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The calcium signals regulate the production and secretion of many signaling molecules like inositol trisphosphate ( $$IP_{3}$$ ) and adenosine triphosphate (ATP) in various cells including pancreatic $$\beta$$ -cells. The calcium signaling mechanisms regulating $$IP_{3}$$, ATP and insulin responsible for various functions of $$\beta$$ -cells are still not well understood. Any disturbance in these mechanisms can alter the functions of $$\beta$$ -cells leading to diabetes and metabolic disorders. Therefore, a mathematical model is proposed by incorporating the reaction-diffusion equation (...) for calcium dynamics and a system of first-order differential equations for $$IP_{3}$$, ATP-production and insulin secretion with initial and boundary conditions. The model incorporates the temporal dependence of $$IP_{3}$$ -production and degradation, ATP production and insulin secretion on calcium dynamics in a $$\beta$$ -cell. The piecewise linear finite element method has been used for the spatial dimension and the Crank-Nicolson scheme for the temporal dimension to obtain numerical results. The effect of changes in source influxes and buffers on calcium dynamics and production of $$IP_{3}$$, ATP and insulin levels in a $$\beta$$ -cell has been analyzed. It is concluded that the dysfunction of source influx and buffers can cause significant variations in calcium levels and dysregulation of $$IP_{3}$$, ATP and insulin production, which can lead to various metabolic disorders, diabetes, obesity, etc. The proposed model provides crucial information about the changes in mechanisms of calcium dynamics causing proportionate disturbances in $$IP_3$$, ATP and insulin levels in pancreatic cells, which can be helpful for devising protocols for diagnosis and treatment of various metabolic diseases. (shrink)

In this pedagogical communication after demonstrating the legitimacy for using the quantum theory of atoms in molecules (QTAIM) to non-Coulombic systems, Hookean H2 +/H3 2+ species are used for AIM analysis. In these systems, in contrast to their Coulombic counterparts, electron density is atom-like and instead of expected two/three topological atoms, just a single topological atom emerges. This observation is used to demonstrate that what is really “seen” by the topological analysis of electron densities is the clustering of (...) electrons. The very trait of monotonic decay of electron density around the “centers” of clustering guarantees the appearance of topological atoms as basin of attraction of the gradient vector field of the electron density. Although observations with Hookean molecules may seem disappointing at first glance, a careful reasoning points to the fact that the QTAIM methodology is extendable to novel domains, by a knowledge of the morphology of underlying densities, beyond the typical Coulombic systems. (shrink)

I argue that molecules may not have structure in isolation. I support this by investigating how quantum models identify structure for isolated molecules. Specifically, I distinguish between two sets of models: those that identify structure in isolation and those that do not. The former identify structure because they presuppose structural information about the target system via the Born- Oppenheimer approximation. However, it is an idealisation to assume structure in isolation because there is no empirical evidence of this. In (...) fact, whenever structure is empirically examined it is always partially determined by factors that are absent in isolation. Together with the growing empirical evidence that isolated molecules behave in non-classical ways, this shows that the quantum models that do not identify structure are more faithful representations of isolated molecules. (shrink)

By comparing chemistry to art, chemists have recently made claims to the aesthetic value, even beauty, of some of their products. This paper takes these claims seriously and turns them into a systematic investigation of the aesthetics of chemical products. I distinguish three types of chemical products - materials, molecules, and molecular models - and use a wide variety of aesthetic theories suitable for an investigation of the corresponding sorts of objects. These include aesthetics of materials, idealistic aesthetics from (...) Plato to Kant and Schopenhauer, psychological approaches of Ernst Gombrich and Rudolf Arnheim, and semiotic aesthetics of Nelson Goodman and Umberto Eco. Although the investigation does not support recent claims, I point out where aesthetics does and can play an import role in chemistry. Particularly, Eco's approach helps us understand that and how aesthetic experience can be a driving force in chemical research. (shrink)

