There is consensus within the chemosciences that olfactory perception is of the molecular structure of chemical compounds, yet within philosophical theories of smell there is little agreement about the nature of smell. The paper critically assesses the current state of debate regarding smells within philosophy in the hopes of setting it upon firm scientific footing. The theories to be covered are: Naïve Realism, Hedonic Theories, Process Theory, Odor Theories, and non-Objectivist Theories. The aforementioned theories will be evaluated based (...) on their explanations of the (a) the olfactory quality of a smell, (b) smells as distal entities, and (c) our experience of smells as intentional objects. The paper concludes with a defense of Molecular Structure Theory that demonstrating its superiority in accounting for each of these three aspects of smell. (shrink)

Perhaps the hottest topic in the philosophy of chemistry is that of the relationship between chemistry and physics. The problem finds one of its main manifestations in the debate about the nature of molecular structure, given by the spatial arrangement of the nuclei in a molecule. The traditional strategy to address the problem is to consider chemical cases that challenge the definition of molecular structure in quantum–mechanical terms. Instead of taking that top-down strategy, in this paper (...) we face the problem of the reduction of molecular structure to quantum mechanics from a bottom-up perspective: our aim is to show how the theoretical peculiarities of quantum mechanics stand against the possibility of molecular structure, defined in terms of the spatial relations of the nuclei conceived as individual localized objects. We will argue that, according to the theory, quantum “particles” are not individuals that can be identified as different from others and that can be reidentified through time; therefore, they do not have the ontological stability necessary to maintain the relations that can lead to a spatially definite system with an identifiable shape. On the other hand, although quantum chemists use the resources supplied by quantum mechanics with successful results, this does no mean reduction: their “approximations” add certain assumptions that are not justified in the context of quantum mechanics or are even inconsistent with the very formal structure of the theory. (shrink)

Whether or not quantum physics can account for molecular structure is a matter of considerable controversy. Three of the problems raised in this regard are the problems of molecular structure. We argue that these problems are just special cases of the measurement problem of quantum mechanics: insofar as the measurement problem is solved, the problems of molecular structure are resolved as well. In addition, we explore one consequence of our argument: that claims about the (...) reduction or emergence of molecular structure cannot be settled independently of the choice of a particular resolution to the measurement problem. Specifically, we consider how three standard putative solutions to the measurement problem inform our under- standing of a molecule in isolation, as well as of chemistry’s relation to quantum physics. (shrink)

The type-level abstraction is a formal way to represent molecular structures in biological practice. Graphical representations of molecular structures of biological objects are also used to identify functional processes of things. This paper will reveal that category theory is a formal mathematical language not only to visualize molecular structures of biological objects as type-level abstraction formally but also to understand how to infer biological functions from the molecular structures of biological objects. Category theory is a toolkit (...) to understand biological knowledge at the type-level formally, not individual token-level, as well as typical heuristic strategies in molecular biology. (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)

One of the most plausible and widely discussed examples of strong emergence is molecular structure. The only detailed account of it, which has been very influential, is due to Robin Hendry and is formulated in terms of downward causation. This paper explains Hendry’s account of the strong emergence of molecular structure and argues that it is coherent only if one assumes a diachronic reflexive notion of downward causation. However, in the context of this notion of downward (...) causation, the strong emergence of molecular structure faces three challenges that have not been met and which have so far remained unnoticed. First, the putative empirical evidence presented for the strong emergence of molecular structure equally undermines supervenience, which is one of the main tenets of strong emergence. Secondly, it is ambiguous how the assumption of determinate nuclear positions is invoked for the support of strong emergence, as the role of this assumption in Hendry’s argument can be interpreted in more than one way. Lastly, there are understandings of causation which render the postulation of a downward causal relation between a molecule’s structure and its quantum mechanical entities, untenable. (shrink)

