that respond differentially to general or context-specific aspects of a situation. I refer to neural cliques that would not be included in the assembly if one were in an analytic mode, but would be if one were in an associative mode, as ‘neurds’. It is posited that the shift to a more associative mode of thought conducive to insight is accomplished by recruiting neurds that respond to abstract or atypical subsymbolic microfeatures of the problem or situation. Since memory is distributed and content-addressable this fosters remindings and the forging of creative connections to potentially relevant items previously encoded in those neurons. Thus it is proposed that creative thought involves neither randomness, nor search through a space of predefined alternatives, but emerges naturally through the recruitment of neurds. It is suggested this occurs when there is a need to resolve conceptual gaps in ones’ internal model of the world, and resolution involves context-driven actualization of the potentiality afforded by its fine-grained associative structure. (shrink)

In recent years, ethical questions related to the development of artificial intelligence are being increasingly discussed. However, there has not been enough corresponding increase in the research and development associated with AI technology that incorporates with ethical discussion. We therefore implemented an organic and dynamic tool for use with knowledge base of AI ethics for engineers to promote engineers’ practice of ethical AI design to realize further social values. Here, “organic” means that the tool deals with complex relationships among (...) different AI ethics. “Dynamic” means that the tool dynamically adopts new issues and helps engineers think in their own contexts. Data in the knowledge base of the tool is standardized based on the ethical design theory that consists of an extension of the hierarchical representation of artifacts to understand ethical considerations from the perspective of engineering, and a description method to express the design ideas. In addition, we apply the dynamic knowledge management model called knowledge liquidization and crystallization. To discuss the effects, we introduce three cases: a case for the clarification of differences in the structures among AI ethics and design ideas, a case for the presentation of semantic distance among them, and a case for the recommendation of the scenario paths that allow engineers to seamlessly use AI ethics in their own contexts. We discuss the effectiveness of the tool. We also show the probability that engineers can reconstruct AI ethics as a more practical one with professional ethicists. (shrink)

Biological objects are often constructive dynamic systems whose structures evolve as a consequence of their internal dynamics, which in turn is affected by the overall structure. As very few tools are presently adapted to tackle constructive dynamic systems, they constitute fascinating challenges for modeling/simulation. In cell biology, the secretory process in eukaryotic cells corresponds to this type of system, as it appears to autonomously generate new structures as a result of its molecular dynamics. Here I briefly (...) review the only documented case of a membrane-bounded intracellular compartment whose very existence strictly depends on its continued functioning. Indeed, the Golgi apparatus of the yeast Saccharomyces cerevisiae appears at steady-state as a continuously renewed set of transitory membrane-bounded structures that self-mature, rather than as a permanent entity. On the basis of this case and of recent advances in related molecular studies, a detailed model is proposed, that encompasses the birth of a yeast Golgi element and bridges its molecular and morphogenetic aspects. This model is extended to briefly outline three evolutionary inventions, from S. cerevisiae to another yeast, Pichia pastoris, on to plant, and on to animal cells: stacking, stabilizing and aggregating the primary Golgi elements. (shrink)

Amit's “Attractor Neural Network” perspective on cognition raises difficult technical problems already met by prior dynamical models. This commentary sketches briefly some of them concerning the internal topological structure of attractors, the constituency problem, the possibility of activating simultaneously several attractors, and the different kinds of dynamical structures one can use to model brain activity: point attractors, strange attractors, synchronized arrays of oscillators, synfire chains, and so forth.

Together with microtubules and actin microfilaments, ∼11 nm wide intermediate filaments (IFs) constitute the integrated, dynamic filament network present in the cytoplasm of metazoan cells. This network is critically involved in division, motility and other cellular processes. While the structures of microtubules and microfilaments are known in atomic detail, IF architecture is presently much less understood. The elementary ‘building block’ of IFs is a highly elongated, rod‐like dimer based on an α‐helical coiled‐coil structure. Assembly of cytoplasmic IF proteins, (...) such as vimentin, begins with a lateral association of dimers into tetramers and gradually into the so‐called unit‐length filaments (ULFs). Subsequently ULFs start to anneal longitudinally, ultimately yielding mature IFs after a compaction step. For nuclear lamins, however, assembly starts with a head‐to‐tail association of dimers. Recently, X‐ray crystallographic data were obtained for several fragments of the vimentin dimer. Based on the dimer structure, molecular models of the tetramer and the entire filament are now a possibility. BioEssays 25:243–251, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

