The vertebrate nervous system performs the most complex functions of any organ system. This feat is mediated by dedicated assemblies of neurons that must be precisely connected to one another and to peripheral tissues during embryonic development. Motor neurons, which innervate muscle and regulate autonomic functions, form an integral part of this neural circuitry. The first part of this review describes the remarkable progress in our understanding of motor neuron differentiation, which is arguably the best understood model of neuronal differentiation (...) to date. During development, the coordinate actions of inductive signals from adjacent non‐neural tissues initiate the differentiation of distinct motor neuron subclasses, with specific projection patterns, at stereotypical locations within the neural tube. Underlying this specialisation is the expression of specific homeodomain proteins, which act combinatorially to confer motor neurons with both their generic and subtype‐specific properties. Ensuring that specific motor neuron subtypes innervate the correct target structure, however, requires precise motor axon guidance mechanisms. The second half of this review focuses on how distinct motor neuron subtypes pursue highly specific projection patterns by responding differentially to spatially discrete attractive and repulsive molecular cues. The tight link between motor neuron specification and axon pathfinding appears to be established by the dominant role of homeodomain proteins in dictating the ways that navigating motor axons interpret the plethora of guidance cues impinging on growth cones. BioEssays 23:582–595, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Entry into mitosis is driven by the activity of kinases, which phosphorylate over 7000 proteins on multiple sites. For cells to exit mitosis and segregate their genome correctly, these phosphorylations must be removed in a specific temporal order. This raises a critical and important question: how are specific phosphorylation sites on an individual protein removed? Traditionally, the temporal order of dephosphorylation was attributed to decreasing kinase activity. However, recent evidence in human cells has identified unique patterns of dephosphorylation (...) during mammalian mitotic exit that cannot be fully explained by the loss of kinase activity. This suggests that specificity is determined in part by phosphatases. In this review, we explore how the physicochemical properties of an individual phosphosite and its surrounding amino acids can affect interactions with a phosphatase. These positive and negative interactions in turn help determine the specific pattern of dephosphorylation required for correct mitotic exit. (shrink)

The mode and timing of germ-cell specification has been studied in diverse organisms, however, the molecular mechanism regulating germ-cell-fate determination remains to be elucidated. In some model organisms, maternal germ-cell determinants play a key role. In mouse embryos, some germ-line-specific gene products exist as maternal molecules and play critical roles in a pluripotential cell population at preimplantation stages. From those cells, primordial germ cells (PGCs) are specified by extracellular signaling mediated by tissue, as well as cell–cell interaction during gastrulation. (...) Thus, establishment of germ-cell lineage in mammalian embryos appears to be regulated by a multistep process, including formation and maintenance of a pluripotential cell population, as well as specification of PGCs. PGCs can be generated from pluripotential embryonic stem (ES) cells in a simple monolayer culture in which tissue interaction does not occur. This raises the possibility that ES cells, as well as, possibly, pluripotential cells in preimplantation embryos, are more closely related to the PGC precursors than pluripotential cells after implantation. BioEssays 27:136–143, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

In their 2002 seminal paper Hauser, Chomsky and Fitch hypothesize that recursion is the only human-specific and language-specific mechanism of the faculty of language. While debate focused primarily on the meaning of recursion in the hypothesis and on the human-specific and syntax-specific character of recursion, the present work focuses on the claim that recursion is language-specific. We argue that there are recursive structures in the domain of motor intentionality by way of extending John R. Searle’s (...) analysis of intentional action. We then discuss evidence from cognitive science and neuroscience supporting the claim that motor-intentional recursion is language-independent and suggest some explanatory hypotheses: linguistic recursion is embodied in sensory-motor processing; linguistic and motor-intentional recursions are distinct and mutually independent mechanisms. Finally, we propose some reflections about the epistemic status of HCF as presenting an empirically falsifiable hypothesis, and on the possibility of testing recursion in different cognitive domains. (shrink)

In The Adapted Mind (1992), Cosmides and Tooby argue for the thesis that biological evolution endowed the human mind with a system of content‐specific computational mechanisms designed to solve long‐standing adaptive problems humans encountered as hunter‐gatherers, and not just a generalized "capacity for culture" or all‐purpose "learning capacity". I analyze three types of arguments they offer: historical arguments for the rise of content‐Specific psychology; programmatic arguments for the aims, theory, concepts, and methods of their evolutionary approach; and (...) experimental arguments for the content‐dependence of reasoning. Their arguments stand or fall on the claim that functionally specialized adaptations must be richly structured in a content‐specific way. (shrink)