We present a mechanical model of a quasi-elastic body which reproduces Maxwell’s equations with charges and currents. Major criticism against mechanical models of electrodynamics is that any presence of charges in the known models appears to violate the continuity equation of the aether and it remains a mystery as to where the aether goes and whence it comes. We propose a solution to the mystery—in the present model the aether is always conserved. Interestingly it turns out that the (...) charge velocity coincides with the aether velocity. In other words, the charges appear to be part of the aether itself. We interpret the electric field as the flux of the aether and the magnetic field as the torque per unit volume. In addition we show that the model is consistent with the theory of relativity, provided that we use Lorentz–Poincare interpretation of relativity theory. We make a statistical-mechanical interpretation of the Lorentz transformations. It turns out that the length of a body is contracted by the electromagnetic field which the molecules of this same body produce. This self-interaction causes also delay of all the processes and clock-dilation results. We prove this by investigating the probability distribution for a gas of self-interacting particles. We can easily extend this analysis even to elementary particles. (shrink)

What does it take for a scientific model to represent? Scientific models have received a great deal of attention in recent philosophical literature. Following Morgan and Morrison’s account of “Models as Mediators”, analysis of how models represent has changed from questioning what properties of models can be said to correlate with the world to asking how models are used to relate to an intended target-system. This turn to a practice-oriented approach of understanding models was a response to a general (...) philosophical problem that attends the empirical application of scientific representations such as models. This problem is twofold. Models, on the one hand, are often said to make false claims about the world.. (shrink)

How much does stimulus input shape perception? The common-sense view is that our perceptions are representations of objects and their features and that the stimulus structures the perceptual object. The problem for this view concerns perceptual biases as responsible for distortions and the subjectivity of perceptual experience. These biases are increasingly studied as constitutive factors of brain processes in recent neuroscience. In neural network models the brain is said to cope with the plethora of sensory information by predicting stimulus regularities (...) on the basis of previous experiences. Drawing on this development, this chapter analyses perceptions as processes. Looking at olfaction as a model system, it argues for the need to abandon a stimulus-centred perspective, where smells are thought of as stable percepts, computationally linked to external objects such as odorous molecules. Perception here is presented as a measure of changing signal ratios in an environment informed by expectancy effects from top-down processes. (shrink)

The goal of synthetic biology is to create artificial organisms. To achieve this it is essential to understand what life is. Metabolism-replacement systems, or (M, R)-systems, constitute a theory of life developed by Robert Rosen, characterized in the statement that organisms are closed to efficient causation, which means that they must themselves produce all the catalysts they need. This theory overlaps in part with other current theories, including autopoiesis, the chemoton, and autocatalytic sets, all of them invoking some idea of (...) closure. A simple model of an (M, R)-system has been implemented in the computer, and behaves in ways that may shed light on the requirements for a prebiotic self-organizing system. In addition to a trivial steady state in which nothing happens, it can establish a non-trivial steady state in which all intermediates have finite concentrations, with their rates of degradation balanced by their rates of synthesis. The system can be regenerated from the set of food components plus a single intermediate, and maintain itself in that state indefinitely, despite continuous degradation. At the very low compartment volumes that may have existed in prebiotic conditions, for example in cavities in minerals, or in micelles formed by simple amphiphiles, statistical fluctuations in the numbers of molecules need to be taken into account. With the stochastic approach there is no non-trivial steady state in strict mathematical terms, because the system will always collapse to the trivial state after sufficient time. However, the average time before collapse is so long for volumes greater than $10^{-19}\;{\textsc{l}}$ (much smaller than the volume of the order of $10^{-15}\;{\textsc{l}}$ for a typical bacterial cell) that for practical purposes the self-maintaining state of non-null concentrations becomes significant, recalling the situation of bistability that is observed in deterministic analysis. In turn, there exists a minimum size below which the self-organizing system cannot maintain itself on chemically relevant time scales. The value of the critical volume depends on the particular concentrations and rate constants assumed, but the principle could apply generally. (shrink)

