An ontological approach to describing neurons and their relationships

The advancement of neuroscience, perhaps one of the most information rich disciplines of all the life sciences, requires basic frameworks for organizing the vast amounts of data generated by the research community to promote novel insights and integrated understanding. Since Cajal, the neuron remains a fundamental unit of the nervous system, yet even with the explosion of information technology, we still have few comprehensive or systematic strategies for aggregating cell-level knowledge. Progress toward this goal is hampered by the multiplicity of names for cells and by lack of a consensus on the criteria for defining neuron types. However, through umbrella projects like the Neuroscience Information Framework (NIF) and the International Neuroinformatics Coordinating Facility (INCF), we have the opportunity to propose and implement an informatics infrastructure for establishing common tools and approaches to describe neurons through a standard terminology for nerve cells and a database (a Neuron Registry) where these descriptions can be deposited and compared. This article provides an overview of the problem and outlines a solution approach utilizing ontological characterizations. Based on illustrative implementation examples, we also discuss the need for consensus criteria to be adopted by the research community, and considerations on future developments. A scalable repository of neuron types will provide researchers with a resource that materially contributes to the advancement of neuroscience

Psychological Innateness and Representations of God: Implications of the Innateness Controversy for the Study Of Religious Concepts

The author examines a means by which cognitive psychological notions of innateness might address the question ofhow the concept ofGod might be said to he \"natural\" or \"instinctive.\" He draws a distinction hetM\'een innate cognitive nuchanisms and innate cognitive content, and examines the concept of innateness from the perspectives of two major cognitive psychological theories of mind: computationalism and connectionism. He argues that, from the cognitive psychological perspective, concept(s) of God (or gods) cannot be said to be strictly innate, but that the development of the God concept does appear to be constrained by innate psychological structures and processes. He concludes by suggesting that the psychological origin of the God-concept may be best described as a sort of \"primal behavior\"—the inevitable product of interaction between innately determined psychological mechanisms and aspects of the environment that are common to all members of a population

Quantum Mechanical Coherence, Resonance, and Mind

Norbert Wiener and J.B.S. Haldane suggested during the early thirties that the profound changes in our conception of matter entailed by quantum theory opens the way for our thoughts, and other experiential or mind-like qualities, to play a role in nature that is causally interactive and effective, rather than purely epiphenomenal, as required by classical mechanics. The mathematical basis of this suggestion is described here, and it is then shown how, by giving mind this efficacious role in natural process, the classical character of our perceptions of the quantum universe can be seen to be a consequence of evolutionary pressures for the survival of the species.Comment: 36 pages, no figures, latexed, uses math_macros.tex (can get math_macros.tex from e-print archive), full postscript available from http://theor1.lbl.gov/www/theorgroup/papers/36915.p

Against Explanatory Minimalism in Psychiatry

The idea that psychiatry contains, in principle, a series of levels of explanation has been criticised both as empirically false but also, by Campbell, as unintelligible because it presupposes a discredited pre-Humean view of causation. Campbell’s criticism is based on an interventionist-inspired denial that mechanisms and rational connections underpin physical and mental causation respectively and hence underpin levels of explanation. These claims echo some superficially similar remarks in Wittgenstein’s Zettel. But attention to the context of Wittgenstein’s remarks suggests a reason to reject explanatory minimalism in psychiatry and reinstate a Wittgensteinian notion of level of explanation. Only in a context broader than the one provided by interventionism is the ascription of propositional attitudes, even in the puzzling case of delusions, justified. Such a view, informed by Wittgenstein, can reconcile the idea that the ascription mental phenomena presupposes a particular level of explanation with the rejection of an a priori claim about its connection to a neurological level of explanation

Bion Theory: an answer to the question Why is there Something rather than Nothing?

Why is there something rather than nothing? This paper explores one particular argument in favor of the answer that 'the existence of nothing' would amount to a logical contradiction. This argument consists of positing the existence of a novel entity, called a bion, of which all contingent things can be composed yet itself is non-contingent. First an overview of historical attempts to compile a systematic and exhaustive list of answers to the question is presented as context. Then follows an analysis of how the antropic principle would manifest itself in a world that consists of information and at the same time conforms to modal realism. Next, a thought experiment introduces bions as the foundation of such a world, showing how under these circumstances the ultimate origin of all existing things would be explained. The non-contingent nature of bions themselves is subsequently argued via a discussion of the principle of non-contradiction. Finally, this theory centered on the existence of bions is integrated into the worldview of Popperian metaphysics. According to the latter's criteria, I conclude that bion theory provides an integral answer to why there is something rather than nothing

New insights into the classification and nomenclature of cortical GABAergic interneurons.

A systematic classification and accepted nomenclature of neuron types is much needed but is currently lacking. This article describes a possible taxonomical solution for classifying GABAergic interneurons of the cerebral cortex based on a novel, web-based interactive system that allows experts to classify neurons with pre-determined criteria. Using Bayesian analysis and clustering algorithms on the resulting data, we investigated the suitability of several anatomical terms and neuron names for cortical GABAergic interneurons. Moreover, we show that supervised classification models could automatically categorize interneurons in agreement with experts' assignments. These results demonstrate a practical and objective approach to the naming, characterization and classification of neurons based on community consensus

Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach

An initiative of the NIH Blueprint for neuroscience research, the Neuroscience Information Framework (NIF) project advances neuroscience by enabling discovery and access to public research data and tools worldwide through an open source, semantically enhanced search portal. One of the critical components for the overall NIF system, the NIF Standardized Ontologies (NIFSTD), provides an extensive collection of standard neuroscience concepts along with their synonyms and relationships. The knowledge models defined in the NIFSTD ontologies enable an effective concept-based search over heterogeneous types of web-accessible information entities in NIF’s production system. NIFSTD covers major domains in neuroscience, including diseases, brain anatomy, cell types, sub-cellular anatomy, small molecules, techniques, and resource descriptors. Since the first production release in 2008, NIF has grown significantly in content and functionality, particularly with respect to the ontologies and ontology-based services that drive the NIF system. We present here on the structure, design principles, community engagement, and the current state of NIFSTD ontologies

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

Neuroeconomics: infeasible and underdetermined

Advocates of neuroeconomics claim to offer the prospect of creating a “unified behavioral theory” by drawing upon the techniques of neuroscience and psychology and combining them with economic theory. Ostensibly, through the “direct measurement” of our thoughts, economics and social science will be “revolutionized.” Such claims have been subject to critique from mainstream and non-mainstream economists alike. Many of these criticisms relate to measurability, relevance, and coherence. In this article, we seek to contribute to this critical examination by investigating the potential of underdetermination, such as the statement that testing involves the conjunction of auxiliary assumptions, and that consequently it may not be possible to isolate the effect of any given hypothesis. We argue that neuroeconomics is especially sensitive to issues of underdetermination. Institutional economists should be cautious of neuroeconomists’ zeal as they appear to over-interpret experimental findings and, therefore, neuroeconomics may provide a false prospectus seeking to reinforce the nostrums of homo economicus