Moritz Schlick’s interpretation of the causality principle is based on Schlick’s understanding of quantum mechanics and on his conviction that quantum mechanics strongly supports an empiricist reading of causation in his sense. The present paper compares the empiricist position held by Schlick with Bas van Fraassen’s more recent conception of constructive empiricism. It is pointed out that the development from Schlick’s understanding of logical empiricism to constructive empiricism reflects a difference between the understanding of quantum mechanics endorsed by Schlick and (...) the understanding that had been established at the time of van Fraassen’s writing. (shrink)

Living organisms act as integrated wholes to maintain themselves. Individual actions can each be explained by characterizing the mechanisms that perform the activity. But these alone do not explain how various activities are coordinated and performed versatilely. We argue that this depends on a specific type of mechanism, a control mechanism. We develop an account of control by examining several extensively studied control mechanisms operative in the bacterium E. coli. On our analysis, what distinguishes a control mechanism (...) from other mechanisms is that it relies on measuring one or more variables, which results in setting constraints in the control mechanism that determine its action on flexible constraints in other mechanisms. In the most basic arrangement, the measurement process directly determines the action of the control mechanism, but in more complex arrangements signals mediate between measurements and effectors. This opens the possibility of multiple responses to the same measurement and responses based on multiple measurements. It also allows crosstalk, resulting in networks of control mechanisms. Such networks integrate the behaviors of the organism but also present a challenge in tailoring responses to particular measurements. We discuss how integrated activity can still result in differential, versatile, responses. (shrink)

This article focuses on the assessment of mechanistic relations with specific attention to medicine, where mechanistic models are widely employed. I first survey recent contributions in the philosophical literature on mechanistic causation, and then take issue with Federica Russo and Jon Williamson’s thesis that two types of evidence, probabilistic and mechanistic, are at stake in the health sciences. I argue instead that a distinction should be drawn between previously acquired knowledge of mechanisms and yet-to-be-discovered knowledge of mechanisms (...) and that both probabilistic evidence and manipulation are essential with respect to newly discovered mechanisms. (shrink)

We are often told that quantum phenomena demand radical revisions of our scientific world view and that no physical theory describing well defined objects, such as particles described by their positions, evolving in a well defined way, let alone deterministically, can account for such phenomena. The great majority of physicists continue to subscribe to this view, despite the fact that just such a deterministic theory, accounting for all of the phe nomena of nonrelativistic quantum mechanics, was proposed by David Bohm (...) more than four decades ago and has arguably been around almost since the inception of quantum mechanics itself. Our purpose in asking colleagues to write the essays for this volume has not been to produce a Festschrift in honor of David Bohm or to gather together a collection of papers simply stating uncritically Bohm's views on quantum mechanics. The central theme around which the essays in this volume are arranged is David Bohm's version of quantum mechanics. It has by now become fairly standard practice to refer to his theory as Bohmian mechanics and to the larger conceptual framework within which this is located as the causal quantum theory program. While it is true that one can have reservations about the appropriateness of these specific labels, both do elicit distinc tive images characteristic of the key concepts of these approaches and such terminology does serve effectively to contrast this class of theories with more standard formulations of quantum theory. (shrink)

Bohmian mechanics, which is also called the de Broglie-Bohm theory, the pilot-wave model, and the causal interpretation of quantum mechanics, is a version of quantum theory discovered by Louis de Broglie in 1927 and rediscovered by David Bohm in 1952. It is the simplest example of what is often called a hidden variables interpretation of quantum mechanics. In Bohmian mechanics a system of particles is described in part by its wave function, evolving, as usual, according to Schrödinger's equation. However, the (...) wave function provides only a partial description of the system. This description is completed by the specification of the actual positions of the particles. The latter evolve according to the.. (shrink)