Three-dimensional material models of molecules were used throughout the 19th century, either functioning as a mere representation or opening new epistemic horizons. In this paper, two case studies are examined: the 1875 models of van ‘t Hoff and the 1890 models of Sachse. What is unique in these two case studies is that both models were not only folded, but were also conceptualized mathematically. When viewed in light of the chemical research of that period not only were both of (...) these aspects, considered in their singularity, exceptional, but also taken together may be thought of as a subversion of the way molecules were chemically investigated in the 19th century. Concentrating on this unique shared characteristic in the models of van ‘t Hoff and the models of Sachse, this paper deals with the shifts and displacements between their operational methods and existence: between their technical and epistemological aspects and the fact that they were folded, which was forgotten or simply ignored in the subsequent development of chemistry. (shrink)

A general equation is derived describing the concentration of all possible complexes of a central molecule with a set of ligands bound to the central molecule. This deduction allows the reaction rate constants for the binding of a given molecule to the central molecule to depend on the species of molecules already bound and the location of the molecules already bound. The model thus allows for structural alteration of the central molecule by binding. Functions describing the concentration (...) dependence of any effect whatever depending on the distribution of complexes are deduced. Possible applications and methods of application are indicated.II est dérivé une équation qui décrit la concentration des toutes les complexes d'une molécule centrale avec une collection de ligands connectés à la molécule centrale. La déduction montre comme les coefficients de la rapidité de reaction entre la molécule centrale et les molécules de la collection dépend de l'espèce et de la location des molécules déjà connectées.La modèle dérivée de l'équation montre les changements structurelles par la connection. Les functions qui décrivent la dependence de chaque effet à la concentration, sont dérivés. Ces effects dépendent aussi à la distribution des complexes. Des applications et des méthodes sont indiqués.Eine allgemeine Vergleichung hat man bekommen welche die Konzentration aller möglichen Komplexen eines zentralen Moleküles mit einer Reihe von „Ligands” verbunden mit dem zentralen Molekül beschreibt. Diese Folgerung gestattet dass die Reaktiongeschwindigkeit Konstanten für die Bindung eines gegebenen Moleküles mit dem zentralen Molekül abhÄngt von den Arten schon gegebenen Molekülen und die Ortsbestimmung der schon gebundenen Molekülen. Das Model zeigt die strukturelle Änderungen des zentralen Moleküls durch Bindung. Funktionen, die die Konzentrationband jedes Effektes beschreiben dass abhÄngt von der Distribution der Komplexen, sind abgeleitet.Mögliche Anwendungen und Methoden von Anwendung sind dargelegt. (shrink)

In the philosophy of chemistry a view is developed according to which laws of nature and scientific theories are peculiar in chemistry. This view was criticized in an earlier issue of the Foundations of Chemistry (Vihalemm, Foundation of Chemistry 5(1): 7–22, 2003) referring to an essay by Maureen and John Christie (Christie and Christie, in N. Bushan and S. Rosenfeld (Eds.), Of Minds and Molecules: New Philosophical Perspectives on Chemistry. Oxford University Press, New York, 2000, pp. 34–50). This criticism (...) was responded by the Christies (Christie and Christie, Foundations of Chemistry 5(2): 165–177, 2003). In the present article the debate is continued. The main issues which need to be elucidated in order to carry the analysis forward are pointed out and discussed. The relevance of a theoretical model of science for the philosophy of chemistry is stressed. (shrink)

The target article presents a model for schizophrenia extending four levels of abstraction: molecules, cells, cognition, and syndrome. An important notion in the model is that of coordination, applicable to both the level of cells and of cognition. The molecular level provides an “implementation” of the coordination at the cellular level, which in turn underlies the coordination at the cognitive level, giving rise to the clinical symptoms.

