This article explores the problem of the foundation of the European Molecular Biology Organization, by reconstructing a broader institutional framework, which includes other international actors – EURATOM, UNESCO and the International Laboratory of Genetics and Biophysics in Naples – and a relevant, but still neglected figure, the Italian geneticist Adriano Buzzati-Traverso. The article considers the tension between centralized and federal models of organization in the field of life sciences not just as an EMBO internal controversy, but rather as (...) a structural issue of European scientific cooperation in fundamental biology in the early 1960s. Along with EMBO, the article analyzes in particular the EURATOM Biology Division Program and the constitution of UNESCO International Cell Research Organization. Adriano Buzzati-Traverso, as founder of ILGB and scientific consultant of EURATOM and UNESCO, played a crucial role in the complex negotiation which ultimately led to the foundation of EMBO. A synchronic treatment of ILGB, EURATOM, UNESCO-ICRO and EMBO opens a window on the early 1960s institutional configuration of molecular biology in Europe, showing how it basically incorporated the “Cold Spring Harbor” decentralized model rather than reproducing the “CERN” centralized model. (shrink)

Recently it has been shown that the classical “stick and ball” viewpoint of molecules is inconsistent with quantum theory (QT). We suggest an unusual reconciliation: The QT state is not a physical property, but instead reflects our state of knowledge about observable aspects of “reality.” We show how this perspective is nevertheless objective. Applied to molecules, the view permits “structure” to exist only when observable evidence is compatible with this feature. Typically one must replace the a priori model (in (...) particular, the dynamical generator) with one consistent with the evidence. We show that such “structure” is stable in the context of first-order perturbation theory. We also indicate how dynamics can be inferred from scattering data—a process alternative to postulating (field-theoretic) models for “environment.”. (shrink)

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 lieu of an abstract, here is a brief excerpt of the content:Introduction to the Special Section on Psychedelics Research and TreatmentDominic SistiAgainst a backdrop of post-pandemic malaise, diseases of despair, and a fragmented mental health care system, psychedelics have enjoyed a resurgence of interest as powerful psychotherapeutic agents and as catalysts of personal growth. The true power of these substances—some of which are considered sacramental by Indigenous peoples—has been shrouded for half a century by cultural mythology, political propaganda, and (...) misuse. From about 1940 to 1970, psychedelics including psilocybin and LSD were studied and used by clinicians to treat a range of psychiatric disorders from alcoholism and depression in adults to "autistic schizophrenia" in children.In June 1971, the Nixon administration's racist and illiberal War on Drugs inaugurated what was essentially a total ban on psychedelics. Society was robbed of half a century of scientific progress, and one can only speculate how differently our society might now function, and how many people might have been spared the trauma of mental illness and incarceration. Thankfully, it appears the time has arrived for psychedelic medicines to be decriminalized and included again in the pharmacopeia.In June 2023, a group of psychedelic researchers, therapists, bioethicists, Indigenous scholars, and advocates met at the Banbury Conference Center at Cold Spring Harbor Laboratory. There, this interdisciplinary group discussed several pressing ethical issues in psychedelics research and treatment that continue to [End Page 114] challenge the field. The aim of this meeting was to develop a bioethical framework for the use of psychedelics in mainstream medical settings. That is, how should psychedelics be employed responsibly by everyday clinicians, including psychiatrists, psychologists, social workers, and other behavioral health-care providers? This special section offers a sampling of three topics in psychedelic bioethics raised by the Banbury group, several of whom appear as coauthors.In our first paper, Logan Neitzke-Spruill and colleagues offer an overview of explanatory models describing the therapeutic mechanisms of psychedelic substances and how each of these models generates unique ethical quandaries. Starting from molecular biology and moving to neural circuitry and networks, neurobiological models now propel contemporary scientific research into psychedelics. Knowing how these substances work on a molecular level may offer promising ways forward in the development of new molecules designed to treat serious mental illnesses and other neurologic conditions. Perhaps neuroplastic mechanisms will be harnessed to develop new therapies without necessitating a psychedelic trip—a controversial premise discussed in our third paper, by Katherine Cheung, Brian Earp, and David Yaden.Such "neuroreductionism" risks ignoring the subjective psychological and spiritual experiences of patients that appear to be pivotal in psychedelic-assisted therapy, often described as mystical and utterly transformative. At the psychological level, these substances engender a kind of vulnerability and suggestibility requiring clear ethical standards to ensure patients' psychological and physical safety. And so too, practitioners will need structural and cultural competency to recognize the spiritual or moral values that inspire patient reactions during and after their psychedelic experiences. Ethically informed psychedelic practitioners will have to navigate between disciplinary silos and explanatory models. One practical upshot is the open question of how best to train psychedelic practitioners who hold this broad set of competencies.To that end, well-trained practitioners will need to be able to disclose in some way the transformative properties of psychedelics to prepare patients for their experiences. But how does one describe the ineffable? This raises the question of how or if it is possible for patients to truly consent to the transformative experience elicited by psychedelics, often described as one of the most important experiences of a person's life. The experience might stimulate significant emotional healing, or it might be horrifying. This sounds like a problem uniquely attached to psychedelics: after all, most pharmaceuticals don't trigger changes in one's fundamental moral values, life choices, and commitments, nor are they intended to. Yet, Brent Kious, Andrew Peterson, and Amy McGuire challenge the view that the psychedelic experience is uniquely transformative and impervious to the disclosure requirements of informed consent, a bedrock of bioethics. Ultimately, the writers show how consent is possible even if the experiences are dramatically different from most medical interventions, endorsing a practical view of consent [End... (shrink)