In this essay, we draw on John Haugeland’s work in order to argue that Burge is wrong to think that exercises of perceptual constancy mechanisms suffice for perceptual representation. Although Haugeland did not live to read or respond to Burge’s Origins of Objectivity, we think that his work contains resources that can be developed into a critique of the very foundation of Burge’s approach. Specifically, we identify two related problems for Burge. First, if (what Burge calls) mere sensory responses (...) are not representational, then neither are exercises of constancy mechanisms, since the differences between them do not suffice to imply that one is representational and the other is not. Second, taken by themselves, exercises of constancy mechanisms are only derivatively representational, so merely understanding how they work is not sufficient for understanding what is required for something, in itself, to be representational (and thereby provide a full solution to the problem of perceptual representation). (shrink)

In this paper, I critically assess different interpretations of Bohmian mechanics that are not committed to an ontology based on the wave function being an actual physical object that inhabits configuration space. More specifically, my aim is to explore the connection between the denial of configuration space realism and another interpretive debate that is specific to Bohmian mechanics: the quantum potential versus guidance approaches. Whereas defenders of the quantum potential approach to the theory claim that Bohmian mechanics is better (...) formulated as quasi-Newtonian, via the postulation of forces proportional to acceleration; advocates of the guidance approach defend the notion that the theory is essentially first-order and incorporates some concepts akin to those of Aristotelian physics. Here I analyze whether the desideratum of an interpretation of Bohmian mechanics that is both explanatorily adequate and not committed to configuration space realism favors one of these two approaches to the theory over the other. Contrary to some recent claims in the literature, I argue that the quasi-Newtonian approach based on the idea of a quantum potential does not come out the winner. (shrink)

We advance an account that grounds cognition, specifically decision-making, in an activity all organisms as autonomous systems must perform to keep themselves viable—controlling their production mechanisms. Production mechanisms, as we characterize them, perform activities such as procuring resources from their environment, putting these resources to use to construct and repair the organism's body and moving through the environment. Given the variable nature of the environment and the continual degradation of the organism, these production mechanisms must be regulated (...) by control mechanisms that select when a production is required and how it should be carried out. To operate on production mechanisms, control mechanisms need to procure information through measurement processes and evaluate possible actions. They are making decisions. In all organisms, these decisions are made by multiple different control mechanisms that are organized not hierarchically but heterarchically. In many cases, they employ internal models of features of the environment with which the organism must deal. Cognition, in the form of decision-making, is thus fundamental to living systems which must control their production mechanisms. (shrink)

Programmed cell death (PCD) is a process aimed at the removal of redundant, misplaced, or damaged cells and it is essential to the development and maintenance of multicellular organisms. In contrast to the relatively well‐described cell death pathway in animals, often referred to as apoptosis, mechanisms and regulation of plant PCD are still ill‐defined. Several morphological and biochemical similarities between apoptosis and plant PCD have been described, including DNA laddering, caspase‐like proteolytic activity, and cytochrome c release from mitochondria. Reactive (...) oxygen species (ROS) have emerged as important signals in the activation of plant PCD. In addition, several plant hormones may exert their respective effects on plant PCD through the regulation of ROS accumulation. The possible plant PCD regulators discussed in this review are integrated in a model that combines plant‐specific regulators with mechanisms functionally conserved between animals and plants. BioEssays 25:47–57, 2003. © 2002 Wiley Periodicals, Inc. (shrink)

Quantum mechanics has recently indicated that temporal order is not always fixed, a finding that has far-reaching philosophical and theological implications. The phenomena, termed “indefinite causal order,” shows that events can be in a superposition with regard to their order. In the experimental setting with which this article is concerned, two events, A and B, were shown to be in the ordering relations “A before B” and “B before A” at the same time. This article introduces an ongoing project that (...) seeks to make sense of this result, with a particular focus on the methodology by which this research will be undertaken. Specific research questions, particularly regarding what indefinite causal order might mean for the metaphysics of time and the doctrine of salvation, are introduced. The collaborative approach detailed brings together the disciplinary skills of a working scientist and a working theologian. What is offered is a collaborative methodology for interaction between science and religion that is more than the sum of its parts. Alister McGrath’s idea of multiple rationalities is employed as an epistemological framework within which this research takes place. Within an epistemologically pluralistic model, collaborative efforts are not only encouraged but necessary. Complex reality requires an equally complex, usually interdisciplinary, explanation. I argue that such dialogue is both theologically justified and culturally valuable and indicates the direction in which this research will be taken. (shrink)

