After observing that the truth conditions of connectives of non–classical logics are generally defined in terms of formulas of first–order logic, we introduce ‘protologics’, a class of logics whose connectives are defined by arbitrary first–order formulas. Then, we introduce atomic and molecular logics, which are two subclasses of protologics that generalize our gaggle logics and which behave particularly well from a theoretical point of view. We also study and introduce a notion of equi-expressivity between two logics based on (...) different classes of models. We prove that, according to that notion, every pure predicate logic with \ variables and constants is as expressive as a predicate atomic logic, some sort of atomic logic. Then, we prove that the class of protologics is equally expressive as the class of molecular logics. That formally supports our claim that atomic and molecular logics are somehow ‘universal’. Finally, we identify a subclass of molecular logics that we call predicate molecular logics and which constitutes its representative core: every molecular logic is as expressive as a predicate molecular logic. (shrink)

In the centennial of Ettore Majorana’s birth (1906–1938?), we re-examine some aspects of his fundamental scientific production in atomic and molecular physics, including a not well known short communication. There, Majorana critically discusses Fermi’s solution of the celebrated Thomas–Fermi equation for electron screening in atoms and positive ions. We argue that some of Majorana’s seminal contributions in molecular physics already prelude to the idea of exchange interactions (or Heisenberg–Majorana forces) in his later works on theoretical nuclear physics. (...) In all his papers, he tended to emphasize the symmetries at the basis of a physical problem, as well as the limitations, rather than the advantages, of the approximations of the method employed. (shrink)

We give an account of the appearance and first developments of the statistical model of atoms proposed by Thomas and Fermi, focusing on the main results achieved by Fermi and his group in Rome. Particular attention is addressed to the unknown contribution to this subject by Majorana, anticipating some important results reached later by leading physicists.

Research into learners' ideas aboutscience suggests that school and collegestudents often hold alternative conceptionsabout `the atom'. This paper discusses whylearners acquire ideas about atoms which areincompatible with the modern scientificunderstanding. It is suggested that learners'alternative ideas derive – at least in part –from the way ideas about atoms are presented inthe school and college curriculum. Inparticular, it is argued that the atomicconcept met in science education is anincoherent hybrid of historical models, andthat this explains why learners commonlyattribute to atoms (...) properties (such as beingthe constituent particles of all substances, orof being indivisible and conserved inreactions) that more correctly belong to otherentities (such as molecules or sub-atomicparticles). Bachelard suggested that archaicscientific ideas act as `epistemologicalobstacles', and here it is argued thatanachronistic notions of the atom survive inthe chemistry curriculum. These conceptualfossils encourage learners to develop an`atomic ontology' (granting atoms `ontologicalpriority' in the molecular model of matter); tomake the `assumption of initial atomicity' whenconsidering chemical reactions; and to developan explanatory framework to rationalisechemical reactions which is based on thedesirability of full electron shells. Theseideas then act as impediments to thedevelopment of a modern chemical perspective onthe structure of matter, and an appreciation ofthe nature of chemical changes at the molecularlevel. (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)

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

By their own account, physicalists are committed to the claim that physics is causally complete, or closed. The claim is presented as an empirical one. However, detailed and explicit empirical arguments for the claim are rare. I argue that molecular models are a key source of evidence but that, on closer inspection, they do not support the completeness claim.

The practice of theoretical research in chemistry largely consists in the construction of models without which experimentation would be impossible. The best-known theoretical models in chemistry are those of the molecular structures of chemical compounds. What is the correspondence between these models and the unobservable entities that they are meant to explain? What is the ontological status of molecular models? The anti-realists question the basis of the realists’ belief in these entities and the truth (...) claims regarding them. Ultimately, the realist/anti-realist debate points to the question of the scope of scientific knowledge. In this paper, I shall show that the description of natural entities offered by the contemporary scientific worldview reveals that molecular modeling presupposes a realistic epistemology that recognizes the limits of scientific objectification. (shrink)