In this article I examine several related views expressed by Robin Hendry concerning molecular structure, emergence and chemical bonding. There is a long-standing problem in the philosophy of chemistry arising from the fact that molecular structure cannot be strictly derived from quantum mechanics. Two or more compounds which share a molecular formula, but which differ with respect to their structures, have identical Hamiltonian operators within the quantum mechanical formalism. As a consequence, the properties of all (...) such isomers yield precisely the same calculated quantities such as their energies, dipole moments etc. The only means through which the difference between the isomers can be recovered is to build their structures into the quantum mechanical calculations, something that is carried out by the application of the Born-Oppenheimer approximation. Consequently, it has been argued by many authors that molecular structure is written in ‘by hand’ rather than derived. Robin Hendry is one such author, but he goes a great deal further by proposing that this situation implies the existence of emergence and downward causation. In the current article I argue that there are alternative explanations which render emergence and downward causation redundant. Such an alternative lies in the notion of quantum decoherence and the appeal to work in the foundations of physics, which posits that the various isomers exist as a superposition until their wavefunctions are collapsed either by observation or by interacting with their environment. Hendry also alludes to a debate among chemists as to whether chemical bonds are real or not, in the sense of directional connections between two or more nuclei in any given molecule. I reject this view and propose that the structural and energetic views of chemical bonding, that have been discussed by some philosophers of chemistry including Hendry, do not refer to any essential ontological differences. I agree that chemists view bonding in a more realistic fashion and may consider bonds to be in some senses real, while physicists may consider bonding in more abstract energetic terms. However, I do not believe that such differences in scientific practice and attitudes should be considered to offer a window as to the ontological status of bonding or whether bonding is real. Finally, I discuss the kinetic energy school of chemical bonding which would seem to challenge any notion of bonds as directional entities, since bonding is no longer regarded as being primarily due to the build-up of electron density between nuclei. (shrink)

Any comprehensive theory of smell must account for (1) the distal nature of smells, (2) how smells are represented within odorous experiences, and (3) the olfactory quality of smells. Molecular Structure Theory (MST) and more recent developments arguably provide an account of these questions. It has been argued that we can account for (3) olfactory quality in light of the molecular structure of chemical compounds that compose the odorant plumes which we perceive as (1) distal mereological (...) complex perduring objects within smellscapes. Additionally it has been argued that olfactory perceptual and cognitive processing implements (2) a non-conceptual representational system that is incompatible with the compositional format employed by semantic processing systems. The theory I have been developing generates a comprehensive account of smell by treating these as nested issues inherent in for the nature of smell (Young, 2016, 2019a-d, 2020). However, the chapter assesses the adequacy of my theory by addressing recent criticisms of MST’s account of olfactory quality (Barwich 2014, 2015; Keller 2015, 2017), the need for positing odor objects (Barwich 2019), and a possible incompatibility between my account of synchronic odor perception in MST and more recent developments focusing on the diachronic experiences of smellscapes. (shrink)

In a recent article entitled “The problem of molecular structure just is the measurement problem”, Alexander Franklin and Vanessa Seifert argue that insofar as the quantum measurement problem is solved, the problems of molecular structure are resolved as well. The purpose of the present article is to show that such a claim is too optimistic. Although the solution of the quantum measurement problem is relevant to how the problem of molecular structure is faced, such (...) a solution is not sufficient to account for the structure of molecules as understood in the field of chemistry. (shrink)

What chemists take as molecular structure is a theoretical construct based on the concepts of chemical bond, atoms in molecules, etc. and hence it should be distinguished from tangible structures around us. The practical adequacy of it has been demonstrated by the established method of retro-synthetic analysis, for instance. But it is not derived a priori from quantum mechanical treatments of the molecule and criticized for being irrelevant to the reality of the molecule. There is persistent skepticism about (...) it. The present study aims to overcome this skepticism by having recourse to the concepts of affordance and phenomenal field. The basic idea of our approach is suggested by the following statement of Niels Bohr: ‘evidence obtained under different experimental conditions cannot be comprehended within a single picture but must be regarded as complementary in the sense that only the totality of the phenomena exhausts the possible information about the objects’. This implies that we should take account of a context in which the cognition of a fact arises when we think about human activities including science. This can be realized by invoking affordances of a complex such as {agent, devices, methods, substances, surroundings}. That is to say, affordances are context-relative dispositional attributes of {agent-material world} complexes as is asserted by Harré and Llored. The phenomenal field is a conceptual device which schematizes the contextual aspect of affordance and, more importantly, serves as a link between the concept of affordance and Kant’s theory of knowledge, by which alone affordances are realized as the dispositional properties of {agent-material world} complexes. Because affordances become actualized in various phenomenal fields, affordances of one and the same object may well be distinct from one another. In conclusion we can take that molecular structure is the affordance of a complex that includes a chemist who is engaged in organic synthesis, whereas a quantum mechanical picture of the molecule may be one of the possible affordances of a complex that includes a quantum chemist who cares about electronic states of the molecule. (shrink)