Are mechanisms for social attention influenced by culture? Evidence that social attention is triggered automatically by bottom-up gaze cues and is uninfluenced by top-down verbal instructions may suggest it operates in the same way everywhere. Yet considerations from evolutionary and cultural psychology suggest that specific aspects of one's cultural background may have consequence for the way mechanisms for social attention develop and operate. In more interdependent cultures, the scope of social attention may be broader, focusing on more (...) individuals and relations between those individuals. We administered a multi-gaze cueing task requiring participants to fixate a foreground face flanked by background faces and measured shifts in attention using eye tracking. For European Americans, gaze cueing did not depend on the direction of background gaze cues, suggesting foreground gaze alone drives automatic attention shifting; for East Asians, cueing patterns differed depending on whether the foreground cue matched or mismatched background cues, suggesting foreground and background gaze information were integrated. These results demonstrate that cultural background influences the social attention system by shifting it into a narrow or broad mode of operation and, importantly, provides evidence challenging the assumption that mechanisms underlying automatic social attention are necessarily rigid and impenetrable to culture. (shrink)

The shared circuits model (SCM) relies on well-regarded theories of perception-action, mirror neurons, and forward models, but the functional/informational level of the model limits its ability to explain complex behavior such as true imitation. Data from our lab and others confirm the more general details of the model, accepted by most, but specify the neural mechanisms involved in perception-action processes.

According to new mechanists, mechanisms explain how specific biological phenomena are produced. New mechanists have had little to say about how mechanisms relate to the organism in which they reside. A key feature of organisms, emphasized by the autonomy tradition, is that organisms maintain themselves. To do this, they rely on mechanisms. But mechanisms must be controlled so that they produce the phenomena for which they are responsible when and in the manner needed by the (...) organism. To account for how they are controlled, we characterize mechanisms as sets of constraints on the flow of free energy. Some constraints are flexible and can be acted on by other mechanisms, control mechanisms, that utilize information procured from the organism and its environment to alter the flexible constraints in other mechanisms so that they produce phenomena appropriate to the circumstances. We further show that control mechanisms in living organisms are organized heterarchically—control is carried out primarily by local controllers that integrate information they acquire as well as that which they procure from other control mechanisms. The result is not a hierarchy of control but an integrated network of control mechanisms that has been crafted over the course of evolution. (shrink)

Ernst Mayr proposed a distinction between “proximate”, mechanistic, and “ultimate”, evolutionary, causes of biological phenomena. This dichotomy has influenced the thinking of many biologists, but it is increasingly perceived as impeding modern studies of evolutionary processes, including study of “niche construction” in which organisms alter their environments in ways supportive of their evolutionary success. Some still find value for this dichotomy in its separation of answers to “how?” versus “why?”questions about evolution. But “why is A?” questions about evolution necessarily take (...) the form “how does A occur?”, so this separation is illusory. Moreover, the dichotomy distorts our view of evolutionary causality, in that, contra Mayr, the action of natural selection, driven by genotype-phenotype-environment interactions which constitute adaptations, is no less “proximate” than the biological mechanisms which are altered by naturally selected genetic variants. Mayr’s dichotomy thus needs replacement by more realistic, mechanistic views of evolution. From a mechanistic viewpoint, there is a continuum of adaptations from those evolving as responses to unchanging environmental pressures to those evolving as the capacity for niche construction, and intermediate stages of this can be identified. Some biologists postulate an association of “phenotypic plasticity” (phenotype-environment covariation with genotype held constant) with capacity for niche construction. Both “plasticity” and niche construction comprise wide ranges of adaptive mechanisms, often fully heritable and resulting from case-specific evolution. Association of “plasticity” with niche construction is most likely to arise in systems wherein capacity for complex learning and behavioral flexibility have already evolved. (shrink)

The use of performance feedback in the workplace has gained popularity over the years, yet school heads have been challenged in providing it to teachers. In the initial interview, they shared that evaluation results can impact teachers’ motivation, and that feedback should be done carefully. However, they failed to clearly articulate a specific mechanism that had been applied in this vital role. Also, no studies have provided clear detail on the feedback mechanism used by school heads in the past. (...) For this reason, a study explored the feedback mechanisms employed by school heads in conveying the performance evaluation results to teachers. This study employed a narrative inquiry, and interviews were conducted with five school heads and five teachers who were chosen purposively for this research. Responses were recorded using a voice recorder. These responses were transcribed and analyzed using thematic narrative analysis. Based on transcripts, the study identified six emergent themes, such as conversational (one-on-one), relational, reflective, technical, reinforcing, and properly situated mechanisms in conveying performance evaluation results to teachers. Thus, a new feedback mechanism framework was developed. (shrink)