This book focuses on the gradual formation of the concept of ‘light quanta’ or ‘photons’, as they have usually been called in English since 1926. The great number of synonyms that have been used by physicists to denote this concept indicates that there are many different mental models of what ‘light quanta’ are: simply finite, ‘quantized packages of energy’ or ‘bullets of light’? ‘Atoms of light’ or ‘molecules of light’? ‘Light corpuscles’ or ‘quantized waves’? Singularities of the field or (...) spatially extended structures able to interfere? ‘Photons’ in G.N. Lewis’s sense, or as defined by QED, i.e. virtual exchange particles transmitting the electromagnetic force? The term ‘light quantum’ made its first appearance in Albert Einstein’s 1905 paper on a “heuristic point of view” to cope with the photoelectric effect and other forms of interaction of light and matter, but the mental model associated with it has a rich history both before and after 1905. Some of its semantic layers go as far back as Newton and Kepler, some are only fully expressed several decades later, while others initially increased in importance then diminished and finally vanished. In conjunction with these various terms, several mental models of light quanta were developed—six of them are explored more closely in this book. It discusses two historiographic approaches to the problem of concept formation: the author’s own model of conceptual development as a series of semantic accretions and Mark Turner’s model of ‘conceptual blending’. Both of these models are shown to be useful and should be explored further. This is the first historiographically sophisticated history of the fully fledged concept and all of its twelve semantic layers. It systematically combines the history of science with the history of terms and a philosophically inspired history of ideas in conjunction with insights from cognitive science. (shrink)

chapter 7. How DNA became an important molecule: Controversies at the origins of molecular biology Eleonora Cresto José María Gil Contributors Author index ...

Studies have shown that as MRI T2 relaxation time lengthens there is a shift toward more unbound or “free-water” and less partitioning of the protein/lipid molecules per unit volume. A shift toward less water partitioning or lengthened MRI T2 relaxation time is linearly related to reduced high frequency EEG amplitude, reduced short distance EEG coherence, increased long distance EEG coherence, and reduced cognitive functioning (Thatcher et al. 1998a; 1998b).

I argue that scientific explanation has a pragmatic dimension that is epistemically relevant. Philosophers with an objectivist approach to scientific explanation (e.g. Hempel, Trout) hold that the pragmatic aspects of explanation do not have any epistemic import. I argue against this view by focusing on the role of models in scientific explanation. Applying recent accounts of modelling (Cartwright, Morgan and Morrison) to a case-study of nineteenth-century physics, I analyse the pragmatic dimension of the process of model construction. I highlight (...) the crucial roles that conceptual tools, skills, and commitments play in this dimension, and show how they contribute to the epistemic aim of science. (shrink)

We review state‐of‐the‐art computational methods for constructing, from image data, generative statistical models of cellular and nuclear shapes and the arrangement of subcellular structures and proteins within them. These automated approaches allow consistent analysis of images of cells for the purposes of learning the range of possible phenotypes, discriminating between them, and informing further investigation. Such models can also provide realistic geometry and initial protein locations to simulations in order to better understand cellular and subcellular processes. To determine the structures (...) of cellular components and how proteins and other molecules are distributed among them, the generative modeling approach described here can be coupled with high throughput imaging technology to infer and represent subcellular organization from data with few a priori assumptions. We also discuss potential improvements to these methods and future directions for research. (shrink)

A model for kinetics of circular substrate cleavage by restriction endonuclease was formulated. The aim of the analysis of the model was to extract kinetic constants for all target sites from time- dependence of fragment concentration in reaction products. That was proved to be possible for molecules with an odd number of fragments only. A symmetry of the molecules with an even number of fragment is the cause. A solution for molecules with an odd number (...) of fragments was found and methods for dealing with the other molecules were suggested. (shrink)

The regulatory NodD proteins of Rhizobium bacteria mediate the activation of a gene set responsible for symbiotic nodule formation by plant signal molecules. Here we discuss the signal recognition and gene activation properties of NodD and present a model summarizing the current knowledge on NodD action.