Formal charge and oxidation state are two means of estimating the charge of an atom in a molecule. Though these concepts have very different origins—formal charge is derived from the ball-and-hook model of bonding and oxidation state is based on the ionic approximation of molecules—they are used to predict reactivity and other molecular properties through their properties as charges. In this submission, it is shown that formal charge and oxidation state are two extreme descriptions of bonding: formal charge (...) represents zero charge transfer between atoms while oxidation state represents complete charge transfer in each bond. These ‘localised electron approximations’ form an incomplete picture of atomic charge. Electronegativity measures the extent of polarity in real bonds; this concept can be introduced to polarise bonds relative to the ‘equal sharing model’. It is shown that the various electronegativity models are fundamentally related. We chose two models to demonstrate numerically that polar bonds yield charges intermediate between the localised electron approximations: Pauling and Mulliken. It is shown that probabilistic interpretation of the Pauling scale (‘scaled Pauling’ method) and use of asymmetric chemical potential (‘modified Mulliken’ method) lead to atomic charges that closely approximate experimental values using simple ‘back of the envelope’ calculations. It is seen that formal charge, oxidation state, and electronegativity-interpolated charge lie on a continuum and are mathematically related. It is therefore concluded that electronegativity introduces (quantum) delocalisation to the localised (classical) picture of electron bonding. (shrink)

Concerning race and its intertwinements with gender, sexual orientation, class, accents, or ability there is a scarcity of social psychological research in Europe. With an intersectional approach studying racism in Europe it is possible to detect specific experiences of discrimination. The prevalent understanding of European racism is connected to migration from the former colonies to the European metropoles and the post-Second-World-War immigration of ‘guest workers.’ Thus, the focus of this research is on work-related discrimination. Against the background of a short (...) historical review, we present the results of the few existing studies on intersectional discrimination within the labor market in Europe and discuss their implications. The pattern of findings is more complex than the assumption that individuals belonging to two or more marginalized social categories are always the most discriminated ones. Gender, sexual orientation, and origin rather interact with the specific job context. These interactions determine whether minority individuals are discriminated against or even preferred over individuals belonging to the majority group. We argue that considering the stereotype content model and social-identity theory helps to structure the sometimes contradictory results of intersectionality research. Therefore, the review presents new perspectives on racism in Europe based on current research, develops hypotheses on the interplay of intersecting identities, and identifies four novel research questions based on racist attributions considering situational variables: These are the role of concrete job contexts in explaining discrimination, the influence of different stereotypes regarding marginalized groups, the explanatory value of sexual orientation as well as class or socioeconomic-status and age in terms of some patterns of results. (shrink)

What role, if any, should centered possible worlds play in characterizing the attitudes? Lewis :513–543, 1979) argued that, in order to account for the phenomena of self-location :474–497, 1977, Noûs 13:3–21, 1979), the contents of the attitudes should be taken to be centered propositions. Stalnaker Assertion: New philosophical essays, Oxford University Press, Oxford, 2011, Context, Oxford University Press, Oxford, 2014), however, has argued that while centered worlds are needed to characterize e.g. belief states, the contents of such states should be (...) understood as ordinary, uncentered propositions. But Stalnaker does not, as is common, provide a semantics of attitude ascriptions based on the models he develops of the attitudinal states themselves. This paper begins to explore the prospects for doing so. It argues that a simple but well-motivated approach does not yield the principles of knowledge and belief Stalnaker endorses; and that a modification which does brings with it worries of its own surrounding communication and learnability. A technical appendix contains novel and pertinent results in doxastic/epistemic logic. (shrink)

An experiment is reported examining dual-process models of belief bias in syllogistic reasoning using a problem complexity manipulation and an inspection-time method to monitor processing latencies for premises and conclusions. Endorsement rates indicated increased belief bias on complex problems, a finding that runs counter to the “belief-first” selective scrutiny model, but which is consistent with other theories, including “reasoning-first” and “parallel-process” models. Inspection-time data revealed a number of effects that, again, arbitrated against the selective scrutiny model. The most (...) striking inspection-time result was an interaction between logic and belief on premise-processing times, whereby belief - logic conflict problems promoted increased latencies relative to non-conflict problems. This finding challenges belief-first and reasoning-first models, but is directly predicted by parallel-process models, which assume that the outputs of simultaneous heuristic and analytic processing streams lead to an awareness of belief - logic conflicts than then require time-consuming resolution. (shrink)

Since 1997 there has been a significant increase in the number and percentage of Kansas farmers who are women. Using Reskin and Roos’ model of “job queues and gender queues” I analyze changes in the agricultural industry in Kansas that resulted in more women becoming “principal farm operators” in the state. I find there are three changes largely responsible for women increasing their representation in the occupation: an increase in the demand for niche products, a decrease in the average farm (...) size, and greater societal acceptance of women as farmers. This study adds to the growing literature on women principal farm operators in developed countries, and is among the first to explore why women are becoming a larger percentage of the occupation in the United States. (shrink)