Human moral behaviour ranges from vicious cruelty to deep compassion, and any explanation of morality must address how our species is capable of such a range. Darwin argued that any social animal, with sufficient intellectual capacity, would develop morality. In agreement, I argue that human morality is unique in the animal kingdom not because of any particular moral capacity, but because some very abstract cognitive abilities that are unique to our species are layered on top of phylogenetically older emotional instincts (...) for aggression and for empathy. I review research on several components of empathy, intersubjectivity and theory of mind, detailing which of these capacities is uniquely human, and highlighting relevant neuroanatomy for each ability. Finally, I describe our abstract cognitive abilities for recursion and metarepresentation, and argue that these are uniquely human. When these abilities interact with our older social abilities (empathy, intersubjectivity) we are able to reason abstractly about others' mental states and how to affect them. Thus, it is these abstract cognitive capacities that give us the ability to be both cruel and compassionate, but it is our ancient ability for empathy that keeps us moral. Morality is, in a very real sense, a gift from our ancestors. (shrink)

The specific mechanisms whereby Pavlovian conditioning leads to adaptive behavior need to be elaborated. There is no evidence that it is via reduction in the “destabilizing effect that time lags have on feedback control” (Domjan et al. 2000, sect. 3.3). The adaptive value of Pavlovian conditioning goes well beyond the regulation of social behavior.

mechanism" is frequently encountered in the social science literature, but there is considerable confusion about the exact meaning of the term. The article begins by addressing the main conceptual issues. Use of this term is the hallmark of an approach that is critical of the explanatory deficits of correlational analysis and of the covering-law model, advocating instead the causal reconstruction of the processes that account for given macro-phenomena. The term "social mechanisms" should be used to refer to recurrent processes (...) generating a specific kind of outcome. Explanation of social macro-phenomena by mechanisms typically involves causal regression to lower-level elements, as stipulated by methodological individualism. While there exist a good many mechanism models to explain emergent effects of collective behavior, we lack a similarly systematic treatment of generative mechanisms in which institutions and specific kinds of structural configurations play the decisive role. Key Words: causal regression • correlational analysis • emergent effects • micro-macro processes • social mechanisms • structural determinants. (shrink)

RESUMEN Dentro de la enorme cantidad de temas reinantes relacionados con el desarrollo científico-tecnológico actual, se encuentra indudablemente el del empleo de la ventilación mecánica no invasiva como medida de soporte vital. Aunque no se trata de una obra especifica que presente un panorama completo y exacto, de todos y cada uno de los problemas relacionados con el empleo de la misma, los autores pretenden con el artículo realizar una breve reflexión del tema desde el enfoque de la ciencia, la (...) tecnología y la sociedad en el momento actual, de manera que constituya un marco útil para el examen de estos temas, su debate, reflexión e intercambio de opiniones en el contexto de los servicios de la salud. ABSTRACT Among the huge number of current issues related to the current scientific-technological development is undoubtedly the use of non-invasive mechanical ventilation as a measure of life support. Although it is not a specific work that presents a complete and accurate picture of each one of the problems related to the use of it. Authors intend with the article to make a brief reflection on the subject from the perspective of science, technology and society at the present time, so that it constitutes a useful framework for the examination of these issues, debate, reflection and exchange of opinions in the context of health services. (shrink)

Perception of temporal patterns is fundamental to normal hearing, speech, motor control, and music. Certain types of pattern understanding are unique to humans, such as musical rhythm. Although human responses to musical rhythm are universal, there is much we do not understand about how rhythm is processed in the brain. Here, I consider findings from research into basic timing mechanisms and models through to the neuroscience of rhythm and meter. A network of neural areas, including motor regions, is regularly (...) implicated in basic timing as well as processing of musical rhythm. However, fractionating the specific roles of individual areas in this network has remained a challenge. Distinctions in activity patterns appear between "automatic" and "cognitively controlled" timing processes, but the perception of musical rhythm requires features of both automatic and controlled processes. In addition, many experimental manipulations rely on participants directing their attention toward or away from certain stimulus features, and measuring corresponding differences in neural activity. Many temporal features, however, are implicitly processed whether attended to or not, making it difficult to create controlled baseline conditions for experimental comparisons. The variety of stimuli, paradigms, and definitions can further complicate comparisons across domains or methodologies. Despite these challenges, the high level of interest and multitude of methodological approaches from different cognitive domains (including music, language, and motor learning) have yielded new insights and hold promise for future progress. (shrink)