We present a molecular model of eukaryotic gene transcription. For the β‐globin locus, we hypothesise that a transcription machine composed of multiple RNA polymerase II (PolII) assembles using the locus control region as a foundation. Transcription and locus remodelling can be achieved by pulling DNA through this multi‐PolII ‘reading head’. Once a transcription complex is formed, it may engage an active gene in several rounds of transcription. Observed intergenic sense and antisense transcripts may be the result of PolII pulling (...) the DNA through the reading head whilst searching for the promoter of a gene. Support for this hypothesis is provided using various data from the literature. In the model, DNA is packed in a 30‐nm chromatin fibre, thus gene regulatory regions separated by kilobases are close in space. This, and the need to store transcription‐induced supercoiling, may explain why functionally interacting regions are often separated by many kilobases. (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)

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

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)

This paper approaches the scientific realism question from a naturalistic perspective. On the basis of a historical case study of the work of James Clerk Maxwell and Ludwig Boltzmann on the kinetic theory of gases, it shows that scientists’ views about the epistemological status of theories and models typically interact with their scientific results. Subsequently, the implications of this result for the current realism debate are analysed. The case study supports Giere’s moderately realist view of scientific models and (...) theories, based on the notion of similarity, and it highlights the crucial role of model users. The paper concludes with a discussion of Boltzmann’s Bildtheorie, the sophisticated form of realism that he developed in response to the scientific problems of kinetic theory. (shrink)

This paper approaches the scientific realism question from a naturalistic perspective. On the basis of a historical case study of the work of James Clerk Maxwell and Ludwig Boltzmann on the kinetic theory of gases, it shows that scientists’ views about the epistemological status of theories and models typically interact with their scientific results. Subsequently, the implications of this result for the current realism debate are analysed. The case study supports Giere’s moderately realist view of scientific models and (...) theories, based on the notion of similarity, and it highlights the crucial role of model users. The paper concludes with a discussion of Boltzmann’s Bildtheorie, the sophisticated form of realism that he developed in response to the scientific problems of kinetic theory. (shrink)

By moving away from the traditional reductionist reading of the quantum theory of atoms in molecules, in this paper we analyze the role played by QTAIM in the relationship between molecular chemistry and quantum mechanics from an emergentist perspective. In particular, we show that such a relationship involves two steps: an intra-domain emergence and an inter-domain emergence. Intra-domain emergence, internal to quantum mechanics, results from the fact that the electron density, from which all the other QTAIM’s concepts are defined, (...) arises from the wavefunction as a coarse-grained magnitude. Inter-domain emergence involves an analogical link, a mapping, between QTAIM’s entities, such as topological atoms and bond paths, and the entities that populate the molecular-chemistry domain, such as chemical atoms and chemical bonds. (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.

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

In the years 1878 and 1879 the American physicist Alfred Marshall Mayer published his experiments with floating magnets as a didactic illustration of molecular actions and forms. A number of physicists made use of this analogy of molecular structure. For William Thomson they were a mechanical illustration of the kinetic equilibrium of groups of columnar vortices revolving in circles round their common centre of gravity . A number of modifications of Mayer's experiments were described, which gave configurations which (...) were more or less analogous to Mayer's arrangements. It was Joseph John Thomson who, in publications between 1897 and 1907, used Mayer's results to obtain a good deal of insight into the general laws which govern the configuration of the electrons in his atomic model. This article is mainly concerned with Mayer's experiments with floating magnets and their use by a number of physicists. Through his experiments Mayer made a significant, although small, contribution to the theory of atomic structure. (shrink)