What chemists take as molecular structure is a theoretical construct based on the concepts of chemical bond, atoms in molecules, etc. and hence it should be distinguished from tangible structures around us. The practical adequacy of it has been demonstrated by the established method of retro-synthetic analysis, for instance. But it is not derived a priori from quantum mechanical treatments of the molecule and criticized for being irrelevant to the reality of the molecule. There is persistent skepticism about (...) it. The present study aims to overcome this skepticism by having recourse to the concepts of affordance and phenomenal field. The basic idea of our approach is suggested by the following statement of Niels Bohr: ‘evidence obtained under different experimental conditions cannot be comprehended within a single picture but must be regarded as complementary in the sense that only the totality of the phenomena exhausts the possible information about the objects’. This implies that we should take account of a context in which the cognition of a fact arises when we think about human activities including science. This can be realized by invoking affordances of a complex such as {agent, devices, methods, substances, surroundings}. That is to say, affordances are context-relative dispositional attributes of {agent-material world} complexes as is asserted by Harré and Llored. The phenomenal field is a conceptual device which schematizes the contextual aspect of affordance and, more importantly, serves as a link between the concept of affordance and Kant’s theory of knowledge, by which alone affordances are realized as the dispositional properties of {agent-material world} complexes. Because affordances become actualized in various phenomenal fields, affordances of one and the same object may well be distinct from one another. In conclusion we can take that molecular structure is the affordance of a complex that includes a chemist who is engaged in organic synthesis, whereas a quantum mechanical picture of the molecule may be one of the possible affordances of a complex that includes a quantum chemist who cares about electronic states of the molecule. (shrink)

What chemists take as molecular structure is a theoretical construct based on the concepts of chemical bond, atoms in molecules, etc. and hence it should be distinguished from tangible structures around us. The practical adequacy of it has been demonstrated by the established method of retro-synthetic analysis, for instance. But it is not derived a priori from quantum mechanical treatments of the molecule and criticized for being irrelevant to the reality of the molecule. There is persistent skepticism about (...) it. The present study aims to overcome this skepticism by having recourse to the concepts of affordance and phenomenal field. The basic idea of our approach is suggested by the following statement of Niels Bohr: ‘evidence obtained under different experimental conditions cannot be comprehended within a single picture but must be regarded as complementary in the sense that only the totality of the phenomena exhausts the possible information about the objects’. This implies that we should take account of a context in which the cognition of a fact arises when we think about human activities including science. This can be realized by invoking affordances of a complex such as {agent, devices, methods, substances, surroundings}. That is to say, affordances are context-relative dispositional attributes of {agent-material world} complexes as is asserted by Harré and Llored. The phenomenal field is a conceptual device which schematizes the contextual aspect of affordance and, more importantly, serves as a link between the concept of affordance and Kant’s theory of knowledge, by which alone affordances are realized as the dispositional properties of {agent-material world} complexes. Because affordances become actualized in various phenomenal fields, affordances of one and the same object may well be distinct from one another. In conclusion we can take that molecular structure is the affordance of a complex that includes a chemist who is engaged in organic synthesis, whereas a quantum mechanical picture of the molecule may be one of the possible affordances of a complex that includes a quantum chemist who cares about electronic states of the molecule. (shrink)