Many areas of science develop by discovering mechanisms and role functions. Cummins' (1975) analysis of role functions-according to which an item's role function is a capacity of that item that appears in an analytic explanation of the capacity of some containing system-captures one important sense of "function" in the biological sciences and elsewhere. Here I synthesize Cummins' account with recent work on mechanisms and causal/mechanical explanation. The synthesis produces an analysis of specifically mechanistic role functions, one that uses (...) the characteristic active, spatial, temporal, and hierarchical organization of mechanisms to add precision and content to Cummins' original suggestion. This synthesis also shows why the discovery of role functions is a scientific achievement. Discovering a role function (i) contributes to the interlevel integration of multilevel mechanisms, and (ii) provides a unique, contextual variety of causal/mechanical explanation. (shrink)

Talk of mechanisms is ubiquitous in the natural sciences. Interdisciplinary fields such as biochemistry and pharmacy frequently discuss mechanisms with the assistance of diagrams. Such diagrams usually depict entities as structures or boxes and activities or interactions as arrows. While some of these arrows may indicate causal or componential relations, others may represent temporal or operational orders. Importantly, what kind of relation an arrow represents may not only vary with context but also be underdetermined by empirical data. In (...) this manuscript, we investigate how an analysis of pharmacological mechanisms in terms of producing and underlying mechanisms—as discussed in the contemporary philosophy of science—may shed light on these issues. Specifically, we shall argue that while pharmacokinetic mechanisms usually describe causal chains of production, pharmacodynamics tends to focus on mechanisms of action underlying the in vivo effects of a drug. Considering the action of thyroid gland hormones in the human body as a case study, we further demonstrate that pharmacodynamic schemes tend to incorporate entities and interactions on multiple levels. Yet, traditional pharmacodynamic schemes are sketched “flat”, i.e., non-hierarchically. We suggest that transforming flat pharmacodynamic schemes into mechanistic multi-level representations may assist in disentangling the different kinds of mechanisms and relations depicted by arrows in flat schemes. The resulting Baumkuchen model provides a powerful and practical alternative to traditional flat schemes, as it explicates the relevant mechanisms and relations more clearly. On a more general note, our discussion demonstrates how pharmacology and related disciplines may benefit from applying concepts from the new mechanist philosophy to guide the interpretation of scientific diagrams. (shrink)

In this paper we analyze and discuss the historical and philosophical development of the notion of logical possibility focusing on its specific meaning in classical and quantum mechanics. Taking into account the logical structure of quantum theory we continue our discussion regarding the Aristotelian Square of Opposition in orthomodular structures enriched with a monadic quantifier. Finally, we provide an interpretation of the Orthomodular Square of Opposition exposing the fact that classical possibility and quantum possibility behave formally in radically different (...) manners. (shrink)

Abstract“Sign stimuli” elicit specific patterns of behavior when an organism's motivation is appropriate. In the toad, visually released prey-catching involves orienting toward the prey, approaching, fixating, and snapping. For these action patterns to be selected and released, the prey must be recognized and localized in space. Toads discriminate prey from nonprey by certain spatiotemporal stimulus features. The stimulus-response relations are mediated by innate releasing mechanisms (RMs) with recognition properties partly modifiable by experience. Striato-pretecto-tectal connectivity determines the RM's recognition (...) and localization properties, whereas medialpallio-thalamo-tectal circuitry makes the system sensitive to changes in internal state and to prior history of exposure to stimuli. RMs encode the diverse stimulus conditions referring to the same prey object through different combinations of “specialized” tectal neurons, involving cells selectively tuned to prey features. The prey-selective neurons express the outcome of information processing in functional units consisting of interconnected cells. Excitatory and inhibitory interactions among feature-sensitive tectal and pretectal neurons specify the perceptual operations involved in distinguishing the prey from its background, selecting its features, and discriminating it from predators. Other connections indicate stimulus location. The results of these analyses are transmitted by specialized neurons projecting from the tectum to bulbar/spinal motor systems, providing a sensorimotor interface. Specific combinations of such projective neurons – mediating feature- and space-related messages – form “command releasing systems” that activate corresponding motor pattern generators for appropriate prey-catching action patterns. (shrink)