J. H. van 't Hoff's 1874 Dutch pamphlet, in which he proposed the spatial arrangement of atoms in a molecule, is one of the most significant documents in the history of chemistry. This essay presents a new narrative of Van 't Hoff's early life and places the appearance of the pamphlet within the context of the 'second golden age' of Dutch science. We argue that the combination of the reformed educational system in The Netherlands, the emergence of graphical molecular (...) modelling within the theoretical and practical culture of chemistry during the 1860s and 1870s, as well as Van 't Hoff's own personal research trajectory, formed the background to his unprecedented attribution of spatial meaning to the traditional concept of atomic 'arrangement'. We also present a new English translation of the pamphlet, for we have found that the existing translation, published by G. M. Richardson in 1901, contains many errors, changes and omissions. The new version offers a more accurate rendition in English of Van 't Hoff's style and argument. (shrink)

Electronegativity is an important physico-chemical concept to study the chemical structure and reactivity. Although, the conundrum related to measurement of electronegativity still persists. In view of this fact, a simple yet rigorous scale of electronegativity, invoking an inverse relationship with atomic nucleophilicity index, has been proposed for 103 elements of the periodic table. The computed data follows periodicity distinctly satisfying all the sine qua non of a standard scale of electronegativity. Further, electronegativity values display a sound similarity with the (...) standard electronegativity scales validating the suitability of the proposed model. Molecular electronegativities of some polyatomic molecules have also been calculated using the proposed scale of electronegativity.Graphic. (shrink)

This paper approaches the scientific realism question from a naturalistic perspective. On the basis of a historical case study of the work of James Clerk Maxwell and Ludwig Boltzmann on the kinetic theory of gases, it shows that scientists’ views about the epistemological status of theories and models typically interact with their scientific results. Subsequently, the implications of this result for the current realism debate are analysed. The case study supports Giere’s moderately realist view of scientific models and (...) theories, based on the notion of similarity, and it highlights the crucial role of model users. The paper concludes with a discussion of Boltzmann’s Bildtheorie, the sophisticated form of realism that he developed in response to the scientific problems of kinetic theory. (shrink)

The concepts of atoms and bonds in molecules which appeared in chemistry during the nineteenth century are unavoidable to explain the structure and the reactivity of the matter at a chemical level of understanding. Although they can be criticized from a strict reductionist point of view, because neither atoms nor bonds are observable in the sense of quantum mechanics, the topological and statistical interpretative approaches of quantum chemistry (quantum theory of atoms in molecules, electron localization function and maximum probability domain) (...) provide consistent definitions which accommodate chemistry and quantum mechanics. (shrink)

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

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims (...) of data science (machine learning in particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

The discrepancy between syntax and semantics is a painstaking issue that hinders a better comprehension of the underlying neuronal processes in the human brain. In order to tackle the issue, we at first describe a striking correlation between Wittgenstein's Tractatus, that assesses the syntactic relationships between language and world, and Perlovsky's joint language-cognitive computational model, that assesses the semantic relationships between emotions and “knowledge instinct”. Once established a correlation between a purely logical approach to the language and computable psychological activities, (...) we aim to find the neural correlates of syntax and semantics in the human brain. Starting from topological arguments, we suggest that the semantic properties of a proposition are processed in higher brain's functional dimensions than the syntactic ones. In a fully reversible process, the syntactic elements embedded in Broca's area project into multiple scattered semantic cortical zones. The presence of higher functional dimensions gives rise to the increase in informational content that takes place in semantic expressions. Therefore, diverse features of human language and cognitive world can be assessed in terms of both the logic armor described by the Tractatus, and the neurocomputational techniques at hand. One of our motivations is to build a neuro-computational framework able to provide a feasible explanation for brain's semantic processing, in preparation for novel computers with nodes built into higher dimensions. (shrink)

Alzheimer's disease results from the degeneration of neurons. Degenerating nerve cells express atypical proteins, and amyloid is deposited. We suggest that some of these events are strongly influenced by genetic factors and age. Animal models should be useful in investigating the pathogenic mechanisms that lead to the brain abnormalities seen in this disease.

