Interpretation of experiments involving use of vacuum ultraviolet radiation to effect ionization of N 2 in terms of measurements of a molecular orbital is erroneous.

In my previous article on the benzene problem, I described how Pauling's valence bond (resonance) theory, sometimes regarded as a modernized version of Kekule's oscillation hypothesis, came to be accepted by chemists by the end of World War II. But the alternative molecular orbital theory, proposed by Mulliken, had already been developed and was regarded as quantitatively superior by many quantum chemists, though it was not as easy to visualize and did not seem to harmonize as well with (...) traditional chemical concepts. During the 1950s and 1960s, thanks to the efforts of Charles Coulson and many other theorists, the molecular orbital approach not only dominated theoretical discussions but also started to be accepted by the chemical community as a whole and became the preferred description for benzene. Possible reasons were: its greater calculational convenience when applied to large molecules; better expository methods directed toward chemists; the spectacular success of the Woodward-Hoffmann rules for pericyclic reactions and Fukui's frontier orbital theory; and the development of a general theory of aromaticity, which predicted properties of similar molecules such as cyclobutadiene (C4H4). The relative importance of these reasons is explored through a mail survey of chemists. (shrink)

Mulliken proposed an Aufbauprinzip for the molecules on the basis of molecular spectroscopy while establishing, point by point, his concept of molecular orbit. It is the concept of electronic state which becomes the lever for his attribution of electronic configurations to a molecule. In 1932, the concept of orbit was transmuted into that of the molecular orbital to integrate the probabilistic approach of Born and to achieve quantitative accuracy. On the basis of the quantum works of (...) Hund, Wigner, Lennard-Jones and group theory, he suggested the fragment method to establish the characteristics of molecular orbital for polyatomic molecules. These developments make it possible to bring elements of thought on the relation between a molecular whole and its parts . An operational realism combined with the second law of thermodynamics can pave the way for interesting tracks in the mereological study of chemical systems. (shrink)

In this paper we will address the problem of the existence of orbitals by analyzing the relationship between molecular chemistry and quantum mechanics. In particular, we will consider the concept of orbital in the light of the arguments that deny its referring character. On this basis, we will conclude that the claim that orbitals do not exist relies on a metaphysical reductionism which, if consistently sustained, would lead to consequences clashing with the effective practice of science in its (...) different branches. (shrink)

The present work is a comment of a recent paper by Fortin and coauthors in which the authors propose the introduction of Bohmian mechanics in the philosophy of chemistry and the use of standard quantum mechanics as a mere instrument of prediction. This way would allow overcoming the obstacles found in linking molecular chemistry and quantum mechanics. Starting from some remarks on the orbital concept, we highlight and discuss some general issues that need to be taken into account (...) when two scientific theories coexist within the same investigation field, i.e. SQM and BM. (shrink)

This manuscript explores the orthogonality constraints on configurations and orbitals subject to the property that states are mutually orthogonal. The orthogonality constraints lead to properties that affect the description of chemical systems. When states are described as linear combinations of configurations, the coefficient matrix diagonalises S−1H. Therefore, single-configuration states are only possible in one-electron systems: non-orthogonal configurations yield single-configuration states only if S−1H is diagonal, but this would violate the orthonormalisation constraint. Further, the coefficient matrix is not constrained to be (...) square. Similarly, the orbitals used to construct configurations may also be orthogonal or non-orthogonal; orbitals are only required to be mutually orthogonal at the one-electron limit. Orthogonal orbitals are generally preferred due to their mathematical and conceptual simplicity, leading to fictitious unoccupied orbitals. Since the Fock operator is orthogonality agnostic, non-orthogonal orbitals can be generated by solving the Fock equation independently for each electron; the virtual orbitals produced by this conception are true excitation orbitals as they are eigensolutions of the Fock operator. Additionally, we show that the number of molecular orbitals generated is not restricted to the number of atomic orbitals employed in the computation. This manuscript explores the mathematical relationships that need to be satisfied under the various orthogonality regimes. We also present mathematical relationships that provide results that are independent of the orthogonality approximation within a particular computational method. (shrink)

This article examines Guattari’s broad political investment with regard to a molecular revolution of institutions through his reflection on one complex event, the 22nd of March Movement at Nanterre. I want to consider this example for two reasons. First, it is general enough to provide a non-clinical foundation for specific kinds of innovations that preoccupy many of his readers who comment on these issues and centre their work on historical clinical examples within the trajectory of institutional psychotherapy from Saint-Alban (...) to La Borde. And second, it is not so far divorced from the orbit of cure where institutional analysts cut their teeth, as it were, in the early 1960s left-wing student groups devoted to health issues. The question of cure, here, remains tied to the recognition of the influence of an institution and how it may be changed, but shifts in my example from clinic to campus and factory and, ultimately, to all of French society. (shrink)