ABSTRACTIn this paper I offer an interventionist perspective on the explanatory structure and explanatory power of dynamical models in cognitive science: I argue that some “pure” dynamical models – ones that do not refer to mechanisms at all – in cognitive science are “contextualized causal models” and that this explanatory structure gives such models genuine explanatory power. I contrast this view with several other perspectives on the explanatory power of “pure” dynamical models. One of the main results is (...) that dynamical models need not refer to underlying mechanisms in order to be explanatory. I defend and illustrate this position in terms of dynamical models of the A-not-B error in developmental psychology as elaborated by Thelen and colleagues, and dynamical models of unintentional interpersonal coordination developed by Richardson and colleagues. (shrink)

Since molecules are inaccessible to immediate observation, our conception of the molecule is brought about by transdiction which entails invention of various transcendental ideas. In organic chemistry we think that molecules consist of atoms, bonds, functional groups, etc. This is, however, not the unique description of the molecule as is shown by quantum mechanical calculations, for example. Then, what description represents the real molecule? Before asking this question, we have to consider what the real molecule is in the first place. (...) Constructive realism distinguishes our cognitive world and the world just given, and claims that we should accept the former as reality. Understanding our cognitive world is possible only through construction of micro-worlds. Atoms, bonds, functional groups, etc., are micro-worlds which make sense in a theoretical framework of organic chemistry. In this study we translate a micro-world to an affordance and paraphrase it as a context-relative dispositional attribute of an {agent-world} complex. Then, we can understand that it is what we take as molecular structure, not what might be out there to be found, that we should accept as reality. Excluding metaphysical fictions from scientific arguments, constructive realism makes science a meaningful activity. Constructive realism claims that, for getting knowledge of the world, we have to integrate information into our own linguistic frame, i.e., to translate it. Strangification is a technique of intentionally taking an accepted proposition out of one scientific system and putting it into a completely different context. As is the case with translation, strangification brings about deeper understanding of philosophical as well as scientific grounds on which the proposition system holds. We apply this method to molecular structure and reveal that it is an ingenious model to describe molecular behavior in multi-molecular systems with strong interactions between molecules. Information provided by strangification is essential to claim the legitimacy of a proposition system. As far as strangification is properly applied, relativism is irrelevant to constructive realism. (shrink)

In his late years, Thomas Kuhn became interested in the process of scientific specialization, which does not seem to possess the destructive element that is characteristic of scientific revolutions. It therefore makes sense to investigate whether and how Kuhn’s insights about specialization are consistent with, and actually fit, his model of scientific progress through revolutions. In this paper, I argue that the transition toward a new specialty corresponds to a revolutionary change for the group of scientists involved in such (...) a transition. I will clarify the role of the scientific community in revolutionary changes and characterize the incommensurability across specialties as possessing both semantic and methodological aspects. The discussion of the discovery of the structure of DNA will serve both as an illustration of my main argument and as reply to one criticism raised against Kuhn—namely, that his model cannot capture cases of revolutionary yet non-disruptive episodes of scientific progress. Revisiting Kuhn’s ideas on specialization will shed new light on some often overlooked features of scientific change. (shrink)

The article presents a verbal and mathematical model of medium-term business cycles (with a characteristic period of 7–11 years) known as Juglar cycles. The model takes into account a number of approaches to the analysis of such cycles; in the meantime it also takes into account some of the authors' own generalizations and additions that are important for understanding the internal logic of the cycle, its variability and its peculiarities in the present-time conditions. The authors argue that the (...) most important cause of cyclical crises stems from strong structural disproportions that develop during economic booms. These are not only disproportions between different economic sectors, but also disproportions between different societal subsystems; at present these are also disproportions within the World System as a whole. The proposed model of business cycle is based on its subdivision into four phases: – recovery phase (which could be subdivided into the start sub-phase and the acceleration sub-phase); – upswing/prosperity/expansion phase (which could be subdivided into the growth sub-phase and the boom/overheating sub-phase); – recession phase (within which one may single out the crash/bust/acute crisis subphase and the downswing sub-phase); – depression/stagnation phase (which we could subdivide into the stabilization subphase and the breakthrough sub-phase). The article provides a detailed qualitative description of macroeconomic dynamics at all the phases; it specifies driving forces of cyclical dynamics and the causes of transition from one phase to another (including psychological causes); a special attention is paid to the turning point from the peak of overheating to the acute crisis, as well as to the turning point from the downswing to recovery. The proposed mathematical model of Juglar cycle takes into account the following effects that are typical for the market economy: • positive feedbacks between various economic processes; • presence of a certain inertia, time lags in reactions of the economic subsystem to the change in conditions; • amplification by the financial subsystem of positive feedbacks and time lags in the economic subsystem; • excessive reaction to changing conditions during the acute crisis sub-phase. The authors suggest that the current crisis turns out to be rather similar to classical Juglar crises; however, there is also a significant difference, as the current crisis occurs at a truly global scale. Yet, due to this truly global scale of the current crisis, the possibilities of regulation with the national state's measures have turned out to be ineffective,whereas the suprastate regulation of financial processes hardly exists. It is shown that all these have led to the reproduction of the current crisis according to a classical Juglar scenario. (shrink)