In this book Joel Spring explores three major international educational ideologies that are shaping global society: neo-liberal educational ideology, human rights education, and environmentalism. _Neo-liberal ideology_ reflects a rethinking of nationalist forms of education as the nation-state slowly erodes under the power of a growing global civil society. Traditional nationalist education attempts to mold loyal and patriotic citizens who are emotionally attached to symbols of the state, whereas the goal of neo-liberal educational ideology is to change nationalist education to (...) serve the needs of the global economy. These changes are fueling a clash between the ideas of free-market and consumer-based neo-liberals and those of human rights and environmental educators. _Human rights education_ is concerned with creating activist global citizens. It is rooted in the idea that inherent in human rights doctrines is a collective responsibility to ensure the rights of all people. _Environmentalism_ is the most radical of the ideologies because it rejects the industrial and consumerist paradigm that has dominated most economic thought, including capitalism and communism. Spring synthesizes and analyzes the effect of these educational ideologies on shaping the future of the global society. In the concluding section, he compares the effect of these ideologies on global society with the possibility of a world divided between conflicting civilizations. _How Educational Ideologies Are Shaping Global Society: Intergovernmental Organizations, NGOs, and the Decline of the Nation-State_ features: *a critical exploration of the transition of schooling from a function of the nation-state to a globalized economic and political system; *a discussion of the major organizations and trading blocs shaping the future globalization of educational policies; *an analysis of the major competing global ideologies of education--including national and corporate models that emphasize training workers for a competitive global free market; the worldwide network of human rights and peace educators who are teaching a global set of ethics; and the environmental movement's efforts to create a common set of educational standards for sustainable development and sustainable consumption; and *an exploration of the possible future of global educational policy and school organizations. By integrating a wide range of previously scattered information within a bold new framework for understanding educational ideologies and their impact on the global society, Spring raises important questions for researchers, professionals, and students in history and philosophy of education, educational policy, educational studies, comparative education, multicultural education, curriculum studies, critical media studies, global studies, human rights education, and related areas. (shrink)

ABSTRACT In this article I consider alternate but often complementary models for women’s republicanism from those discussed by Sandrine Bergès. In particular, I make use of Bergès’s insights about extending philosophical inquiry beyond traditional texts to analyse how militant political action was both informed by and informed the creation of philosophical texts, and consider the possibility of bringing direct action into the realm of philosophical investigation.

The authors focus on the ways in which various models of the distribution of power in society treat interest groups and evaluate their significance.

US citizens perceive their society to be one of the most diverse and religiously tolerant in the world today. Yet seemingly intractable religious intolerance and moral conflict abound throughout contemporary US public life - from abortion law battles, same-sex marriage, post-9/11 Islamophobia, public school curriculum controversies, to moral and religious dimensions of the Black Lives Matter and Occupy Wall Street movements, and Tea Party populism. Healthy Conflict in Contemporary American Society develops an approach to democratic discourse and coalition-building across deep (...) moral and religious divisions. Drawing on conflict transformation in peace studies, recent American pragmatist thought, and models of agonistic democracy, Jason Springs argues that, in circumstances riven with conflict between strong religious identities and deep moral and political commitments, productive engagement may depend on thinking creatively about how to constructively utilize conflict and intolerance. The result is an approach oriented by the recognition of conflict as a constituent and life-giving feature of social and political relationships. (shrink)

In the United States “restorative justice” typically refers to small-scale measures that divert alleged wrongdoers from a standard path through the criminal justice system by funneling them into alternative justice programs. These aim not to punish the offender, but to constructively address the harm that wrongdoing may have caused to individuals or to the community, engaging with the wrongdoer to come to a response that might heal and repair the harm. -/- Yet restorative justice initiatives generally fail to challenge and (...) transform the racist system of mass incarceration. This book argues that these initiatives have the potential to do so, but that we need to better understand what restorative justice is, and how it should be implemented. It claims that restorative justice can achieve its desired effect only insofar as it provides a mode of association between people that is, at its core, moral and spiritual. The book explores the ways in which restorative justice ethics and practices exhibit moral and spiritual dynamics, and what difference such “lived religious” dynamics can make for purposes of transforming structural violence. -/- Looking to Chicago’s restorative justice network as a model for developing these transformational and sustainable social changes, the volume showcases real-life examples of the kinds of practices and initiatives needed to shift the entrenched dynamics that fuel the prison-industrial complex across the United States. The book argues that restorative justice has the capacity to transform systemic injustices inscribed in U.S. mass incarceration in ways that mediate the "prison reform" vs "prison abolition" dichotomy. (shrink)

There is a deluge of AI-assisted decision-making systems, where our data serve as proxy to our actions, suggested by AI. The closer we investigate our data (raw input, or their learned representations, or the suggested actions), we begin to discover “bugs”. Outside of their test, controlled environments, AI systems may encounter situations investigated primarily by those in other disciplines, but experts in those fields are typically excluded from the design process and are only invited to attest to the ethical features (...) of the resulting system or to comment on demonstrations of intelligence and aspects of craftmanship after the fact. This communicative impasse must be overcome. Our idea is that philosophical and engineering considerations interact and can be fruitfully combined in the AI design process from the very beginning. We embody this idea in the role of a philosopher engineer. We discuss the role of philosopher engineers in the three main design stages of an AI system: deployment management (what is the system’s intended use, in what environment?); objective setting (what should the system be trained to do, and how?); and training (what model should be used, and why?). We then exemplify the need for philosopher engineers with an illustrative example, investigating how the future decisions of an AI-based hiring system can be fairer than those contained in the biased input data on which it is trained; and we briefly sketch the kind of interdisciplinary education that we envision will help to bring about better AI. (shrink)

Identifying sporting talent remains a difficult task due to the complex nature of sport. Technical skill assessments are used throughout the talent pathway to monitor athletes in an attempt to more effectively predict future performance. These assessments however, largely focus on the isolated execution of key skills devoid of any game context. When assessments are representative of match-play and applied in a setting where all four components of competition (i.e., technical, tactical, physiological and psychological) are assessed within an integrated approach, (...) prediction of talent is more likely to be successful. This article explores the current talent identification technical skill assessments, with a particular focus on Australian Football, and proposes a 5-level performance assessment model for athlete assessment. The model separates technical game skill on a continuum from Level-1 (i.e., laboratory analysis) to Level-5 (i.e., match-play). These levels, using the assumptions of the expert performance model and representative learning design theory, incorporate a step-wise progression of performance demands to more closely represent match-play conditions. The proposed model will provide researchers and practitioners with a structured framework to consider when assessing, or developing, new assessments of technical game-based skill. (shrink)