Heisenberg’s explanation of how two coupled oscillators exchange energy represented a dramatic success for his new matrix mechanics. As matrix mechanics transmuted into wave mechanics, resulting in what Heisenberg himself described as …an extraordinary broadening and enrichment of the formalism of the quantum theory , the term resonance also experienced a corresponding evolution. Heitler and London’s seminal application of wave mechanics to explain the quantum origins of the covalent bond, combined with Pauling’s characterization of the effect, introduced resonance into the (...) chemical lexicon. As the Valence Bond approach gave way to a soon-to-be dominant Molecular Orbital method, our understanding of the term resonance, as it might apply to our understanding the chemical bond, has also changed. (shrink)

The rapidly changing field of genetics affects society through advances in health-care and through implications of genetic research. This study addresses the impacts of new genetic discoveries and technologies on different segments of today's society. The book begins with a chapter on genetic complexity, and subsequent chapters discuss moral and ethical questions arising from today's genetics from the perspectives of health care professionals, the media, the general public, special interest groups and commercial interests.

BackgroundThe pursuit of a cure for HIV is a high priority for researchers, funding agencies, governments and people living with HIV (PLWH). To date, over 250 biomedical studies worldwide are or have been related to discovering a safe, effective, and scalable HIV cure, most of which are early translational research and experimental medicine. As HIV cure research increases, it is critical to identify and address the ethical challenges posed by this research.MethodsWe conducted a scoping review of the growing HIV cure (...) research ethics literature, focusing on articles published in English peer-reviewed journals from 2013 to 2021. We extracted and summarized key developments in the ethics of HIV cure research. Twelve community advocates actively engaged in HIV cure research provided input on this summary and suggested areas warranting further ethical inquiry and foresight via email exchange and video conferencing.DiscussionDespite substantial scholarship related to the ethics of HIV cure research, additional attention should focus on emerging issues in six categories of ethical issues: (1) social value (ongoing and emerging biomedical research and scalability considerations); (2) scientific validity (study design issues, such as the use of analytical treatment interruptions and placebos); (3) fair selection of participants (equity and justice considerations); (4) favorable benefit/risk balance (early phase research, benefit-risk balance, risk perception, psychological risks, and pediatric research); (5) informed consent (attention to language, decision-making, informed consent processes and scientific uncertainty); and (6) respect for enrolled participants and community (perspectives of people living with HIV and affected communities and representation).ConclusionHIV cure research ethics has an unfinished agenda. Scientific research and bioethics should work in tandem to advance ethical HIV cure research. Because the science of HIV cure research will continue to rapidly advance, ethical considerations of the major themes we identified will need to be revisited and refined over time. (shrink)

El propósito del presente trabajo consiste en abordar la pregunta por la ontología de la química cuántica. Para ello nos concentraremos en el concepto de enlace químico desde la perspectiva de los dos enfoques a través de los cuales la ecuación de Schrödinger se aplica a los sistemas químicos moleculares: la teoría del enlace de valencia (EV) y la teoría del orbital molecular (OM). Sobre la base de la presentación de ambos enfoques y su comparación, señalaremos que, a (...) pesar de su denominación tradicional, no pueden considerarse estrictamente como teorías científicas, sino que se ajustan mejor a la noción de modelo; en particular, son modelos que incorporan conceptos y leyes tanto del ámbito de la mecánica cuántica como del de la química estructural. Estas consideraciones nos permitirán argumentar que la química cuántica no posee un referente ontológico autónomo, sino que se trata de un ámbito científico cuya vigencia descansa sobre su éxito práctico en el cálculo y la predicción. Finalmente, indicaremos de qué modo los enfoques EV y OM del enlace químico abren una nueva perspectiva respecto de la noción misma de modelo en ciencias empíricas. (shrink)

Most contemporary chemists consider quantum mechanics to be the foundational theory of their discipline, although few of the calculations that a strict reduction would seem to require have ever been produced. In this essay I discuss contemporary algebraic and diagrammatic representations of molecular systems derived from quantum mechanical models, specifically configuration interaction wavefunctions for ab initio calculations and molecular orbital energy diagrams. My aim is to suggest that recent dissatisfaction with reductive accounts of chemical theory may stem (...) from both the inability of standard accounts of reduction to incorporate the diverse forms of representation found in chemical practice and our philosophical predilection to analyze all connections between theories in terms of logical reduction. (shrink)

Mereology is the logic of part—whole concepts as they are used in many different contexts. The old chemical metaphysics of atoms and molecules seems to fit classical mereology very well. However, when functional attributes are added to part specifications and quantum mechanical considerations are also added, the rules of classical mereology are breached in chemical discourses. A set theoretical alternative mereology is also found wanting. Molecular orbital theory requires a metaphysics of affordances that also stands outside classical mereology.