What chemists take as molecular structure is a theoretical construct based on the concepts of chemical bond, atoms in molecules, etc. and hence it should be distinguished from tangible structures around us. The practical adequacy of it has been demonstrated by the established method of retro-synthetic analysis, for instance. But it is not derived a priori from quantum mechanical treatments of the molecule and criticized for being irrelevant to the reality of the molecule. There is persistent skepticism about (...) it. The present study aims to overcome this skepticism by having recourse to the concepts of affordance and phenomenal field. The basic idea of our approach is suggested by the following statement of Niels Bohr: ‘evidence obtained under different experimental conditions cannot be comprehended within a single picture but must be regarded as complementary in the sense that only the totality of the phenomena exhausts the possible information about the objects’. This implies that we should take account of a context in which the cognition of a fact arises when we think about human activities including science. This can be realized by invoking affordances of a complex such as {agent, devices, methods, substances, surroundings}. That is to say, affordances are context-relative dispositional attributes of {agent-material world} complexes as is asserted by Harré and Llored. The phenomenal field is a conceptual device which schematizes the contextual aspect of affordance and, more importantly, serves as a link between the concept of affordance and Kant’s theory of knowledge, by which alone affordances are realized as the dispositional properties of {agent-material world} complexes. Because affordances become actualized in various phenomenal fields, affordances of one and the same object may well be distinct from one another. In conclusion we can take that molecular structure is the affordance of a complex that includes a chemist who is engaged in organic synthesis, whereas a quantum mechanical picture of the molecule may be one of the possible affordances of a complex that includes a quantum chemist who cares about electronic states of the molecule. (shrink)

According to scientific realists, the predictive success of mature theories provides a strong epistemic basis for thinking that such theories are approximately true. However, we know that many theories once regarded as well-confirmed and predictively successful were eventually replaced with successor theories, and some claim this undermines the epistemic confidence we should have in the approximate truth of current science. Selective scientific realists in turn argue that if one can show that the predictive success of some rejected theory T is (...) a function of theoretical claims consistent with current science, then T’s failure doesn’t undermine the claim that current successful theories are approximately true. As such, Selective Scientific Realism (SSR) can be tested through historical examples. Showing that the predictive success of a failed theory is the result of theoretical features later rejected provides a counterexample to SSR. Conversely, SSR is supported if its explanation of the predictive success of failed theories--namely, that the factors which lead to predictive success in the failed theory survive in the successor theory--is able to handle a wide array of historical cases. (shrink)

Gap junctions are ubiquitous plasma membrane specializations that allow cells to exchange small molecules and ions directly. The isolation, biochemical characterization and molecular cloning of the major protein of rat liver gap junctions lead to a clearer view of these membrane zones that allow cells to ‘talk’ to each other and co‐ordinate their activities in tissues and organs.

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)

In this article I examine several related views expressed by Robin Hendry concerning molecular structure, emergence and chemical bonding. There is a long-standing problem in the philosophy of chemistry arising from the fact that molecular structure cannot be strictly derived from quantum mechanics. Two or more compounds which share a molecular formula, but which differ with respect to their structures, have identical Hamiltonian operators within the quantum mechanical formalism. As a consequence, the properties of all (...) such isomers yield precisely the same calculated quantities such as their energies, dipole moments etc. The only means through which the difference between the isomers can be recovered is to build their structures into the quantum mechanical calculations, something that is carried out by the application of the Born-Oppenheimer approximation. Consequently, it has been argued by many authors that molecular structure is written in ‘by hand’ rather than derived. Robin Hendry is one such author, but he goes a great deal further by proposing that this situation implies the existence of emergence and downward causation. In the current article I argue that there are alternative explanations which render emergence and downward causation redundant. Such an alternative lies in the notion of quantum decoherence and the appeal to work in the foundations of physics, which posits that the various isomers exist as a superposition until their wavefunctions are collapsed either by observation or by interacting with their environment.Hendry also alludes to a debate among chemists as to whether chemical bonds are real or not, in the sense of directional connections between two or more nuclei in any given molecule. I reject this view and propose that the structural and energetic views of chemical bonding, that have been discussed by some philosophers of chemistry including Hendry, do not refer to any essential ontological differences. I agree that chemists view bonding in a more realistic fashion and may consider bonds to be in some senses real, while physicists may consider bonding in more abstract energetic terms. However, I do not believe that such differences in scientific practice and attitudes should be considered to offer a window as to the ontological status of bonding or whether bonding is real. Finally, I discuss the kinetic energy school of chemical bonding which would seem to challenge any notion of bonds as directional entities, since bonding is no longer regarded as being primarily due to the build-up of electron density between nuclei. (shrink)