Two experiments are reported that employed think-aloud methods to test predictions concerning relevance effects and rationalisation processes derivable from Evans' (1996) heuristic-analytic theory of the selection task. Evans' account proposes that card selections are triggered by relevance-determining heuristics, with analytic processing serving merely to rationalise heuristically cued decisions. As such, selected cards should be associated with more references to both their facing and their hidden sides than rejected cards, which are not subjected to analytic rationalisation. Experiment 1 used a standard (...) selection-task paradigm, with negative components permuted through abstract conditional rules. Support was found for all heuristic-analytic predictions. This evidence was shown to be robust in Experiment 2, where "select - don't select" decisions were enforced for all cards. Both experiments also clarify the role played by secondary heuristics in cueing the consideration of hidden card values during rationalisation. We suggest that whilst Evans' heuristic-analytic model and Oaksford and Chater's (e.g., 2003) optimal data selection model can provide compelling accounts of our protocol findings, the mental models theory fares less well as an explanation of our full dataset. (shrink)

In the last decades, Systems Biology (including cancer research) has been driven by technology, statistical modelling and bioinformatics. In this paper we try to bring biological and philosophical thinking back. We thus aim at making diferent traditions of thought compatible: (a) causality in epidemiology and in philosophical theorizing—notably, the “sufcient-component-cause framework” and the “mark transmission” approach; (b) new acquisitions about disease pathogenesis, e.g. the “branched model” in cancer, and the role of biomarkers in this process; (c) the burgeoning of omics (...) research, with a large number of “signals” and of associations that need to be interpreted. In the paper we summarize frst the current views on carcinogenesis, and then explore the relevance of current philosophical interpretations of “cancer causes”. We try to ofer a unifying framework to incorporate biomarkers and omic data into causal models, referring to a position called “evidential pluralism”. According to this view, causal reasoning is based on both “evidence of diference-making” (e.g. associations) and on “evidence of underlying biological mechanisms”. We conceptualize the way scientists detect and trace signals in terms of information transmission, which is a generalization of the mark transmission theory developed by philosopher Wesley Salmon. Our approach is capable of helping us conceptualize how heterogeneous factors such as micro and macro-biological and psycho-social—are causally linked. This is important not only to understand cancer etiology, but also to design public health policies that target the right causal factors at the macro-level. (shrink)

Although it is now generally acknowledged that new biomedical technologies often produce new definitions and sometimes even new concepts of disease, this observation is rarely used in research that anticipates potential ethical issues in emerging technologies. This article argues that it is useful to start with an analysis of implied concepts of disease when anticipating ethical issues of biomedical technologies. It shows, moreover, that it is possible to do so at an early stage, i.e. when a technology is only just (...) emerging. The specific case analysed here is that of ‘molecular medicine’. This group of emerging technologies combines a ‘cascade model’ of disease processes with a ‘personal pattern’ model of bodily functioning. Whereas the ethical implications of the first are partly familiar from earlier—albeit controversial—forms of preventive and predictive medicine, those of the second are quite novel and potentially far-reaching. (shrink)

The diploblastic Cnidaria form one of the most ancient metazoan phyla and thus provide a useful outgroup for comparative studies of the molecular control of development in the more complex, and more often studied, triploblasts. Among cnidarians, the reef building coral Acropora is a particularly appropriate choice for study. Acropora belongs to the Anthozoa, which several lines of evidence now indicate is the basal class within the phylum Cnidaria, and has the practical advantages that its reproduction is predictable, external (...) and accessible and that the base content of its genome is not strongly biased. The Acropora system has already provided insights into ancestral linkages of homeobox genes and the evolution of the Pax genes, and has the potential to provide further new perspectives on the age, role in development, and evolution of these and other gene families. BioEssays 22:291–296, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

Wason's standard 2-4-6 task requires discovery of a single rule and leads to around 20% solutions, whereas the dual goal (DG) version requires discovery of two rules and elevates solutions to over 60%. We report an experiment that aimed to discriminate between competing accounts of DG facilitation by manipulating the degree of complementarity between the to-be-discovered rules. Results indicated that perfect rule complementarity is not essential for task success, thereby undermining a key tenet of the goal complementarity account of DG (...) facilitation. The triple heterogeneity account received a good degree of support since more varied triple exploration was associated with facilitatory DG conditions, in line with this account's prediction that task success is associated with the creative search of the problem space. The contrast class account (an extension of Oaksford & Chater's, 1994, iterative counterfactual model) was also corroborated in that the generation of descending triples was demonstrated to be the dominant predictor of DG success. We focus our discussion on conceptual ideas relating to the way in which iterative counterfactual testing and contrast class identification may work together to provide a powerful basis for effective hypothesis testing. (shrink)

Despite its strengths, Leech et al.'s model fails to address the important benefits that derive from self-explanation and task feedback in analogical reasoning development. These components encourage explicit, self-reflective processes that do not necessarily link to knowledge accretion. We wonder, therefore, what mechanisms can be included within a connectionist framework to model self-reflective involvement and its beneficial consequences.