Recent publications by several leading philosophers of chemistry have focused on the definition, scope, utility, and nomenclature of issues dealing with acidity and basicity. In this paper, molecular orbital theory is used to explain all acid–base reactions, concluding that the interaction of the highest occupied molecular orbital (HOMO) of one substrate, “the base,” with the lowest unoccupied molecular orbital (LUMO) of a second substrate, “the acid,” determines the reactivity of such systems. This paradigm provides (...) an understanding of all acid–base reactions as well as other reactions which, on the surface, may not seem like acid–base reactions but which have fundamental underpinnings of that kind of chemistry. Rather than being unable to determine a unified understanding of acidity and basicity as suggested in the philosophy of chemistry literature, we propose that acidity and basicity fit securely in a classification of many other reactions that, using classical chemistry knowledge, pre-quantum chemistry, would not be possible. We strongly support the use of all scientific knowledge and experience in the development of the ideas in the philosophy science. We further suggest increased interactions between philosophers of science and scientists, so that all scholars benefit from the values, knowledge, and perspectives of other disciplines. (shrink)

A selective history of the benzene problem is presented, starting with August Kekulé's proposal of a hexagonal structure in 1865 and his hypothesis of 1872 that the carbon–carbon bonds oscillate between single and double. Only those theories are included that were accepted or at least discussed by a significant number of chemists. Special attention is given to predictions, their empirical tests, and the effect of the outcomes of those tests on the reception of the theories. At the end of the (...) period covered by this article, chemists generally accepted the valence bond theory proposed by Linus Pauling; some of them considered this a more sophisticated version of Kekulé's oscillation hypothesis. The sequel describes the replacement of the valence bond theory by the molecular orbital theory in the period ending around 1980. (shrink)

Developments in the application of quantum mechanics to the understanding of the chemical bond are traced with a view to examining the evolving conception of the covalent bond. Beginning with the first quantum mechanical resolution of the apparent paradox in Lewis’s conception of a shared electron pair bond by Heitler and London, the ensuing account takes up the challenge molecular orbital theory seemed to pose to the classical conception of the bond. We will see that the threat of (...) delocalisation can be overstated, although it is questionable whether this should be seen as reinstating the issue of the existence of the chemical bond. More salient are some recent developments in a longstanding discussion of how to understand the causal aspects of the bonding interaction—the nature of the force involved in the covalent link—which are taken up in the latter part of the paper. (shrink)

Most contemporary chemists consider quantum mechanics to be the foundational theory of their discipline, although few of the calculations that a strict reduction would seem to require have ever been produced. In this essay I discuss contemporary algebraic and diagrammatic representations of molecular systems derived from quantum mechanical models, specifically configuration interaction wavefunctions for ab initio calculations and molecular orbital energy diagrams. My aim is to suggest that recent dissatisfaction with reductive accounts of chemical theory may stem (...) from both the inability of standard accounts of reduction to incorporate the diverse forms of representation found in chemical practice and our philosophical predilection to analyze all connections between theories in terms of logical reduction. (shrink)

Two different models for chemical bond were developed almost simultaneously after the Schrödinger formulation of quantum theory. These are known as the valence bond (VB) and molecular orbital (MO) theories. Initially chemists preferred the VB theory and ignored the MO theory. Now the VB theory is almost dropped out of currency. The context of discovery and Linus Pauling’s overpowering influence gave the VB theory its initial advantage. The current universal acceptance of the MO theory is due to its (...) ability to provide direct interpretation of many different types of experiments now being pursued. In current research both localized bonds and delocalized charge distributions play important roles and the MO theory has been successful in giving a good account of both. (shrink)

In modern German ‘Anschauung’ is translated as intuition. But in Kant’s technical philosophical context, it means an intuition derived from previous visualizations of physical processes in the world of perceptions. The nineteenth century chemists’ predilection for Kantian Anschauung led them to develop an intuitive representation of what exists beyond the bounds of the senses. Molecular structure is one of the illuminating outcomes. (Ochiai 2021, pp. 1–51) This mental habit seems to be dominant among chemists even in the twentieth century, (...) as is illustrated by the electronic theory of organic chemistry and the frontier orbital theory as well. The former assumes that (1) bonds are paired electrons shared by bonded atoms—in fact, electrons in molecules are not localized in bonds; (2) the difference of electronegativities between bonded atoms causes electron drifts—expressed by the curly arrow—that result in bond formation or bond cleavage. The latter focuses on the orbitals that make the greatest contribution to the energy of a system undergoing electron delocalization, while the LCAO method says, as is suggested by the word Linear Combination of Atomic Orbitals, molecular orbitals should be constructed from all of the atomic orbitals that have the appropriate symmetry. In other words, every molecular orbital contributes to some extent to the electronic state of a molecule. The curly arrow in the electronic theory and the orbital lobe in the frontier orbital theory illustrate an intuitive character of these theories. Although both theories rely on such simple and qualitative models rather than mathematically rigid quantum mechanical calculations, they are successful in explaining, predicting, and designing chemical reactions. What makes these prima facie intuitive theories so successful? In this study we address this problem from a historical and philosophical as well as scientific point of view. The key to solve this problem is that they are concerned with only bond formation or bond cleavage, in which the localized-bond principle holds. (shrink)

