The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The two parts of this particle constitute a single chapter in H.J. Berman, Law and Revolution: The Formation of the Western Legal Tradition, published by Harvard University Press.

v. 1. Nicomachean ethics. Politics. The Athenian Constitution. Rhetoric. On Poetics.--v. 2. Logic.--v. 3. Physics. Metaphysics. On the soul. Short physical treaties.--v. 4. On the heavens. On generation and corruption. Meteorology. Biological treatises.

When the whole is greater than the sum of the parts--indeed, so great that the sum far transcends the parts and represents something utterly new and different--we call that phenomenon emergence. When the chemicals diffusing in the primordial waters came together to form the first living cell, that was emergence. When the activities of the neurons in the brain result in mind, that too is emergence. In The Emergence of Everything, one of the leading scientists involved in the study of (...) complexity, Harold J. Morowitz, takes us on a sweeping tour of the universe, a tour with 28 stops, each one highlighting a particularly important moment of emergence. For instance, Morowitz illuminates the emergence of the stars, the birth of the elements and of the periodic table, and the appearance of solar systems and planets. We look at the emergence of living cells, animals, vertebrates, reptiles, and mammals, leading to the great apes and the appearance of humanity. He also examines tool making, the evolution of language, the invention of agriculture and technology, and the birth of cities. And as he offers these insights into the evolutionary unfolding of our universe, our solar system, and life itself, Morowitz also seeks out the nature of God in the emergent universe, the God posited by Spinoza, Bruno, and Einstein, a God Morowitz argues we can know through a study of the laws of nature. Written by one of our wisest scientists, The Emergence of Everything offers a fascinating new way to look at the universe and the natural world, and it makes an important contribution to the dialogue between science and religion. (shrink)

Cartesian mind body dualism and modern versions of this viewpoint posit a mind thermodynamically unrelated to the body but informationally interactive. The relation between information and entropy developed by Leon Brillouin demonstrates that any information about the state of a system has entropic consequences. It is therefore impossible to dissociate the mind's information from the body's entropy. Knowledge of that state of the system without an energetically significant measurement would lead to a violation of the second law of thermodynamics.

Celebrating the remarkable career of jurist Harold J. Berman, the essays in this volume demonstrate that Berman's contributions to Russian studies, international trade law, legal history, philosophy of law, and law and religion have firmly established him as part of the tradition of our greatest American jurists.

Christmas gives us that 'sweet little Jesus Boy' and Lent follows that with the 'gentle Jesus, meek and mild.' He was neither of those. In point of fact, he was the 'tough guy from Nazareth.' He was consistently abrasive, if not abusive, to his mother (Lk 2:49; Jn 2:4; Mt 12:48) and aggressively hard on males, particularly those in authority. In Mark 8 he cursed and damned Peter for failing to get Jesus' esoteric definition of Messiah correct. Nobody else understood (...) it either. Jesus had made it up himself and not adequately explained it to anybody until then. He called the religious authorities snakes, corrupt tombs, filthy chinaware, fakes, and Mosaic legalists who had forgotten God's real revelation of universal grace and salvation in the Abraham Covenant. He tore up the temple in the middle of a worship service and cursed those present for turning God's house of prayer into a den of thieves, when actually they were kind, helping out-of-town tourists obtain the proper sacrifices for the liturgical rituals. Jesus was persistently aggressive, often angry and not infrequently irrational, killing an innocent fig tree with his curse, for example. He constantly attacked the Pharisees and their proposals for renewing the spiritual vitality of the Jewish Community. He abused numerous people by healing them on the Sabbath just to make his political point against the religious leaders. He could just as well have healed them on Tuesday, if he really wanted to heal them. By healing the blind man in John 9 on the Sabbath, for example, he caused the man to be driven out of his synagogue, his family, and his community of faith; isolated and abandoned as if he were a leper. Even when he said surprising things about children, his focus was not on the children but on his disciples, using the children as tools for making an assertive teaching point. Jesus' life was one of perpetually aggressive claims for his vision of God's reign. He constantly and intentionally provoked conflict and disruption of the status quo, spiritually and politically. He refused to negotiate, compromise, palliate, or mollify his insistence upon keeping his elbow perpetually in the eye of the people in power. In all this he would not back down. The principle by which Jesus operated was absolute and that is why he did not back down, even though they killed him for this very reason. His principle was simply that the renewal of Jewish spirituality could only come from a return to the Abrahamic Covenant, which declared (Gn 12; Rm 8) that God is gracious and universally forgiving towards all humankind, unconditional to our conduct and behaviour, and radically in that it removes all fear, guilt, and shame from the equation of our relationship with God (Mi 7:18-20). He saw that the Pharisees and Scribes were absolutely wrong in assuming that the Mosaic legal system would renew the Jewish relationship with God. He was not the gentle Jesus, meek and mild. He was that tough guy from Nazareth! He had good reason and he was willing to go the distance for what he stood for, even to death on the cross. (shrink)

Scientific realism is usually a thesis or theses advanced about our best natural science. In contrast, this book defends scientific realism applied to the social and behavioral sciences. It does so, however, by applying the same argument strategy that many have found convincing for the natural sciences, namely, by arguing that we can only explain the success of the sciences by postulating their approximate truth. The particular success that Trout emphasizes for the social sciences is the effective use of statistical (...) testing. Social scientists apply diverse statistical measurement tools to social reality; they are able to refine and improve those measurements over time. The best explanation for such success is that the social sciences give us an approximately true account of some of the laws and entities of the social world. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Resolution of the entropy‐evolution problem was a significant issue for Pierre Teilhard de Chardin throughout his scientific career. Although never truly satisfied with his solution, he proposed that all energy must be psychic and contain two components. Tangential energy is related to physical energy. Radial energy in some way accounts for increasing complexity and consciousness in evolution. Analysis of developments in thermodynamics, statistical mechanics, and information theory show that Gibbs free energy contains both calorimetric and noetic components, thus validating Teilhard's (...) intuition. (shrink)

Integrating science, philosophy, and religion, the author shows the reader how to look at the most basic phenomena of life in new ways.