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)

Molecular vibrations and quantum tunneling may link ligand binding to the function of pharmacological receptors. The well‐established lock‐and‐key model explains a ligand's binding and recognition by a receptor; however, a general mechanism by which receptors translate binding into activation, inactivation, or modulation remains elusive. The Vibration Theory of Olfaction was proposed in the 1930s to explain this subset of receptor‐mediated phenomena by correlating odorant molecular vibrations to smell, but a mechanism was lacking. In the 1990s, inelastic electron tunneling (...) was proposed as a plausible mechanism for translating molecular vibration to odorant physiology. More recently, studies of ligands’ vibrational spectra and the use of deuterated ligand analogs have provided helpful information to study this admittedly controversial hypothesis in metabotropic receptors other than olfactory receptors. In the present work, based in part on published experiments from our laboratory using planarians as an experimental organism, I will present a rationale and possible experimental approach for extending this idea to ligand‐gated ion channels. (shrink)

One might poetically muse that computers have the essence both of logic and machines. Through the case of the history of Separation Logic, we explore how this assertion is more than idle poetry. Separation Logic works because it merges the software engineer’s conceptual model of a program’s manipulation of computer memory with the logical model that interprets what sentences in the logic are true, and because it has a proof theory which aids in the crucial problem of scaling the reasoning (...) task. Scalability is a central problem, and some would even say the central problem, in appli- cations of logic in computer science. Separation Logic is an interesting case because of its widespread success in verification tools. For these two senses of model—the engineering/conceptual and the logical—to merge in a genuine sense, each must maintain their norms of use from their home disciplines. When this occurs, both the logic and engineering benefit greatly. Seeking this intersection of two different senses of model provides a strategy for how computer scientists and logicians may be successful. Furthermore, the history of Separation Logic for analysing programs provides a novel case for philosophers of science of how software engineers and computer scientists develop models and the components of such models. We provide three contributions: an exploration of the extent of models merging that is necessary for success in computer science; an introduction to the technical details of Separation Logic, which can be used for reasoning about other exhaustible resources; and an introduction to the problems, process, and results of computer scientists for those outside the field. (shrink)

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)

Hodgkin and Huxley’s 1952 model of the action potential is an apparent dream case of covering-law explanation. The model appeals to general laws of physics and chemistry (specifically, Ohm’s law and the Nernst equation), and the laws, coupled with details about antecedent and background conditions, entail many of the significant properties of the action potential. However, Hodgkin and Huxley insist that their model falls short of an explanation. This historical fact suggests either that there is more to explaining the action (...) potential than subsuming it under a general laws or that Hodgkin and Huxley were wrong about the explanatory import of their model. In this paper, I defend Hodgkin and Huxley’s view that their model alone does not explain the action potential (contra Weber 2005). I argue further that neuroscientists lacked crucial explanatory details about the action potential until they could describe the molecular and ionic mechanisms by virtue of which their model holds (see Bogen 2005). Mathematical generalizations are important epistemic tools for assessing mechanistic explanations, but they are neither necessary nor sufficient for adequate explanations, even at the lowest levels of organization where biological phenomena are integrated with physics and chemistry. (shrink)

The use of informatic metaphors and models derived from mid-20th-century cyberscience in molecular biology has been the subject of much controversy. Many social critics have argued that informatic discourses implicitly privilege a disembodied or implicitly masculine conception of life that is most fully realized in contemporary genomics. In this paper, I offer a different perspective on these issues by returning to the 18th-century work of Gregor Mendel, who conducted a series of experiments that are generally regarded as having (...) laid down the basic rules of heredity underlying genetic science. I attempt to show that a nascent informatic understanding of the body is already present in Mendel’s work, and that the implications of his approach for the politics of gender and social life are much more ambiguous than is generally recognized. More specifically, I argue that the meaning of ‘sex’, and of its relation to the organic body, is implicitly at stake in Mendel’s thought. I suggest that his text contains certain unresolved questions of sexual propriety that are today still being worked out in the context of contemporary genomics. (shrink)

Conrad Hal Waddington was a British developmental biologist who mainly worked in Cambridge and Edinburgh, but spent the late 1930s with Morgan in California learning about Drosophila. He was the first person to realize that development depended on the then unknown activities of genes, and he needed an appropriate model organism. His major experimental contributions were to show how mutation analysis could be used to investigate developmental mechanisms in Drosophila, and to explore how developmental mutation could drive evolution, his other (...) deep interest. Waddington was, however, predominantly a thinker, and set out to provide a coherent framework for understanding the genetic bases of embryogenesis and evolution, developing his ideas in many books. Perhaps his best-known concept is the epigenetic landscape: here a ball rolls down a complex valley, making path choices. The rolling ball represents a cell’s development over time, while the topography represents the changing regulatory environment that controls these choices. In its later forms, the role of each feature in the landscape was controlled by the effects of sets of interacting genes, an idea underpinning contemporary approaches to systems biology. Waddington was the first developmental geneticist and probably the most important developmental biologist of the pre-molecular age. (shrink)

In a number of membrane-bound viruses, ion channels are formed by integral membrane proteins. These channel proteins include M2 from influenza A, NB from influenza B, and, possibly, Vpu from HIV-1. M2 is important in facilitating uncoating of the influenza A viral genome and is the target of amantadine, an anti-influenza drug. The biological roles of NB and Vpu are less certain. In all cases, the protein contains a single transmembrane α-helix close to its N-terminus. Channels can be formed by (...) homo-oligomerization of these proteins, yielding bundles of transmembrane helices that span the membrane and surround a central ion-permeable pore. Molecular modeling may be used to integrate and interpret available experimental data concerning the structure of such transmembrane pores. This has proved successful for the M2 channel domain, where two independently derived models are in agreement with one another, and with solid-state nuclear magnetic resonance (NMR) data. Simulations based on channel models may yield insights into possible ion conduction and selectivity mechanisms. BioEssays 20:992–1000, 1998. © 1998 John Wiley & Sons, Inc. (shrink)

During the past few decades, philosophers of biology have debated the issue of reductionism versus anti-reductionism, with both sides often claiming a ‘pluralist’ position. However, both sides also tend to focus on a single research paradigm, which analyzes living things in terms of certain macromolecular components. I offer a case study where biologists pursue other analytic pathways, in a tradition of quantitative genetics that originates with the initially purely mathematical theories of R. A. Fisher, J. B. S. Haldane, and Sewall (...) Wright in the 1930s. Aster Models offers a class of statistical models designed for studying the fitness of plant and animal populations, by integrating the measurements of separate, sequential, non-normally distributed fitness components in novel ways. Their work generates important theoretical and practical results that do not require elaboration by molecular biology, and thus serves as a counterexample to the claims of philosophers whose ‘pluralism’ still harbors reductionist assumptions. (shrink)