Roald Hoffmann's contributions to chemistry are well known; this Nobel laureate has published more than 500 articles and two books. As an "applied theoretical chemist," he has made significant contributions to our understanding of chemical bonding and reactivity, and taught two generations of chemists how to use molecular orbitals for real chemistry. Less well known, however, are Hoffmann's important and insightful contributions to the areas of scholarship surrounding chemistry. Over a career that spans nearly fifty years, Roald Hoffmann has (...) thought and written copiously about the broader context of chemistry and its relationship to the arts and poetry. This book contains Hoffmann's essays and is organized around several major themes: chemical reasoning and explanation, writing and communicating in science, ethics, art and science, and chemical education. A few are unpublished lectures that are valuable additions to the volume. The editors have the full cooperation of Roald Hoffmann in this project. Most of the published work will be reprinted verbatim, but a few of the essays will be revised to eliminate redundancy. The unpublished lectures will also be edited since they were originally intended to be delivered orally at specific occasions. The editors will provide an introduction to the book, and some introductory material for each section. In introducing the material, they will highlight the intrinsic importance and interest of the ideas, as well as the places where Hoffmann's thought makes novel contributions to cognate areas. (shrink)

Summary Linus Pauling played a key role in creating valence-bond theory, one of two competing theories of the chemical bond that appeared in the first half of the 20th century. While the chemical community preferred his theory over molecular-orbital theory for a number of years, valence-bond theory began to fall into disuse during the 1950s. This shift in the chemical community's perception of Pauling's theory motivated Pauling to defend the theory, and he did so in a peculiar way. (...) Rather than publishing a defence of the full theory in leading journals of the day, Pauling published a defence of a particular model of the double bond predicted by the theory in a revised edition of his famous textbook, The Nature of the Chemical Bond. This paper explores that peculiar choice by considering both the circumstances that brought about the defence and the mathematical apparatus Pauling employed, using new discoveries from the Ava Helen and Linus Pauling Papers archive. (shrink)

SummaryKekulé first suggested a hexagonal structure for benzene in 1865. For over a half-century after, chemists struggled to reconcile proposed structures for benzene and other aromatic compounds with their resistance to chemical transformation and tendency to maintain the type during reaction. The combined structural and reactivity features of these compounds were eventually covered by the term ‘aromaticity’. Kekulé, Bamberger and Thiele had each proposed a criterion for aromaticity; all were either empirically contradicted or incapable of evaluation. In the 1930s, two (...) rival quantum mechanical methods succeeded in establishing a physical basis for aromaticity. Using valence bond theory, Pauling attributed benzene's stability to its being a resonance hybrid of several Lewis structures. Calculating resonance energies was challenging but manipulating Lewis structures was not; that procedure provided qualitative insights into aromatic structure and reactivity. Resonance theory appealed especially to organic chemists and eclipsed Hückel's contemporaneous molecular orbital approach, which remained relatively inaccessible. In the 1950s, however, simple rules derived from Hückel's mathematics, combined with proton NMR data, provided seemingly universal criteria for aromaticity. In the event, post-1950 discoveries of non-organic, three-dimensional compounds such as ferrocene and the fullerenes that exhibit aromatic properties led chemists to doubt the utility and universality of ‘aromaticity’ as a concept. A recent consensus maintains that aromaticity is a multi-variable phenomenon that cannot be reduced to a strict definition, a property it shares with other core chemical concepts such as ‘acidity’ and ‘reactivity’. (shrink)

It is often assumed that chemistry was a typical positivistic science as long as chemists used atomic and molecular models as mere fictions and denied any concern with their real existence. Even when they use notions such as molecular orbitals chemists do not reify them and often claim that they are mere models or instrumental artefacts. However a glimpse on the history of chemistry in the longue durée suggests that such denials of the ontological status of chemical entities (...) do not testify for any specific allegiance of chemists to positivism. Rather it suggests that the dilemma positivism vs realism is inappropriate for characterizing the ontology of chemistry. This alternative shaped at the turn of the twentieth century in the context of controversies about atomic physics does not take into account the major concern of chemists, i.e. making up things. Only by considering what matters for chemists, their matters of concern rather than their matter theories, can we expect to get an insight on their ontological assumptions. The argumentation based on historical data is twofold. It is wellknown that generating new substances out of initial ingredients which is the raison d'être of chemistry raised a vexing puzzle which has been alternatively solved with the Aristotelian notion of mixt and the Lavoisieran notion of compound. I argue that an essential tension remains intrinsic in chemistry between the two conceptual frameworks. The second section tries to make sense of the long tradition in chemistry of ontological noncommitment. I argue that what is usually considered as a denial of the existence of the basic units of matter would be better characterized as a focus on more important actors on the chemical stage. (shrink)