According to classical molecular chemistry, molecules have a structure, that is, they are sets of atoms with a definite arrangements in space and held together by chemical bonds. The concept of molecular structure is central to modern chemical thought given its impressive predictive power. It is also a very useful concept in chemistry education, due to its role in the rationalization and visualization of microscopic phenomena. However, such a concept seems to find no place in the (...) ontology described by quantum mechanics, since it appeals to classical notions such as the position of the atomic nuclei or the individuality of electrons. Although this problem has attracted the attention of several authors, the discussion is far from settled. Some authors adopt an explicitly reductionist position and advocate to reconstruct the concept of molecular structure within the framework of the quantum theory. Others, although acknowledging the conceptual discontinuity between quantum mechanics and molecular chemistry, keep the hope of future reduction alive. From an explicitly non-reductionist position, on the contrary, others authors conceive molecular structure as an emergent phenomenon. The purpose of this article is to propose a different line of argumentation to address this problem. By contrast to reduction and emergence, the admission of a multiplicity of ontologies, not necessarily linked by hierarchical connections, cancels the need of finding a relation of dependence between the molecular level and the quantum level. This ontologically pluralist position can be applied to the issue of molecular structure, in order to argue that it is possible to admit the existence of structure in the ontology of molecular chemistry, in spite of the fact that it does not exist in the quantum world. (shrink)

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)

Część II pracy objaśnia molekularne podłoże pamięci w oparciu o założenia Neuro-Elektro- Dynamiki postulowanej przez Aura i Yoga. Wskazano na biofizyczne mechanizmy generacji wspomnień, refleksji i odczuć dzięki efatycznym sprzężeniom synaptycznym, spełniającym wymagania indukowania impresjonów Vadakkana. Wykazano, że działanie mechanizmu selekcyjnego WTA może być dobrym modelem opisującym funkcję przełączania uwagi. Wskazano na relacje między pamięcią roboczą, krótkoterminową i trwałą i ich spójność z molekularnymi procesami zapamiętywania i rozpoznawania wzorców. Wskazano, że trwała pamięć epizodyczna wymaga konwersji sekwencji czasowych sygnałów bottom-up do (...) rozkładu przestrzennego tworzącego impresjony dynamiczne. Odwrotna transformacja tych impresjonów umożliwia przypominanie epizodów z przeszłości. Omówiono znaczenie wrodzonych struktur sieci neuronowych zapewniających dziedziczenie zachowań instynktownych. Struktury te nie wykluczają zachowania plastyczności umysłu umożliwiającej efektywne uczenie. (shrink)

The concepts of molecular structure and molecular shape are ubiquitous in the chemical literature, where they are often taken as synonyms, with unavoidable drawbacks in chemistry teaching. A third concept, molecular topology, is less frequent but it is a reference term in molecular research domains such as Quantitative Structure–Activity Relationships. The present paper proposes an epistemological analysis of these three notions, aimed at clarifying the nature of their relationship, as well as the contiguities and (...) differences between them. At first, we discuss the various acceptations of the terms molecular structure and molecular shape. Then, we examine some crucial milestones in the history of these concepts and we analyse the relationship between structure, shape and topology from an epistemological viewpoint. We point out the distinguishing features of each concept and we show that their semantic openness, that may be fruitful in a specialized context, turns into a source of incoherence and inaccuracy in the teaching context, fostered by the misleading use of these terms made by textbooks. Eventually, we propose a criterion fit to discriminate between the conceptual domains of molecular shape, molecular structure and molecular topology. (shrink)

Traditional approaches to theory structure and theory change in science do not fare well when confronted with the practice of certain fields of science. We offer an account of contemporary practice in molecular biology designed to address two questions: Is theory change in this area of science gradual or saltatory? What is the relation between molecular biology and the fields of traditional biology? Our main focus is a recent episode in molecular biology, the discovery of enzymatic (...) RNA. We argue that our reconstruction of this episode shows that traditional approaches to theory structure and theory change need considerable refinement if they are to be defended as generally applicable. 1This paper emerged from discussions between us, and we are both equally responsible for its errors. We would like to thank Yvonne Paterson for helpful comments. (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)