Love, fear, hope, calculus, and game shows-how do all these spring from a few delicate pounds of meat? Neurophysiologist Ian Glynn lays the foundation for answering this question in his expansive An Anatomy of Thought, but stops short of committing to one particular theory. The book is a pleasant challenge, presenting the reader with the latest research and thinking about neuroscience and how it relates to various models of consciousness. Combining the aim of a textbook with the style (...) of a popularization, it provides all the lay reader needs to know to participate in the philosophical debate that is redefining our attitudes about our minds. Drawing on the rich history of neurological case studies, Glynn picks through the building blocks of our nervous system, examines our visual and linguistic systems, and probes deeply into our higher thought processes. The stories of great scientists, like Ramon y Cajal, and famous patients, like Sperry's split-brained epileptics, illuminate the scientific issues Glynn selects as essential for understanding consciousness. Some might argue that his lengthy explorations of natural selection overemphasize evolutionary explanations of psychological phenomena, but they must also agree that evolutionary psychology has distanced itself mightily from social Darwinism in recent years and merits a reappraisal. The great consciousness debate may form the core of the 21st-century Zeitgeist; get ready for it with An Anatomy of Thought. -Rob Lightner From Publishers Weekly How do we know? What do we think? How could a philosophical problem-'the mind-body problem,' say-induce a headache? What can evolutionary theory, molecular biology, the history of medicine and experimental psychology tell us about the features of human consciousness, and (once again) how do we know? Glynn, a physician and Cambridge University professor, meticulously attempts to answer these questions and more, setting forth the results of all sorts of research relevant to our brains-from 19th-century dissections to Oliver Sacks-like case studies, work with monkeys and supercomputers, and the enduring puzzles of philosophy, which he rightly saves for near the end. After explaining evolution by natural selection and 'clearing away much dross,' Glynn lays out the experiments and theories that have shown 'how nerve cells can carry information about the body, how they can interact' and how sense organs work; demonstrates the 'mixture of parallel and hierarchical organization' in our brains and 'the striking localization of function within it'; considers where neuroscience is likely to go; and admits that, among the many fields of exciting research just ahead, 'we can be least confident of progress toward a complete, scientific explanation of our sensations and thoughts and feelings.' Other recent explaining-the-brain books have sometimes advanced simplistic, or implausibly grand, claims about the nature and features of consciousness in general. Instead, Glynn offers a patient, informative, well-laid-out researcher's-eye view of what we have learned, how we figured it out and what we still don't know about neurons, senses, feelings, brains and minds. (Apr.) Copyright 2000 Reed Business Information, Inc. From Library Journal The nature of consciousness, which perennially troubles the minds of scientists and philosophers, is the subject of an ever-growing body of literature. Two of the latest entries approach the topic from different perspectives. Glynn, a professor of physiology and head of the Physiological Laboratory at Cambridge, offers a comprehensive summary of what we know about the brain-both its evolution and its mechanisms. Among the topics he covers are natural selection, molecular evolution, nerves and the nervous system, sensory perception, and the specific structures responsible for our intellect. Using the mechanisms involved in vision and speech as models, Glynn skillfully describes various neurological deficiencies that can lead to 'disordered seeing' and problems with the use of language. He carefully distinguishes what we know through experimental evidence from what we know through the observation of patients with neurological damage. He also describes some of the major theories that attempt to explain why these structures arose. While his book concentrates on the structures that make up the mind, Glynn is well aware that some physical events appear explicable only in terms of conscious mental events-a situation that conflicts with the laws of modern physics. Only briefly, however, does he consider the various approaches that have been taken to deal with the issues of mind/body and free will. In contrast, this is the primary focus of The Physics of Consciousness. After reviewing the fundamentals of classic physics, Walker (who has a Ph.D. in physics) summarizes elements of the new physics in which our knowledge of space, time, matter, and energy are all dependent on the moment of observation. Walker explores the meaning of consciousness as a characteristic of the observer. In this context both the observer and the act of measurement are critical. In essence, Walker leads his reader on a journey through his concept of a 'quantum mind,' which can both affect matter (including other minds) and can be affected by other distant matter/minds. To break up what would otherwise be an extremely dense text, Walker also relates the very touching story of the loss of his high-school sweetheart to leukemia. Indeed, it is his memory of their relationship that drives Walker to seek an understanding of ultimate reality. At times, he has a tendency to be dogmatic-as when he concludes, 'our consciousness, our mind, and the will of God are the same mind.' While An Anatomy of Thought is appropriate for most academic libraries, the Physics of Consciousness will be most accessible to readers with some knowledge of advanced physics. -Laurie Bartolini, Illinois State Lib., Springfield Copyright 2000 Reed Business Information, Inc. From Booklist The codiscoverers of natural selection-Charles Darwin and Alfred Wallace-disagreed over the possibility of finding an evolutionary explanation for the human mind. Glynn here argues Darwin's side of the debate, tracing an eons-long path of development starting from simple amino acids floating in primal seas and extending through the erect hominids in which the powers of a massive brain first manifest themselves. Patiently adducing evidence of an evolutionary origin for the underlying molecular machinery, Glynn dissects the nerve centers that make possible speech and hearing, sight, and reading. Pressing deeper, he lays bare the cortical foundations of personality. But those who deal with the mind must attend also to the arguments advanced by philosophers. And it is when he turns from dendrites to syllogisms (especially the vexing mind-body paradox) that Glynn's empirical reasoning fails him. In the end, he concedes his perplexity in trying to conceive of an evolutionary origin for human consciousness. This concession may set the shade of Alfred Wallace to chortling, but it will draw readers into an honest confrontation with a profound enigma. Bryce Christensen. (shrink)