This paper combines naturalized metaphysics and a philosophical reflection on a recently evolving interdisciplinary branch of quantum chemistry, ab initio molecular dynamics. Bridging the gaps among chemistry, physics, and computer science, this cutting-edge research field explores the structure and dynamics of complex molecular many-body systems through computer simulations. These simulations are allegedly crafted solely by the laws of fundamental physics, and are explicitly designed to capture nature as closely as possible. The models and algorithms employed, however, involve (...) many approximations and significant degrees of idealization of their target systems. Therefore, for philosophers of science the pivotal question of whether relying only on the fundamental laws of physics supports a reductionist or realist stance arises. One conceivable answer to this question is that the irreducible approximations and idealizations support rather anti-realist positions. After reviewing an influential attitude in the philosophy of computer simulations and the debate concerning scientific realism, I offer a fair interpretation of such ab initio modelling in quantum chemistry within a naturalistic metaphysical framework that gives rise to a specific type of ontic structural realism. (shrink)

I explored the relationship between the “Black Axe” Confraternity and cybercrime, with a particular emphasis on the structural dynamics of the Business Email Compromise (BEC) schemes. I investigated whether a conventional hierarchical system governs the membership and remuneration for BEC roles as perpetrators by interviewing an accused “leader” of the “Black Axe” affiliated cybercriminal incarcerated in a prominent Western nation. I supplemented the analysis of interview data with insights from tapped phone records monitored by a law enforcement entity. I merged (...) Actor-network theory and Social Network theory as analytical frameworks and thematically analyzed data to produce six overarching themes: (1) The fluidity of Structure and Adaptive Roles in BEC, (2) Challenges in Visualizing Criminal Networks, (3) Globalization and Transnational Dimensions, (4) Social and Cultural Influences, (5) Internal Cybersecurity Threats and Money Laundering, and (6) Remuneration and Influences of Cryptocurrency, casting a brighter light on the topic. Unlike traditional organized crime, BEC scammers have adopted a nonhierarchical model that is flexible and fluid. I found no evidence of a rigid hierarchy dictating positions and remuneration for BEC roles. Instead, I observed that cybercriminals involved in BEC activities functioned horizontally, promoting fluidity, maneuverability, collaboration, and specialization across various facets of their illicit pursuits. I also highlighted the cross-border links BEC offenders have with other criminal actors facilitated by Black Axe organizational machinery. My research adds value to the existing body of knowledge, utilizing a unique dataset comprising direct testimonies of a high-profile BEC offender affiliated with the ‘hard–to–access,’ Black Axe gang. (shrink)

Dynamical activities within living eukaryotic cells are organized by microtubules, main structural components of the cytoskeleton and cylindrical polymers of the protein tubulin. Evidence and theoretical models suggest that states of tubulin may play the role of “bits” in classical microtubule computational automata. The advent of quantum information devices, key roles played by quantum processes in protein dynamics, and coherent ordering in the cell cytoplasm further suggest that microtubules may function as quantum computational devices, and that mesoscopic and macroscopic quantum (...) states are characteristic of living systems. In this paper new results from molecular dynamics simulation based on recently obtained atomic structure of tubulin are presented which provide support for classical and quantum modes of microtubule information processing. (shrink)

Irregularity may occur on the earth’s surface in the form of mountains due to the imperfection of the earth’s crust. To explore the influence of horizontally polarized shear waves on mountains, we considered the fluid-saturated porous medium over an orthotropic semi-infinite medium with rigid and soft mountain surfaces for wave propagation. The mountain surface is defined mathematically as a periodic function of the time domain. The physical interpretation of materials’ structure has been explained in rectangular Cartesian coordinate system (...) originated at the contact interface of layer and half-space. The displacement of the mountains has been derived by solving energy equations analytically. The influence of rigid and soft mountain surfaces on the phase velocity of shear waves has been demonstrated graphically. (shrink)

The balance between births and deaths in an age-structured population is strongly influenced by the spatial distribution of sub-populations. Our aim was to describe the demographic process of a fish population in an hierarchical dendritic river network, by taking into account the possible movements of individuals. We tried also to quantify the effect of river network changes (damming or channelling) on the global fish population dynamics. The Salmo trutta life pattern was taken as an example for.We proposed a model (...) which includes the demographic and the migration processes, considering migration fast compared to demography. The population was divided into three age-classes and subdivided into fifteen spatial patches, thus having 45 state variables. Both processes were described by means of constant transfer coefficients, so we were dealing with a linear system of difference equations. The discrete case of the variable aggregation method allowed the study of the system through the dominant elements of a much simpler linear system with only three global variables: the total number of individuals in each age-class. (shrink)