One important aspect of biological explanation is detailed causal modeling of particular phenomena in limited experimental background conditions. Recognising this allows one to appreciate that a sufficient condition for a reduction in biology is a molecular model of (1) only the demonstrated causal parameters of a biological model and (2) only within a replicable experimental background. These identities—which are ubiquitous in biology and form the basis of ruthless reductions (Bickle, Philosophy and neuroscience: a ruthlessly reductive account, 2003)—are criticised as (...) merely “local” (Sullivan, Synthese 167:511–539, 2009) or “fragmentary” (Schaffner, Synthese, 151(3):377–402, 2006). However, in an instructive case, a biological model is preserved in molecular terms, demonstrating a complex phenomenon that has been successfully reduced. (shrink)

This paper examines processes of translation through which molecular genetic technologies and practices are incorporated into environmental health research and regulation. Specifically, it considers how scientists, risk assessors, and regulators have used genetically modified mouse models to translate across scientific disciplines, articulate emergent molecular forms, standards, and practices with the extant? gold standard,? and establish roles for molecular knowledge in risk assessment and regulation. Noting variation both within and between regulatory agencies in responses to data from (...) these models, the article describes also the role of public-private networks and their effects on professional and institutional imperatives which shape regulators? responses to the potential applications of these models. The conclusions address the importance of translation for understanding the wider implications of the molecularization of environmental health science. (shrink)

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims (...) of data science (machine learning in particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

Nanotechnology thrives in the realm of the virtual. Throughout its history, the field has been shaped by futuristic visions of technological revolution, hyperbolic promises of scientific convergence at the molecular scale, and science fiction stories of the world rebuilt atom by atom. Even today, amid the welter of innovative nanomaterials that increasingly appear in everyday consumer products—the nanoparticles enhancing our sunscreens, the carbon nanotubes strengthening our tennis rackets, the antimicrobial nano-silver lining our socks, the nanofilms protecting our wrinkle-free trousers—the (...) public rhetoric of nanotechnology constantly reminds us that such precision-engineered materials merely represent a trace or a premonition of the amazing future still to come... (shrink)

In both the philosophical and visual sense, ‘seeing is believing’ does not apply to nanotechnology, for there is nothing even remotely visible to create proof of existence. On the atomic and molecular scale, data is recorded by sensing and probing in a very abstract manner, which requires complex and approximate interpretations. More than in any other science, visualization and creation of a narrative becomes necessary to describe what is sensed, not seen. Nevertheless, many of the images generated in (...) science and popular culture are not related to data at all, but come from visualizations and animations frequently inspired or created directly from science fiction. Likewise, much of this imagery is based on industrial models and is very mechanistic in nature, even though nanotechnology research is at a scale where cogs, gears, cables, levers and assembly lines as functional components appear to be highly unlikely. However, images of mechanistic nanobots proliferate in venture capital circles, popular culture, and even in the scientific arena, and tend to dominate discourse around the possibilities of nanotechnology. The authors put forward that this new science is ultimately about a shift in our perception of reality from a purely visual culture to one based on sensing and connectivity. (shrink)

Nanoscience has enabled the understanding of organisation of the atomic and molecular world. Due to the unique chemical, electronic and magnetic properties nanomaterials have wide applications in the chemical, manufacturing, medical sector etc., Single walled carbon nanotubes, buckyballs, ZnSe quantum dots, TiO 2 nanoparticle based products are nearing commercialisation. Research is on-going worldwide on suitable delivery systems for nanomaterial based drugs. Nanomaterials are highly reactive in biological systems due to the large surface area. While the benefits of nanomaterials (...) are evident there are studies which indicate the potential risk to biological systems. Substances known to be harmless in bulk can be potentially toxic in certain fibrous and nanoparticle form. Risk assessment studies with nanomaterials largely focus on mouse models. There are very few studies on their effects on aquatic species and plants which form the largest in the productivity chain with respect to the ecological pyramid. This study reviews the research done worldwide in the area of risk assessment of nanomaterials, particularly the effects on aquatic and plant systems. Risk assessment is the foundation for regulatory decision making. A general comparison of the regulatory regime in nanotechnology is performed to understand the extent of development. (shrink)