The present paper has two aims. First, we reconstruct the core of molecular genetics (MOLGEN) i.e. the array of theoretical assumptions which underly all or most applications of molecular genetics. Second, we define a reduction relation p reducing character-factor genetics (CFG) to MOLGEN. That p is a reduction relation is proved by establishing that p satisfies the two major conditions which are discussed in the literature as necessary or ‘essential’ for reduction. This substantiates the claim that molecular (...) genetics is ‘better than’ or ‘more progressive-than’ character-factor genetics-which is commonly held true today. The paper continues, and relies heavily on the definitions given in part 1 (Balzer and Dawe [1985]). The enumeration of the definitions and sections in the present paper continues that of part 1. References to definitions with numbers smaller than 8 and to sections number I-4 always refer to part 1. (shrink)

A large proportion of tumour‐associated antigens seem to be determined by carbohydrate structures. Advances in the study of the antigenicity of cell‐surface carbohydrates have been hampered by the absence of advanced monoclonal hybridoma technology comparable to that available for the study of protein antigens. Monoclonal antibodies have been raised against a carbohydrate epitope (43–9F) that is associated with the proliferative features of squamous lung carcinomas. These were used in turn to generate anti‐idiotype antibodies with homology to 43–9F. The method and (...) its possible applications are described, together with a procedure to detect rare cell membrane variants within large populations. (shrink)

A molecular dynamics (MD) approach which determines automatically the complex magnetic structures in itinerant electron systems is applied to Fe-Cr alloys with use of 250 atoms in a MD unit cell (5×5×5 bcc lattice). It is demonstrated that the Fe-Cr alloys show various complex magnetic structures due to competing interactions: the collinear ferromagnetism (F) of matrix Fe with antiparallel Cr moments beyond 80 at.% Fe, the coexistence of non-collinear structure of Cr and collinear F of Fe between 50 (...) and 75 at.% Fe, the coexistence of broken antiferromagnetism (AF) of Cr and the F of Fe between 25 and 45 at.% Fe, the coexistence of F of Fe and antiferromagnetic long-range order of Cr around 20 at.% Fe, the AF of Cr matrix with non-collinear Fe moments (spin-glass like structure) between 5 and 15 at.% Fe, and the AF below 5 at.% Fe. In the concentration region between 5 and 20 at.% Fe, ferromagnetic Fe pairs which are stabilized with different amplitudes of local moments are found. The magnetic phase diagram and calculated magnetic moments are shown to be consistent with the neutron, Mössbauer, and photoemission experiments. (shrink)

Advances in molecular technologies have the potential to help remedy health inequities through earlier detection and prevention; if, however, their delivery and uptake are not more carefully considered, there is a very real risk that existing inequities in access and use will be further exacerbated. We argue this risk relates to the way that information and knowledge about the technology is both acquired and shared, or not, between health practitioners and their patients.A healthcare system can be viewed as a (...) complex social network comprising individuals with different worldviews, hierarchies, professional cultures and subcultures and personal beliefs, both for those giving and receiving care. When healthcare practitioners are not perceived as knowledge equals, they would experience informational prejudices, and the result is that knowledge dissemination across and between them would be impeded. The uptake and delivery of a new technology may be inequitable as a result. Patients would also experience informational prejudice when they are viewed as not being able to understand the information that is presented to them, and information may be withheld.Informational prejudices driven by social relations and structures have thus far been underexplored in considering equitable implementation and uptake of new molecular technologies. Every healthcare interaction represents an opportunity for experiencing informational prejudice, and with it the risk of being inappropriately informed for undertaking such screening or testing. Making knowledge acquisition and information dissemination, and experiences of informational prejudice, explicit through sociologically framed investigations would extend our understandings of equity, and offer ways to affect network relationships and structures that support equity in delivery and uptake. (shrink)