It is often assumed that chemistry was a typical positivistic science as long as chemists used atomic and molecular models as mere fictions and denied any concern with their real existence. Even when they use notions such as molecular orbitals chemists do not reify them and often claim that they are mere models or instrumental artefacts. However a glimpse on the history of chemistry in the longue durée suggests that such denials of the ontological status of chemical entities (...) do not testify for any specific allegiance of chemists to positivism. Rather it suggests that the dilemma positivism vs realism is inappropriate for characterizing the ontology of chemistry. This alternative shaped at the turn of the twentieth century in the context of controversies about atomic physics does not take into account the major concern of chemists, i.e. making up things. Only by considering what matters for chemists, their matters of concern rather than their matter theories, can we expect to get an insight on their ontological assumptions. The argumentation based on historical data is twofold. Generating new substances out of initial ingredients which is the raison d’être of chemistry raised a vexing puzzle which has been alternatively solved with the Aristotelian notion of mixt and the Lavoisieran notion of compound. I will argue that an essential tension remains intrinsic in chemistry between the two conceptual frameworks. But how are we to make sense of the long tradition of ontological non-commitment in chemistry? I argue that what is usually considered as a denial of the existence of the basic units of matter is better characterized as a focus on more important actors on the chemical stage. (shrink)

A possible atomic mechanism underlying the Re- and Ru-induced strengthening effects on the n - n ' interface in Ni-based single-crystal superalloys has been investigated using the DMol3 molecular orbital package based on density functional theory. The calculation of bonding properties has been performed on a cluster designed to model Re and Ru strengthening effects within the interface. The stronger Re--Ni bonds are formed mainly as a result of d- hybridization, while the Ni--Ni bonding become weaker accompanying the (...) Re substitution. The vertical and horizontal bond orders for a local environmental cluster are proposed and developed for the description of the strengthening effect on the n - n ' interface, with larger bond order values achieving better effect. Results show that both Re and Ru significantly strengthen the interface. It is also shown that the strengthening effect of Re is better than that of Ru, and this is explained in terms of the charge transfer of electrons between orbitals of Ru atom according to Mulliken population analysis. The calculation results provide a basis for understanding the atomic mechanism of Re- and Ru-induced n - n ' interfacial strengthening. (shrink)

The importance of watching and understanding color of chemical compounds and linking it to diverse physical and chemical properties is illustrated here using transition metal oxides at the highest achievable oxidation state of a metal. Analyses are based on qualitative thinking supported by Molecular Orbital theory in its simplest implementation. Graphic abstract.

It is argued that some elusive “entropic” characteristics of chemical bonds, e.g., bond multiplicities (orders), which connect the bonded atoms in molecules, can be probed using quantities and techniques of Information Theory (IT). This complementary perspective increases our insight and understanding of the molecular electronic structure. The specific IT tools for detecting effects of chemical bonds and predicting their entropic multiplicities in molecules are summarized. Alternative information densities, including measures of the local entropy deficiency or its displacement relative to (...) the system atomic promolecule, and the nonadditive Fisher information in the atomic orbital resolution(called contragradience) are used to diagnose the bonding patterns in illustrative diatomic and polyatomic molecules. The elements of the orbital communication theory of the chemical bond are briefly summarized and illustrated for the simplest case of the two-orbital model. The information-cascade perspective also suggests a novel, indirect mechanism of the orbital interactions in molecular systems, through “bridges” (orbital intermediates), in addition to the familiar direct chemical bonds realized through “space”, as a result of the orbital constructive interference in the subspace of the occupied molecular orbitals. Some implications of these two sources of chemical bonds in propellanes, π-electron systems and polymers are examined. The current–density concept associated with the wave-function phase is introduced and the relevant phase-continuity equation is discussed. For the first time, the quantum generalizations of the classical measures of the information content, functionals of the probability distribution alone, are introduced to distinguish systems with the same electron density, but differing in their current(phase) composition. The corresponding information/entropy sources are identified in the associated continuity equations. (shrink)

Robin Hendry has presented an account of two equally valid ways of understanding the nature of chemical bonding, consisting of what the terms the structural and the energetic views respectively. In response, Weisberg has issued a “challenge to the structural view”, thus implying that the energetic view is the more correct of the two conceptions. In doing so Weisberg identifies the delocalization of electrons as the one robust feature that underlies the increasingly accurate quantum mechanical calculations starting with the Heitler-London (...) method and moving on to such approaches as the valence bond and molecular orbital theories of chemical bonding. The present article provides a critical evaluation of Weisberg’s article and concludes that he fails to characterize the nature of chemical bonding in several respects. I claim that Hendry’s structural and energetic views remain as equally viable ways of understanding chemical bonding. Whereas the structural view is more appropriate for chemists, the energetic view is preferable to physicists. Neither view is more correct unless one subscribes to the naively reductionist view of considering that the more physical energetic view is the more correct one. (shrink)