Despite the miraculous progress of science—it’s practitioners continue to run into mistakes, either discrediting research unduly or making leaps of causal inference where none are warranted. In this we isolate two of the reasons for such behavior involving the misplaced understanding of the role of mechanisms and mechanistic knowledge in the establishment of cause-effect relationships. We differentiate causal knowledge into causes, effects, mechanisms, cause-effect relationships, and causal stories. Failing to understand the role of mechanisms in this picture, (...) including their absence of knowledge or incorrect specification, leads to errors of wrongly excluding cause-effect relationships or wrongly inferring their existence. We highlight the primary of causality over mechanistic knowledge and causal stories in scientific reasoning. (shrink)

Mechanisms consist of component parts and processes organized in a specific way to produce changes that may give rise to one or more phenomena. I aim to examine the generative mechanism of generative material models in the production of new material models. A generative material model in biology is a living material model that is capable of generating new material models. I contend that generative mechanisms of a generative material model are not to be conflated with biological (...) mechanisms: the former is a mechanism manipulated and altered by the modeler while the latter is a naturally occurring mechanism. I examine the ways in which idealization may contribute to the generative mechanism in generating new model organisms. I articulate that the component parts and activities in a generative mechanism are to a large extent shaped by idealization in generative material modeling. Although biological mechanisms do have a role to play in the generation of model organisms, I propose that we shall view the generative mechanism as a hybrid of biological mechanisms and modeling activities. I shall argue that the notion of generative mechanisms as hybrid mechanisms is different from the extant conceptions of mechanisms in various aspects. (shrink)

The explanatory value of niche construction can be strengthened by firm footing in semiotic theory. Anthropologists have a unique perspective on the integration of such diverse approaches to human action and evolutionary processes. Here, we seek to open a dialogue between anthropology and biosemiotics. The overarching aim of this paper is to demonstrate that niche construction, including the underlying mechanism of reciprocal causation, is a semiotic process relating to biological development as well as cognitive development and cultural change. In making (...) this argument we emphasize the semiotic mechanisms underlying the niche concept. We argue that the “niche” in ecology and evolutionary biology can be consistent with the Umwelt of Jakob von Uexkull. Following John Deely we therefore suggest that investigations into the organism—environment interface constituting niche construction should emphasize the semiotic basis of experience. Peircean signs are pervasive and allow for flexible interpretations of phenomena in relation to the perceptual and cognitive capacities of the behaving organism, which is particularly pertinent for understanding the relation of proximate/ultimate selective forces as co-productive. Additionally, theoretical work by Kinji Imanishi on the evolution of daily life and Gregory Bateson’s relational view of evolution both support the linkage between proximate and ultimate evolutionary processes of causation necessitated by the niche construction perspective. We will then apply this theoretical framework to two specific examples: 1) hominin evolution, including uniquely human cultural behaviors with niche constructive implications; and 2) the multispecies and anthropocentric niche of human-dog coevolution from which complex cognitive capacities and semiotic relationships emerged. The intended outcome of this paper is the establishment of concrete semiotic mechanisms and theory underlying niche constructive behavior which can then be applied to a broad spectrum of organisms to contextualize the reciprocal relation between proximate and ultimate drivers of behavior. (shrink)

The claim that mechanisms are essential good science is widespread. I argue, however, that these claims are ambiguous in multiple ways. I sort out different version of the mechanism idea: (1) mechanisms that are horizontal —between cause and effect— and mechanisms that are vertical —they realize in lower-level terms causal properties—: and (2) different purposes or uses mechanisms may have. I then focus on the claim that various senses of mechanism are necessary for the confirmation of (...) causal claims. The paper shows that mechanisms can be useful, essential, or harmful depending on context, using the now standard graphical causal structure framework. These conclusions also support the larger philosophy of science moral that methodological norms in science are often context specific and empirical, not a priori and universal. (shrink)