The English language has adopted the word Tardis for something that looks simple from the outside but is much more complicated when inspected from the inside. The word comes from a BBC science fiction series, in which the Tardis is a machine for traveling in time and space, that looks like a phone booth from the outside. This paper claims that simulation models are a Tardis in a way that calls into question their transferability. The argument is developed taking (...) Molecular Modeling and Simulation as an example. There, simulation models are force fields that describe the molecular interactions and that look like simple and highly modular mathematical expressions. To make them work, they contain parameters that are adjusted to match certain data. The role of these parameters and the way they are obtained is seriously under-appreciated. It is constitutive for the model and central for its applicability and performance. Hence, the model is more than it seems so that working with adjustable parameters deeply affects the ontology of simulation models. This is particularly crucial for the transferability of the models: the information on how a model was trained is like luggage the model must carry on its voyage. (shrink)

In the 1960s molecular population geneticists used Monte Carlo experiments to evaluate particular diffusion equation models. In this paper I examine the nature of this comparative evaluation and argue for three claims: first, Monte Carlo experiments are genuine experiments: second, Monte Carlo experiments can provide an important meansfor evaluating the adequacy of highly idealized theoretical models; and, third, the evaluation of the computational adequacy of a diffusion model with Monte Carlo experiments is significantlydifferent from the evaluation of (...) the emperical adequacy of the same diffusion model. (shrink)

A peer instruction model was used whereby 78 residence dons (36 males, 42 females) provided instruction regarding academic integrity for 324 students (125 males, 196 females) under their supervision. Quantitative and qualitative analyses were conducted to assess survey responses from both the dons and students regarding presentation content, quality, and learning. Overall, dons consistently identified information-based slides about academic integrity as the most important material for the presentations, indicating that fundamental information was needed. Although student ratings of the usefulness of (...) the presentations were middling, students did indicate knowledge gains. Both interest and personal value for academic integrity were highly predictive of positive evaluations of the presentations. Dons and students provided suggestions for improvement and identified more global concerns. (shrink)

We apply molecular code theory to a rule-based model of the human inner kinetochore and study how complex formation in general can give rise to molecular codes. We analyze 105 reaction networks generated from the rule-based inner kinetochore model in two variants: with and without dissociation of complexes. Interestingly, we found codes only when some but not all complexes are allowed to dissociate. We show that this is due to the fact that in the kinetochore model proteins can (...) only bind at kinetochores by attaching to already attached proteins and cannot form complexes in free solution. Using a generalized linear mixed model we study which centromere protein can take which role in a molecular code . By this, associations between CENPs and code roles are found. We observed that CenpA is a major risk factor while CenpQ is a major protection factor . Finally we show, using an abstract model of copolymer formation, that molecular codes can also be realized solely by the formation of stable complexes, which do not dissociate. For example, with particular dimers as context a molecular code mapping from two different monomers to two particular trimers can be realized just by non-selective complex formation. We conclude that the formation of protein complexes can be utilized by the cell to implement molecular codes. Living cells thus facilitate a subsystem allowing for an enormous flexibility in the realization of mappings, which can be used for specific regulatory processes, e.g. via the context of a mapping. (shrink)

In the 1940s and 1950s, nuclear magnetic resonance , one of the most important analytical techniques in chemistry, grew to maturity in the intermediate research field of chemical physics. Chemists and physicists adapted the new technology to the experimental culture of molecular spectroscopy which was based on a pragmatic experimental style. In molecular spectroscopy, the purpose of experiments was the establishment of methods that suited both the physicists' quest for precision and theoretical model building and the chemists' longing (...) for empirical data and understanding of structural formulae and reaction courses. In this process, an experimental style emerged that can be characterized as reliance on self‐built instrumentation, theoretical foundation in quantum mechanics, and proof of utility in the solution of structural and dynamical questions. This article focuses on the early development of NMR at Harvard University, with particular emphasis on the contributions of the first chemist working in the field of NMR, Herbert S. Gutowsky. (shrink)

Using Gebharter’s representation, we consider aspects of the problem of discovering the structure of unmeasured submechanisms when the variables in those submechanisms have not been measured. Exploiting an early insight of Sober’s, we provide a correct algorithm for identifying latent, endogenous structure—submechanisms—for a restricted class of structures. The algorithm can be merged with other methods for discovering causal relations among unmeasured variables, and feedback relations between measured variables and unobserved causes can sometimes be learned.

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.

In The Logic of Life, François Jacob reconstructed the history of heredity from the seventeenth century to the present, emphasizing the role of physics in the development of biology. Quantum mechanics provided questions, methods, and techniques to molecular biologists. In the 1960s, physics also provided the organizational model. Jacob worked on the creation of the European Molecular Biology Laboratory, on the model of CERN (European Organization for Nuclear Research). I argue that reflection on the relation between molecular (...) biology and physics played a part in the making of The Logic of Life. Between the mid-1960s and the early 1970s, Jacob focused on relations between the “genealogy” of his molecular biology work and the development of physics at scientific, institutional, and historical levels. He thus brought molecular biology to the attention of a larger public, following the history of the Institut Pasteur, whose public mission had to be reaffirmed to grant its survival. With The Logic of Life, Jacob became an influential intellectual who engaged with scholars in human sciences. He promoted his view of the development of molecular biology as a model for a possible new discipline: bioanthropology. (shrink)