Is integrative biology a good idea, or even possible? There has been much interest lately in the unifica- tion of biology and the integration of traditionally separate disciplines such as molecular and develop- mental biology on one hand, and ecology and evolutionary biology on the other. In this paper I ask if and under what circumstances such integration of efforts actually makes sense. I develop by example an analogy with Aristotle’s famous four “causes” that one can investigate concerning any object (...) or phenomenon: material (what something is made of), formal (what distinguishes that particular object from others), efficient (how was the object made) and final (why was the object made). The example is provided by ongoing research on different aspects of flowering time in the model system Arabidop- sis, a small weed belonging to the mustard family. I show that understanding how flowering time is controlled is an epistemologically different sort of question from why and how it evolved, and that the two research agendas can be pursued largely independently of each other. Toward the end, I propose that the real goal of integrative biology is to understand the boundary layers between levels of biologi- cal analysis, something to which modern philosophy of science can contribute significantly. (shrink)

The aim of the presentation is to focus on the differences between two scientific contexts: the genetic engineering context of the 1970s, with specific attention paid to the use of the recombinant DNA technique to generate genetically modified molecules, and the current genome editing context, with specific attention paid to the use of CRISPR-Cas9 technology to modify human germ line cells genetically. In both events, scientists have been involved in discussions that have gone beyond mere professional deontology touching on (...) specific policy issues such as freedom of research, responsibility for the consequences of research, the right of the public to participate in the evaluation of the goals of research methods, the relationship between cost and benefit and possible social consequences. The comparison between these two scientific contexts suggests the need of handling such issues by defining procedures that meet the criteria of democracy and responsibility towards society. The underlying objective should be to effectively launch actions and interventions based not on a hierarchical approach but rather a reticular conception of knowledge. (shrink)

Several paradoxes of infinity have recently featured in this journal involving gases distributed in a denumerable infinite series of compartments. I shall demonstrate in this paper that:a) None of these new paradoxes applies where the gases comply with both Boyle’s law and Avogadro’s law. As several of these new paradoxes expressly require compliance with Boyle’s law, it is unclear, in principle, as to whether there is a plausible model of gas that is able to uphold them all.b) Notwithstanding a), (...) any of the above paradoxes can be reinstated by acknowledging that there are two distinct, non-equivalent concepts of ideal gas. Indeed, the various infinity puzzles actually enable a distinction to be made between the two concepts. (shrink)

In this thesis I examine a number of topics that bear on explanation and understanding in molecular and cell biology, in order to shed new light on explanatory practice in those areas and to find novel angles from which to approach relevant philosophical debates. The topics I look at include mechanism, emergence, cellular complexity, and the informational role of the genome. I develop a perspective that stresses the intimacy of the relations between ontology and epistemology. Whether a phenomenon looks mechanistic, (...) or complex, or indeed emergent, is largely an epistemic matter, yet has an objective basis in features of the world. After reviewing several concepts of mechanism I consider the influential recent account of Machamer, Darden and Craver (MDC). That account makes interesting proposals concerning the relationship between mechanistic explanation and intelligibility, which are consistent with the results of the investigation I undertake into the science surrounding protein folding. In relation to a number of other issues pertaining to biological systems I conclude that the MDC account is insufficiently nuanced, however, leading me to outline an alternative approach to mechanism. This emphasizes the importance of structure—function relations and addresses issues raised by reflection on the nature of cellular complexity. These include the distinction between structure and process and the different possible bases on which system organization may be maintained. The account I give of emergence construes the phenomenon in terms of psychological deficit: phenomena are emergent when we lack the capacity to trace through and model their causal structures using our cognitive schemas. I conclude by developing these ideas into a preliminary and partial account of explanation and understanding. This aspires to cover the significant fraction of work in molecular and cell biology that correlates biological structures, processes and functions by visualizing phenomena and making them imaginable. (shrink)

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts (...) from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease. (shrink)

To explore how molecules became signs I will ask: “What sort of process is necessary and sufficient to treat a molecule as a sign?” This requires focusing on the interpreting system and its interpretive competence. To avoid assuming any properties that need to be explained I develop what I consider to be a simplest possible molecular model system which only assumes known physics and chemistry but nevertheless exemplifies the interpretive properties of interest. Three progressively more complex variants of (...) this model of interpretive competence are developed that roughly parallel an icon-index-symbol hierarchic scaffolding logic. The implication of this analysis is a reversal of the current dogma of molecular and evolutionary biology which treats molecules like DNA and RNA as the original sources of biological information. Instead I argue that the structural characteristics of these molecules have provided semiotic affordances that the interpretive dynamics of viruses and cells have taken advantage of. These molecules are not the source of biological information but are instead semiotic artifacts onto which dynamical functional constraints have been progressively offloaded during the course of evolution. (shrink)

