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)

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.

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)

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)

This chapter contains section titled: Upbringing English Works, Dutch Sources The Fable Last Work and Legacy.

Two overriding considerations shaped the development of early research on the biological effects of microwave radiation—possible medical application and uncertainty about the hazards of exposure to radar. Reports in the late 1940s and early 1950s of hazards resulting from microwave exposure led to the near abandonment of medical research related to microwave diathermy at the same time that military and industrial concern over hazards grew, culminating in the massive research effort known as ‘the Tri-Service program’ . Both the early focus (...) on medical application and the later search for hazards played important roles in dictating how this field of research developed as a science. (shrink)

Hare used his thesis of universalizability to generate specific normative results and a defense of utilitarianism. To accomplish the latter task, he enjoined that one consider oneself in various roles in a given situation, and that the concluding judgment must be one that is affirmable in any of the various roles. In effect this means that one must, says Hare, give equal weight to the interests of all involved parties, an axiom of utilitarianism. The paper argues that he did not (...) succeed. (shrink)

The two parts of this article constitute a single chapter in H.J. Berman, Law and Revolution: The Formation of the Western Legal Tradition.

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.

Hare's important book Freedom and Reason has arguments applying the thesis of universalizability (a kind of neutrality principle) to a variety of cases. The procedure involves considering persons in different roles. I argue from a consideration of Hare's multilateral case (judge and thief) that the thesis by itself cannot enable one to reach the conclusion Hare intends. I argue that Hare's arguments require additional principles or premises to reach their desired conclusion. All of this bears on the possibility of extracting (...) utilitarianism from rather formal principles about neutrality of judgments. My arguments suggest this is not the case. (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.