In a number of membrane-bound viruses, ion channels are formed by integral membrane proteins. These channel proteins include M2 from influenza A, NB from influenza B, and, possibly, Vpu from HIV-1. M2 is important in facilitating uncoating of the influenza A viral genome and is the target of amantadine, an anti-influenza drug. The biological roles of NB and Vpu are less certain. In all cases, the protein contains a single transmembrane α-helix close to its N-terminus. Channels can be formed by (...) homo-oligomerization of these proteins, yielding bundles of transmembrane helices that span the membrane and surround a central ion-permeable pore. Molecular modeling may be used to integrate and interpret available experimental data concerning the structure of such transmembrane pores. This has proved successful for the M2 channel domain, where two independently derived models are in agreement with one another, and with solid-state nuclear magnetic resonance (NMR) data. Simulations based on channel models may yield insights into possible ion conduction and selectivity mechanisms. BioEssays 20:992–1000, 1998. © 1998 John Wiley & Sons, Inc. (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)

Many lymphokine genes have now been cloned from activated T cells and their products have been expressed in mammalian cells. Use of these recombinant lymphokines has provided the opportunity to evaluate both the spectrum of their biological activities and the mechanisms of their action in promoting proliferation and differentiation of hemopoietic and lymphoid cells. Characterization of the structure of lymphokine genes will provide information about their regulated expression in T‐cell activation.

We present a conceptual model of the ways in which built and social environments shape the development of self-regulation in early childhood. Importantly, in centering children of color growing up in historically disinvested neighborhoods, we first describe how systemic structures of racism and social stratification have shaped neighborhood built and social environment features. We then present evidence linking these neighborhood features to children’s development of self-regulation. Furthermore, we take a multilevel approach to examining three potential pathways linking neighborhood contexts to (...) self-regulation: school environment and resources, home environment and resources, and child health behaviors. Finally, we consider how racial-ethnic-cultural strengths and multilevel interventions have the potential to buffer children’s development of self-regulation in disinvested neighborhood contexts. Advancing multilevel approaches to understand the development of self-regulation among children of color living in historically disinvested neighborhoods is an important step in efforts to promote equity in health and education. (shrink)

Sudden infant death syndrome (SIDS) has been mainly described from a risk perspective, with a focus on endogenous, exogenous, and temporal risk factors that can interact to facilitate lethal outcomes. Here we discuss the limitations that this risk-based paradigm may have, using two of the major risk factors for SIDS, prone sleep position and bed-sharing, as examples. Based on a multipronged theoretical model encompassing evolutionary theory, developmental biology, and cultural mismatch theory, we conceptualize the vulnerability to SIDS as an imbalance (...) between current physiologic-regulatory demands and current protective abilities on the part of the infant. From this understanding, SIDS appears as a developmental condition in which competencies relevant to self-protection fail to develop appropriately in the future victims. Since all of the protective resources in question are bound to emerge during normal infant development, we contend that SIDS may reflect an evolutionary mismatch situation—a constellation in which certain modern developmental influences may overextend the child’s adaptive (evolutionary) repertoire. We thus argue that SIDS may be better understood if the focus on risk factors is complemented by a deeper appreciation of the protective resources that human infants acquire during their normal development. We extensively analyze this evolutionary-developmental theory against the body of epidemiological and experimental evidence in SIDS research and thereby also address the as-of-yet unresolved question of why breastfeeding may be protective against SIDS. (shrink)

It is discerned what light can bring the recent historical reconstructions of maxwellian optics and electromagnetism unification on the following philosophical/methodological questions. I. Why should one believe that Nature is ultimately simple and that unified theories are more likely to be true? II. What does it mean to say that a theory is unified? III. Why theory unification should be an epistemic virtue? To answer the questions posed genesis and development of Maxwellian electrodynamics are elucidated. It is enunciated that the (...) Maxwellian Revolution is a far more complicated phenomenon than it may be seen in the light of Kuhnian and Lakatosian epistemological models. Correspondingly it is maintained that maxwellian electrodynamics was elaborated in the course of the old pre-maxwellian programmes’ reconciliation: the electrodynamics of Ampére-Weber, the wave theory of Young-Fresnel and Faraday’s programme. To compare the different theoretical schemes springing from the different language games James Maxwell had constructed a peculiar neutral language. Initially it had encompassed the incompressible fluid models; eventually – the vortices ones. The three programmes’ encounter engendered the construction of the hybrid theory at first with an irregular set of theoretical schemes. However, step by step, on revealing and gradual eliminating the contradictions between the programmes involved, the hybrid set is “put into order” (Maxwell’s term). A hierarchy of theoretical schemes starting from ingenious crossbreeds (the displacement current) and up to usual hybrids is set up. After the displacement current construction the interpenetration of the pre-maxwellian programmes begins that marks the commencement of theoretical schemes of optics, electricity and magnetism real unification. Maxwell’s programme surpassed that of Ampére-Weber because it did absorb the ideas of the Ampére-Weber programme, as well as the presuppositions of the programmes of Young-Fresnel and Faraday properly co-ordinating them with each other. But the opposite statement is not true. The Ampére-Weber programme did not assimilate the propositions of the Maxwellian programme. Maxwell’s victory over his rivals became possible because the gist of Maxwell’s unification strategy was formed by Kantian epistemology looked in the light of William Whewell and such representatives of Scottish Enlightenment as Thomas Reid and Sir William Hamilton. Maxwell did put forward as basic synthetic principles the ideas that radically differed from that of Ampére-Weber approach by their open, flexible and contra-ontological, genuinly epistemological, Kantian character. For Maxwell, ether was not the ultimate building block of physical reality, from which all the charges and fields should be constructed. “Action at a distance”, “incompressible fluid”, “molecular vortices”, etc. were contrived analogies for Maxwell, capable only to direct the researcher at the “right” mathematical relations. Key words: J.C. Maxwell, unification of optics and electromagnetism, I. Kant, T. Reid, W. Hamilton . (shrink)

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We (...) focus on the articulation and development of mechanistic models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)