A selective history of the benzene problem is presented, starting with August Kekule's proposal of a hexagonal structure in 1865 and his hypothesis of 1872 that the carbon-carbon bonds oscillate between single and double. Only those theories are included that were accepted or at least discussed by a significant number of chemists. Special attention is given to predictions, their empirical tests, and the effect of the outcomes of those tests on the reception of the theories. At the end of the (...) period covered by this article, chemists generally accepted the valence bond (resonance) theory proposed by Linus Pauling; some of them considered this a more sophisticated version (and thus a vindication) of Kekule's oscillation hypothesis. The sequel (to be published in the following issue) describes the replacement of the valence bond theory by the molecular orbital theory in the period ending around 1980. (shrink)

The aim of the present paper is to analyze the problem of the relationship between chemistry and physics, by focusing on the widely discussed case of the atomic orbitals. We will begin by remembering the difference between the physical and the chemical interpretation of the concept of orbital. Then, we will refer to the claim made in 1999 that atomic orbitals have been directly imaged for the first time. On this basis, we will analyze the problem from a new (...) approach, by comparing the concept of orbital used in physics with the concept of orbital used in chemistry. Such an analysis will allow us to argue for an ontological pluralism that admits the coexistence of different ontologies without priorities or metaphysical privileges. From this philosophical framework, the concepts of chemical orbital and physical orbital correspond to two different ontologies. As a consequence, chemical orbitals are real entities belonging to the ontology of molecular chemistry, and can be observed like any other entity not belonging to the quantum mechanical ontology. DOI:10.5007/1808-1711.2010v14n3p309. (shrink)

It is customary to distinguish experimental from purely observational sciences. The former include physics and molecular biology, the latter astronomy and palaeontology. Experiments involve actively intervening in the course of nature, as opposed to observing events that would have happened anyway. When a molecular biologist inserts viral DNA into a bacterium in his laboratory, this is an experiment; but when an astronomer points his telescope at the heavens, this is an observation. Without the biologist’s handiwork the bacterium would (...) never have contained foreign DNA; but the planets would have continued orbiting the sun whether or not the astronomer had directed his telescope skyward. The observational/experimental distinction would probably be difficult to make precise 1, as the notion of an ‘intervention’ is not easily defined, but it is intuitively fairly clear, and is frequently invoked by scientists and historians of science. Experimentation, or ‘putting questions to nature’, is often cited as a hallmark of the modern scientific method, something that permitted the enormous advances of the last 350 years. And it is sometimes said that the social sciences lag behind the natural because controlled experiments cannot be done so readily in the former. Moreover in certain sciences, e.g. epidemiology, students are explicitly taught that experimental data is preferable to observational data, particularly for doing causal inference. So the distinction between observational and experimental science has quite wide currency, and is often regarded as methodologically significant. Surprisingly, mainstream philosophy of science has had rather little to say about the observational/experimental distinction. 2 For example, discussions of confirmation usually invoke a notion of ‘evidence’, to be contrasted with ‘theory’ or ‘hypothesis’; the aim is to understand how the evidence bears on the hypothesis. But whether this ‘evidence’ comes from observation or experiment generally plays no role in the discussion; this is true …. (shrink)

This essay addresses issues concerningexplanation by exploring how explanatorystructures function within contemporarychemistry. Three examples are discussed:explanations of the behavior of gases using theideal gas law, explanations of trends inchemical properties using the periodic table,and explanations of molecular geometry usingdiagrammatic orbital schemes. In each case,the general explanatory structure, rather thanparticular explanations, occupies center stagein the analysis. It is argued that thisquasi-empirical investigation may be morefruitful than previous analyses that attempt toisolate the essential features of individualexplanations. There are two reasons (...) for thisconclusion, each discussed in some detail. First, the traditional analyses rely on highlyprecarious reasoning. Second, empiricallygrounded investigations provide a more naturalconnection to the core aim of analyses ofexplanation, namely to provide a rationale forthe widely expressed preference for explanatorytheories in science. (shrink)

The preparation of layers of amorphous Se by plasma-enhanced CVD using the hydride H2Se as precursor gas is described. Information concerning the structure of the films was obtained from Raman spectroscopy. The spectra of amorphous Se indicated that the dominant molecular structure is the eight-membered ring and/or a chain with Se8 molecular fragments. This material exhibited reversible photodarkening when illuminated at 77 K. In order to explain this phenomenon, we propose a mechanism which takes into account the role (...) of the lone-pair electron orbitals of Se in their contribution to structural ordering. Illumination can cause a distortion in the normal bonding direction between nearest-neighbour Se atoms and induce in this way intrinsic defect states located at the band edges. In the photo-darkened state, optical transition will occur between these defect states. (shrink)