'Structure' and 'function' are both ambiguous terms. Discriminating different meanings of these terms sheds light on research and explanatory practice in molecular biology, as well as clarifying central theoretical concepts in the life sciences like the sequence-structure-function relationship and its corresponding scientific "dogmas". The overall project is to answer three questions, primarily with respect to proteins: What is structure? What is function? What is the relation between structure and function? The results of addressing these questions (...) lead to an answer to the title question, what the statement 'structure determines function' means. (shrink)

In the debate on causal explanation in biology, in the past two decades largely influenced by the new mechanist approach, the concept of a pathway has recently reemerged as a promising research agenda, 551-572, 2018; The British Journal for the Philosophy of Science, 72, 131-158, 2021). Ross’ account of biological explanation differentiates several autonomous types of causal structures that play explanatory and other roles across the life sciences. NM, however, prioritizes mechanisms as vehicles of biological explanations. According to this program, (...) the causal architecture of biological pathways and other causal structures, such as cascades and processes, can be interpreted with at least one of the NM’s mechanism concepts. In other words, these alternative causal structures are not sufficiently distinctive to merit the explanatory autonomy with regard to the NM corresponding concepts. We examine the explanatory practice of molecular biology and concur with Ross that there are indeed distinct types of causal structures, not all falling under the concept of a mechanism. Nonetheless, we show that the concept of mechanism is referring to a privileged causal structure, at the center of explanatory efforts in molecular biology. Pathways and other causal concepts, while somewhat distinct from mechanisms themselves, are explanatorily relevant to the degree in which they exhibit mechanistic features, are parts of a mechanistic architecture, or may lead to a mechanistic arrangement. What emerges in that manner is a hierarchy of causal structures with mechanisms at the explanatory top, and lower levels differing in the degree in which they contribute to mechanistic arrangements. (shrink)

Theoretical frames for analyzing information in biological and molecular multicomponent structures are proposed. The mathematical foundations of the proposal are presented. Both the information encoded in structures is defined and the method of calculating the amount of this information is introduced. The proposed approach is applied to the operation of a molecular multicomponent machine.

In a recent essay in this journal, John Maynard Smith argues that the often expressed idea that the genome is the repository of meaningful information is not merely a heuristically useful metaphor. Instead, he contends, it is a central idea in contemporary microbiology. While I am in general agreement with Maynard Smith on this issue, his account suffers, I believe, from using an inappropriate concept of ‘information.’ One result of this is that the concept of genomic information becomes burdened by (...) a conceptual load that the biological facts cannot support. When, however, the appropriate concept of information is used, then these burdens are shed, and the result is an account that is in substantial agreement with the heart of Maynard Smith's thesis. (shrink)

Many biologically active compounds including neurotransmitters, metabolic precursors, and certain drugs are accumulated intracellularly by transporters that are coupled to the transmembrane Na+ gradient. Amino acid neurotransmitter transporters play a key role in the regulation of extracellular amino acid concentrations and termination of neurotransmission in the CNSAbbreviations: CNS, central nervous system; GABA, γ‐aminobutyric acid; cDNA, complementary deoxyribonucleic acid; mRNA, messenger ribonucleic acid; NMDA, N‐methyl‐D‐aspartate; PKC, protein kinase C; PMA, phorbol 12‐myristate 13‐acetate; DAG, diacyl glycerol; R59022, DAG kinase inhibitor; AA, arachidonic (...) acid; ACHC, cis‐3‐aminocyclohexanecarboxylic acid; GAT‐A, ACHC‐sensitive GABA transporter; GAT‐B, β‐alanine‐sensitive GABA transporter; GLY‐1 and GLYT‐1, glycine transporters; PROT‐1, proline transporter; BGT‐1, betaine transporter.. Transporters for the major amino acid neurotransmitters glutamate, GABA, and glycine are found in both neurons and glial cells. Recent work has resulted in the identification of cDNAs encoding several amino acid neurotransmitter transport proteins, all of which belong to the Na+‐and Cl−‐dependent transporter gene family. The diversity of this family suggests a degree of transporter heterogeneity that is greater than that indicated by biochemical and pharmacological studies. (shrink)