Almost all computational models of the mind and brain ignore details about neurotransmitters, hormones, and other molecules. The neglect of neurochemistry in cognitive science would be appropriate if the computational properties of brains relevant to explaining mental functioning were in fact electrical rather than chemical. But there is considerable evidence that chemical complexity really does matter to brain computation, including the role of proteins in intracellular computation, the operations of synapses and neurotransmitters, and the effects of neuromodulators such as (...) hormones. Neurochemical computation has implications for understanding emotions, cognition, and artificial intelligence. (shrink)

Atoms and molecules are particular kinds of restricted n-body systems, which generally behave as quasi-separable, unlike other n-body systems, e.g., Newtonian ones. The Coulomb repulsion and the Pauli exclusion principle in atoms and molecules are responsible for that separability. Additionally, chemical bonds, especially covalent bonds, enhance the separability of molecules. Independent particle models do not describe atoms and molecules since first-order energy corrections are high. However, these corrections obtained by the first-order perturbation or mean-field strongly converge, (...) implying a one-electron effective potential description. Consequently, stable states of atoms and molecules can be reasonably described by one-electron effective potentials, which strongly differ from other n-body problems. We discuss the peculiarities of the correlation motion of generic systems in the context of the four fundamental forces. In particular, we have shown that the two components (attraction and repulsion) of the electromagnetic force confer a relatively low correlation motion to atoms and molecules. We discuss the physical and chemical nature of atoms and molecules, comparing the degrees of separability between different systems. For example, the separability of Newtonian systems is generally possible in particular classes of restricted systems due to relative mass differences. However, for atoms and molecules, the separability is much broader. (shrink)

We have been using feather development as a model for understanding the molecular basis of pattern formation and to explore the roles of homeoproteins, retinoids and adhesion molecules in this process. Two kinds of homeobox (Hox) protein gradients in the skin have been identified: a ‘microgradient’ within a single feather bud and a ‘macrogradient’ across the feather tract. The asynchronous alignment of different Hox macrogradients establishes a unique repertoire of Hox expression patterns in skin appendages within the integument, (...) designated here as the ‘Hox codes of skin appendages’. It is hypothesized that these Hox codes contribute to the phenotypic determination of skin appendages. High doses of retinoic acid cause a morphological transformation between feather and scale, while low doses of retinoic acid cause an alteration of the axial orientation of skin appendages. We have tested the ability of molecules directly involved in the feather formation process to mediate the action of the Hox codes, and surmise that adhesion molecules are potential candidates. Using specific Fabs to suppress the activity of adhesion molecules, we have found that L‐CAM is involved in the formation of the hexagonal pattern, N‐CAM is involved in mediating dermal condensations, tenascin is involved in feather bud growth and elongation, and integrin β‐1 is essential for epithelial‐mesenchymal interactions. More work is in progress to fully understand the molecular pathways regulating the feather formation process. (shrink)

This thesis attempts to address the philosophical implications of the N, N-Dimethyltryptamine (DMT) research of Dr. Rick Strassman. Strassman concludes that the psychedelic properties of DMT represent a proper biological starting point for discussing spiritual and near-death experiences. My research attempts to incorporate philosophical elements from the philosophy of mind and philosophy of religion/mysticism to give an accurate account of some of the philosophical issues worth exploring for future research. One of the essential patterns in this thesis is to trace (...) the research and conclusions of Strassman, compare them with the philosophical issues in the contemporary philosophy of mind and to address the problems of spiritual qualia and mystical experience. Part of the issue stems from understanding a theoneurological (brain mediated prophetic/spiritual communication) account for spiritual experiences within the framework of naturalism/supernaturalism philosophy. Here, I decipher the problems of qualitative distinctions amongst spiritual and nonspiritual experiences and how consciousness plays an essential role in this process. (shrink)