Slater’s method is an integral part of the undergraduate experience. In actuality, Slater’s method is part of an atomic model and not simply a set of rules. Slater’s rules are a simple means for computing the effective nuclear charge experienced by an orbital. These rules are based on the shell-like structure of the Slater atom in which outer shell electrons are incapable of shielding inner electrons. Slater’s model provides a qualitative description of the valence electrons in multi-electron atoms with (...) tremendous ease. The model is useful for explaining atomic properties such as ionisation energy, electron affinity and atomic radius qualitatively. Slater’s rules also correctly reproduce the Madelung rule of filling and the ionisation sequence (4s before 3d); however, these rules are not able to reproduce the anomalous configurations of atoms such as Cr and Cu. It is found that the atomic properties that Slater’s model reproduces are all related to the exponential decay factor of the Slater orbital. We find—from estimating the polarity of a diatomic molecule using a simple model—that molecular polarity is related to the difference in the exponential decay factors of the valence orbitals of the two atoms, implying that the decay factor acts as the electronegativity of the atom. (shrink)

The aim of the present paper is to analyze the problem of the relationship between chemistry and physics, by focusing on the widely discussed case of the atomic orbitals. We will begin by remembering the difference between the physical and the chemical interpretation of the concept of orbital. Then, we will refer to the claim made in 1999 that atomic orbitals have been directly imaged for the first time. On this basis, we will analyze the problem from a new (...) approach, by comparing the concept of orbital used in physics with the concept of orbital used in chemistry. Such an analysis will allow us to argue for an ontological pluralism that admits the coexistence of different ontologies without priorities or metaphysical privileges. From this philosophical framework, the concepts of chemical orbital and physical orbital correspond to two different ontologies. As a consequence, chemical orbitals are real entities belonging to the ontology of molecular chemistry, and can be observed like any other entity not belonging to the quantum mechanical ontology. (shrink)

Without directly addressing the Demarcation Problem for logic—the problem of distinguishing logical vocabulary from others—we focus on distinctive aspects of logical vocabulary in pursuit of a second goal in the philosophy of logic, namely, proposing criteria for the justification of logical rules. Our preferred approach has three components. Two of these are effectively Belnap’s, but with a twist. We agree with Belnap’s response to Prior’s challenge to inferentialist characterisations of the meanings of logical constants. Belnap argued that for a logical (...) constant to exist, its rules must be conservative over a previously given consequence relation and guarantee the uniqueness of the constant. The twist is that we require logical vocabulary to be provably conservative, not over a previously given formal consequence relation, but over a previously given meaningful vocabulary of a language. Uniqueness is also a feature defined in terms of provability: if two syntactically distinguished expressions are governed by the same rules, then formulas with them as main operators are interderivable. Belnap’s criteria are not only those for the existence of a logical constant, but more: they are what distinguishes logical vocabulary from all other expressions. It is the defining mark of a logical constant that it is provably conservative over the fragment of the language which excludes it and that its rules guarantee its uniqueness. The third component is the topic neutrality of logic. The provable conservativeness of logic over a previously given vocabulary of a language is motivated, in part, by appeal to molecularism in the theory of meaning. Molecularity is a feature endorsed by the theory of meaning as a whole, so it does not distinguish logical constants from other expressions. The same is true for conservativeness. We argue that molecularity, and hence conservativeness, are implicit presuppositions of speakers’ use of language: the addition of new vocabulary to a language is presupposed to be conservative. But this presupposition is one that we should be able reflectively to endorse (such as when attempting a rational reconstruction of the use of the vocabulary). Thus, where conservativeness is found to fail, this defect should be remedied and the use of the vocabulary corrected (as in classical negation) or excised altogether (as in pejoratives). We go on to characterise a notion of topic neutrality, which we argue applies to logical vocabulary. We then note that reflective endorsement of the conservativeness of a topic neutral vocabulary requires a proof that the vocabulary is conservative relative to any base vocabulary. Thus we require that logical vocabulary be demonstrably conservative. Allying this requirement, distinctive of logic, to a general consideration about the commitments of assertion yields a mode of justification for logical constants akin to some conceptions of Harmony, i.e., to the idea that the consequences of assertion of a logical complex need to be warranted by the grounds and ought to be the strongest consequences warranted by the grounds. Intuitionistic logic acquires a somewhat familiar justification but emanating from a new motivation. (shrink)