The ‘universal cell reaction’ (UCR), a coordinated biphasic response to external (noxious and other) stimuli observed in all living cells, was described by Nasonov and his colleagues in the mid‐20th century. This work has received no attention from cell biologists in the West, but the UCR merits serious consideration. Although it is non‐specific, it is likely to be underpinned by precise mechanisms and, if these mechanisms were characterized and their relationship to the UCR elucidated, then our understanding (...) of the integration of cellular function could be improved. As a step towards identifying such mechanisms, I review some recent advances in understanding cell mechanics and the stress response and I suggest potentially testable hypotheses. There is a particular need for time‐course studies of cellular responses to different stimulus doses or intensities. I also suggest a correspondence with hormesis; re‐investigation of the UCR using modern biophysical and molecular‐biological techniques might throw light on this much‐discussed phenomenon. BioEssays 29:324–333, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

The contribution describes some aspects related to the representation of special curves; recalling mechanisms created specifically for the design of these curves, which have particular characteristics. Through the construction of a simple apparatus, consisting of two pendulums—which oscillate at the same time- it is possible to graphically reproduce Lissajous’ experiments on the commuting vibrations of the diapasons. This equipment was first built by Samuel Charles Tisley (London 1829-Unknown), under the name of harmonographer. The contribution aslo illustrates the essential characteristics (...) of the harmonograph—born as a means of analysing vibrations—but which, by its principle belongs to mechanics, for its applications to acoustic science and geometry for the ability to draw “harmonious” curves. (shrink)

Despite its uniform appearance, the cerebellar cortex is highly heterogeneous in terms of structure, genetics and physiology. Purkinje cells (PCs), the principal and sole output neurons of the cerebellar cortex, can be categorized into multiple populations that differentially express molecular markers and display distinctive physiological features. Such features include action potential rate, but also their propensity for synaptic and intrinsic plasticity. However, the precise molecular and genetic factors that correlate with the differential physiological properties of PCs remain elusive. In this (...) article, we provide a detailed overview of the cellular mechanisms that regulate PC activity and plasticity. We further perform a pathway analysis to highlight how molecular characteristics of specific PC populations may influence their physiology and plasticity mechanisms. (shrink)

Backgrounds: Transcranial direct current stimulation is a non-invasive brain stimulation technique for the treatment of several psychiatric disorders, e.g., mood disorders and schizophrenia. Therapeutic effects of tDCS are suggested to be produced by bi-directional changes in cortical activities, i.e., increased/decreased cortical excitability via anodal/cathodal stimulation. Although tDCS provides a promising approach for the treatment of psychiatric disorders, its neurobiological mechanisms remain to be explored.Objectives: To review recent findings from neurophysiological, chemical, and brain-network studies, and consider how tDCS ameliorates psychiatric (...) conditions.Findings: Enhancement of excitatory synaptic transmissions through anodal tDCS stimulation is likely to facilitate glutamate transmission and suppress gamma-aminobutyric acid transmission in the cortex. On the other hand, it positively or negatively modulates the activities of dopamine, serotonin, and acetylcholine transmissions in the central nervous system. These neural events by tDCS may change the balance between excitatory and inhibitory inputs. Specifically, multi-session tDCS is thought to promote/regulate information processing efficiency in the cerebral cortical circuit, which induces long-term potentiation by synthesizing various proteins.Conclusions: This review will help understand putative mechanisms underlying the clinical benefits of tDCS from the perspective of neurotransmitters, network dynamics, intracellular events, and related modalities of the brain function. (shrink)

There has been a burst of work in the last couple of decades on mechanistic explanation, as an alternative to the traditional covering-law model of scientific explanation. That work makes some interesting claims about mechanistic explanations rendering phenomena ‘intelligible’, but does not develop this idea in great depth. There has also been a growth of interest in giving an account of scientific understanding, as a complement to an account of explanation, specifically addressing a three-place relationship between explanation, world, and the (...) scientific community. The aim of this paper is to use the contextual theory of scientific understanding to build an account of understanding phenomena using mechanistic explanations. This account will be developed and illustrated by examining the mechanisms of supernovae, which will allow synthesis of treatment of the life sciences and social sciences on the one hand, where many accounts of mechanisms were originally developed, and treatment of physics on the other hand, where the contextual theory drew its original inspiration. (shrink)

Insights into the role of sleep in the molecular mechanisms of memory consolidation may come from studies of activity-dependent synaptic plasticity, such as long-term potentiation (LTP). This commentary posits a specific contribution of sleep to LTP stabilization, in which mRNA transported to dendrites during wakefulness is translated during sleep. Brain-derived neurotrophic factor may drive the translation of newly transported and resident mRNA.