The use of physical models of molecular structures as research tools has been central to the development of biochemistry and molecular biology. Intriguingly, it has received little attention from scholars of science. In this paper, I argue that these physical models are not mere three-dimensional representations but that they are in fact very special research tools: they are cognitive augmentations. Despite the fact that they are external props, these models serve as cognitive tools that augment (...) and extend the modeler’s cognitive capacities and performance in molecular modeling tasks. This cognitive enhancement is obtained because of the way the modeler interacts with these models, the models’ materiality contributing to the solving of the molecule’s structure. Furthermore, I argue that these material models and their component parts were designed, built and used specifically to serve as cognitive facilitators and cognitive augmentations. (shrink)

The general perception of how innovative assisted reproductive technologies are introduced is through a carefully controlled series of experiments in an animal model, such as the mouse. Only after the technique has been proven can one consider confirmatory studies on mammals closely related to humans, such as rhesus monkeys or other nonhuman primates. With this background of a peer-reviewed body of well-established published data, there is sufficient foundation and rationale to propose a clinical investigation to a responsible human subjects institutional (...) review board. IRBs weigh the benefits and risks of the new methods to human subjects, and then consider the appropriate informed consent procedures for the particular case. Only after a large number of clinical studies are performed at multiple sites and are peer reviewed can the efficacy and safety of the innovative approach be clearly evaluated. At that time, the potential therapy can be responsibly offered to suitable beneficiaries. (shrink)

The general perception of how innovative assisted reproductive technologies are introduced is through a carefully controlled series of experiments in an animal model, such as the mouse. Only after the technique has been proven can one consider confirmatory studies on mammals closely related to humans, such as rhesus monkeys or other nonhuman primates. With this background of a peer-reviewed body of well-established published data, there is sufficient foundation and rationale to propose a clinical investigation to a responsible human subjects institutional (...) review board. IRBs weigh the benefits and risks of the new methods to human subjects, and then consider the appropriate informed consent procedures for the particular case. Only after a large number of clinical studies are performed at multiple sites and are peer reviewed can the efficacy and safety of the innovative approach be clearly evaluated. At that time, the potential therapy can be responsibly offered to suitable beneficiaries. (shrink)

To ensure their survival in natural habitats, plants must recognize and respond to a wide variety of insect herbivores. Aphids and other Hemiptera pose a particular challenge, because they cause relatively little direct tissue damage when inserting their slender stylets intercellularly to feed from the phloem sieve elements. Plant responses to this unusual feeding strategy almost certainly include recognition of aphid salivary components and the induction of phloem‐specific defenses. Due to the excellent genetic and genomic resources that are available for (...) Arabidopsis thaliana (Arabidopsis), this plant was chosen as a model system to study the metabolic and transcriptional responses to infestation by two aphids, Myzus persicae (green peach aphid, a broad generalist) and Brevicoryne brassicae (cabbage aphid, a crucifer‐feeding specialist). Future research on Arabidopsis–aphid interactions will lead to the identification of aphid‐specific elicitors, components of the defense‐signaling pathway, and additional metabolic responses that are induced by aphid infestation. BioEssays 29:871–883, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