The autophagy initiation complex is brought about via a highly ordered and stepwise assembly process. Two crucial signaling molecules, mTORC1 and AMPK, orchestrate this assembly by phosphorylating/dephosphorylating autophagy‐related proteins. Activation of Atg1 followed by recruitment of both Atg9 vesicles and the PI3K complex I to the PAS (phagophore assembly site) are particularly crucial steps in its formation. Ypt1, a small Rab GTPase in yeast cells, also plays an essential role in the formation of the autophagy initiation complex through multiple regulatory (...) pathways. In this review, our primary focus is to discuss how signaling molecules initiate the assembly of the autophagy initiation complex, and highlight the significant roles of Ypt1 in this process. We end by addressing issues that need future clarification. (shrink)

Some strategies to turn any logic into a paraconsistent system are examined. In the environment of universal logic, we show how to paraconsistentize logics at the abstract level using a transformation in the class of all abstract logics called paraconsistentization by consistent sets. Moreover, by means of the notions of paradeduction and paraconsequence we go on applying the process of changing a logic converting it into a paraconsistent system. We also examine how this transformation can be performed using multideductive abstract (...) logics. To conclude, the conceptual notion paraconsistent orbit of a logic is proposed. (shrink)

In 1969 Jasia Reichardt curated an exhibition at the Institute of Contemporary Art in London called Play Orbit. Although it has not achieved the landmark status of Reichardt's Cybernetic Serendipity, which was presented in London a year earlier, it caught the intellectual and artistic mood of a newly emergent constituency of (largely British) artists who had benefited from a post-war revision of art education and a de-centring of intellectual energy away from the economic capitals. It may be that Play Orbit (...) will eventually be regarded in much the same way as Cybernetic Serendipity that is, as a significant footnote in the history of contemporary art. By turning artists' attention to toys through this project, the categories of painting and sculpture dissolved and the Modernist imperative of the enduring observation that had informed the arts and letters in a centred intellectual regime was seen for what it was: a colonial anachronism. The unapologetic relativism of play and the provisional truths of games coalesced in Play Orbit as confrontations to the essentialist materialism of the prevailing orthodoxy. In this sense Play Orbit, and its extensive catalogue of images and essays, foreshadowed not only the critical style that followed the influence of Continental Theory in the mid 1970s but also anticipated the agenda of virtually all that has been written about games in the last decade. For all its apparent whimsy and reification of idiosyncrasy, Play Orbit can now be seen as, above all, a constructively political intervention levered through the arts. For example, one of the more enduring and least contested impacts of the intellectual revisions of the last thirty years that Play Orbit foreshadowed is evident in the practice of history not least the practice of history as a game to be played. This paper elaborates on these assertions and asks how games and games theory might be connected with their own political and intellectual history, and how contemporary artists who choose to benefit from the licence that play endows might situate their work within what might be called Art Ludistory: a political play on the history of play. (shrink)

This chapter contains section titled: The Neutral Theory of Molecular Evolution The Molecular Clock The Neutral Null Model Controversy in Molecular Evolution Acknowledgment References Further Reading.

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)

Despite the transformation in biological practice and theory brought about by discoveries in molecular biology, until recently philosophy of biology continued to focus on evolutionary biology. When the Human Genome Project got underway in the late 1980s and early 1990s, philosophers of biology -- unlike historians and social scientists -- had little to add to the debate. In this landmark collection of essays, Sahotra Sarkar broadens the scope of current discussions of the philosophy of biology, viewing molecular biology (...) as a unifying perspective on life that complements that of evolutionary biology. His focus is on molecular biology, but the overriding question behind these papers is what molecular biology contributes to all traditional areas of biological research.Molecular biology -- described with some foresight in a 1938 Rockefeller Foundation report as a branch of science in which "delicate modern techniques are being used to investigate ever more minute details" -- and its modeling strategies apparently argue in favor of physical reductionism. Sarkar's first three chapters explore reductionism -- defending it, but cautioning that reduction to molecular interactions is not necessarily a reduction to genetics. The next sections of the book discuss function, exploring how functional explanations pose a problem for reductionism; the informational interpretation of biology and how it interacts with reductionism; and the tension between the unifying framework of molecular biology and the received framework of evolutionary theory. The concluding chapter is an essay in the emerging field of developmental evolution, exploring what molecular biology may contribute to the transformation of evolutionary theory as evolutionary theory takes into account morphogenetic development. (shrink)

The article disputes the recent claim featured in "Nature" magazine and many other science magazines to the effect that atomic orbitals have been observed for the first time. The claim is incorrect in view of the unconvincing nature of the evidence adduced and since atomic orbitals are deemed unobservable in principle by quantum mechanics. In addition, the possible educational drawbacks of this incorrect claim are discussed.

Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era.

The main focus of the book is the presentation of the 'inertial' view of population growth. This view provides a rather simple model for complex population dynamics, and is achieved at the level of the single species without invoking species interactions. An important part of this account is the maternal effect. Investment of mothers in the quality of their daughters makes the rate of reproduction of the current generation depend not only on the current environment, but also on the environment (...) experienced by the previous generation. (shrink)