Abstract.Since the gene splicing debates of the 1980s, the public has been exposed to an ongoing sequence of genetic and reproductive technologies. Many issue areas have outcomes that lose track of people's inner values or engender opposing religious viewpoints defying final resolution. This essay relocates the discussion of what is an acceptable application from the individual to the societal level, examining technologies that stand to address large numbers of people and thus call for policy resolution, rather than individual fiat, in (...) their application. A major source of guidance is the “Genetic Frontiers” series of professional dialogues and conferences held by the National Conference for Community and Justice from 2002 to 2004. Genetic testing, human gene therapy, genetic engineering of plants and animals, and stem cell technology are examined. While differences in perspective on the beginning of life persist, a stepwise approach to the examination of genetic testing reveals areas of general agreement. Stewardship of life, human co‐creativity with the divine, and social justice help define the bounds of application of genetic engineering and therapy; compassionate care plays a major role in establishing stem cell policy. Active, sustained dialogue is a useful resource for enabling sharing of religious values and crystallization of policies. (shrink)

The estrangement between genetic scientists and theologians originating in the 1960s is reflected in novel combinations of human thought (subject) and genes (investigational object), paralleling each other through the universal process known in chaos theory as self-similarity. The clash and recombination of genes and knowledge captures what Philip Hefner refers to as irony, one of four voices he suggests transmit the knowledge and arguments of the religion-and-science debate. When viewed along a tangent connecting irony to leadership, journal dissemination, and the (...) activities of the "public intellectual" and the public at large, the sequence of voices is shown to resemble the passage of genetic information from DNA to mRNA, tRNA, and protein, and from cell nucleus to surrounding environment. In this light, Hefner's inquiry into the voices of Zygon is bound up with the very subject matter Zygon covers. (shrink)

In the target article “How molecules became signs” I offer a molecular “thought experiment” that provides a paradigm for resolving the major incompatibilities between biosemiotic and natural science accounts of living processes. To resolve these apparent incompatibilities I outline a plausible empirically testable model system that exemplifies the emergence of chemical processes exhibiting semiotic causal properties from basic nonliving chemical processes. This model system is described as an autogenic virus because of its virus-like form, but its nonparasitic (...) self-repair and reproductive dynamics. The 16 commentaries responding to this proposal recognize its material plausibility but are divided on its value in resolving this basic biosemiotic challenge. In response, I have addressed some of the most serious criticisms raised and have attempted to diagnose the major sources of incompatible assumptions that distinguish the autogenic paradigm from other major paradigms. In particular, I focus on four main issues: the significance of the shift from a cellular to a viral perspective, the relevance of intrinsic versus extrinsic initiation and channeling of interpretive work, the insufficiency of molecular replication as a basis for grounding biological semiosis, and a (universal?) three step scaffolding logic that enables referential displacement of sign vehicle properties without loss of referential continuity (as exemplified by DNA-protein relations). Although I can’t conclude that this is the only way that biosemiotic properties can emerge from physical-chemical relations that otherwise lack these properties, I contend that this approach offers a biologically plausible demonstration that it is possible. (shrink)

Aristotle is oftentimes viewed through a strictly philosophical lens as heir to Plato and has having introduced logical rigor where an emphasis on the theory of Forms formerly prevailed. It must be appreciated that Aristotle was the son of a physician, and that his inculcation of the thought of other Greek philosophers addressing health and the natural elements led to an extremely broad set of biologically- and medically-related writings. As this article proposes, Aristotle deepened the fourfold theory of the elements (...) with anatomic and physiologic observations. In books like History of Animals, Parts of Animals, and the lost Anatomai, he actively dissected organisms and recorded his findings. The corpus of medically-related literature Aristotle developed had a direct influence on subsequent Greek thinkers, including Galen, and on Medieval Islamic and modern Western practitioners such as William Harvey. Aristotle's ideas continue to influence modern medical thinkers in Europe and America through both his interpretation by European philosophers gaining the attention of medical humanists, and his writings' enduring impact on medical researchers balancing scientific with more personalistic approaches to medicine. (shrink)