In the context of 1960s research on biological membranes, scientists stumbled upon a curiously coloured material substance, which became called the “purple membrane.” Interactions with the material as well as chemical analyses led to the conclusion that the microbial membrane contained a photoactive molecule similar to rhodopsin, the light receptor of animals’ retinae. Until 1975, the find led to the formation of novel objects in science, and subsequently to the development of a field in the molecular life sciences that (...) comprised biophysics, bioenergetics as well as membrane and structural biology. Furthermore, the purple membrane and bacteriorhodopsin, as the photoactive membrane transport protein was baptized, inspired attempts at hybrid bio-optical engineering throughout the 1980s. A central motif of the research field was the identification of a functional biological structure, such as a membrane, with a reactive material substance that could be easily prepared and manipulated. Building on this premise, early purple membrane research will be taken as a case in point to understand the appearance and transformation of objects in science through work with material substances. Here, the role played by a perceptible material and its spontaneous change of colour, or reactivity, casts a different light on objects and experimental practices in the late twentieth century molecular life sciences. With respect to the impact of chemical working and thinking, the purple membrane and rhodopsins represent an influential domain straddling the life and chemical sciences as well as bio- and material technologies, which has received only little historical and philosophical attention. Re-drawing the boundary between the living and the non-enlivened, these researches explain and model organismic activity through the reactivity of macromolecular structures, and thus palpable material substances. (shrink)

Molecular biologists exploit information conveyed by mechanistic models for experimental purposes. In this article, I make sense of this aspect of biological practice by developing Keller’s idea of the distinction between ‘models of’ and ‘models for’. ‘Models of (phenomena)’ should be understood as models representing phenomena and are valuable if they explain phenomena. ‘Models for (manipulating phenomena)’ are new types of material manipulations and are important not because of their explanatory force, but because (...) of the interventionist strategies they afford. This is a distinction between aspects of the same model. In molecular biology, models may be treated either as ‘models of’ or as ‘models for’. By analysing the discovery and characterization of restriction–modification systems and their exploitation for DNA cloning and mapping, I identify the differences between treating a model as a ‘model of’ or as a ‘model for’. These lie in the cognitive disposition of the modeller towards the model: a modeller will look at a model as a ‘model of’ if interested in its explanatory force, or as a ‘model for’ if interested in the material manipulations it can possibly afford. (shrink)

Caenorhabditis elegans (C. elegans) is a tiny worm that has become the focus of a large number of worldwide research projects examining its genetics, development, neuroscience, and behavior. Recently several groups of investigators have begun to tie together the behavior of the organism and the underlying genes, neural circuits, and molecular processes implemented in those circuits. Behavior is quintessentially organismal--it is the organism as a whole that moves and mates--but the explanations are devised at the molecular and neurocircuit (...) levels, and tested in populations using protocols that span many levels of aggregation. Following a brief review of the main relevant features of C. elegans, I describe some of these circuits, and then discuss two contrasting approaches in behavioral genetics and neural network analysis of the worm. Finally, I outline the rudiments of a "field and focus" explanation model using the two contrasting approaches. (shrink)

Between 1905 and 1913, French physicist Jean Perrin's experiments on Brownian motion ostensibly put a definitive end to the long debate regarding the real existence of molecules, proving the atomic theory of matter. While Perrin's results had a significant impact at the time, later examination of his experiments questioned whether he really gained experimental access to the molecular realm. The experiments were successful in determining the mean kinetic energy of the granules of Brownian motion; however, the values for (...) molecular magnitudes Perrin inferred from them simply presupposed that the granule mean kinetic energy was the same as the mean molecular kinetic energy in the fluid in which the granules move. This stipulation became increasingly questionable in the years between 1908 and 1913, as significantly lower values for these magnitudes were obtained from other experimental results like alpha-particle emissions, ionization, and Planck's blackbody radiation equation. In this case study in the history and philosophy of science, George E. Smith and Raghav Seth here argue that despite doubts, Perrin's measurements were nevertheless exemplars of theory-mediated measurement-the practice of obtaining values for an inaccessible quantity by inferring them from an accessible proxy via theoretical relationships between them. They argue that it was actually Perrin more than any of his contemporaries who championed this approach during the years in question. The practice of theory-mediated measurement in physics had a long history before 1900, but the concerted efforts of Perrin, Rutherford, Millikan, Planck, and their colleagues led to the central role this form of evidence has had in microphysical research ever since. Seth and Smith's study thus replaces an untenable legend with an account that is not only tenable, but more instructive about what the evidence did and did not show. (shrink)