Definitions of Dream: A Paradigm for Comparing Field Descriptive Specific Studies of Dream

A single definition for dreaming is most likely impossible given the wide spectrum of fields engaged in the study of dreaming, and the diversity in currently applied definitions. Many studies do not specify a definition, yet results are likely to be comparable only when comparable definitions of the topic are used. The alternative is to develop a classification system organizing the multiplicity of definitions for dream. A dream should not be exclusively defined as a non-conscious electrophysiologic state. Dreaming is, at least in part, a mental experience that can be described during waking consciousness. Definitions for dreaming should be utilized in research and discussion which address the various axes which define dreaming: Wake/sleep, Recall, and Content.     

Planning horizons and end conditions for sustained yield studies in continuous cover forests

The contemporary forestry preoccupation with non-declining even-flow during yield simulations detracts from more important questions about the constraints that should bind the end of a simulation. Whilst long simulations help to convey a sense of sustainability, they are inferior to stronger indicators such as the optimal state and binding conditions at the end of a simulation. Rigorous definitions of sustainability that constrain the terminal state should allow flexibility in the planning horizon and relaxation of non-declining even-flow, allowing both greater economic efficiency and better environmental outcomes. Suitable definitions cannot be divorced from forest type and management objectives, but should embrace concepts that ensure the anticipated value of the next harvest, the continuity of growing stock, and in the case of uneven-aged management, the adequacy of regeneration.     

Inbreeding and relatedness coefficients: what do they measure?

This paper reviews and discusses what is known about the relationship between identity in state, allele frequency, inbreeding coefficients, and identity by descent in various uses of these terms. Generic definitions of inbreeding coefficients are given, as ratios of differences of probabilities of identity in state. Then some of their properties are derived from an assumption in terms of differences between distributions of coalescence times of different genes. These inbreeding coefficients give an approximate measurement of how much higher the probability of recent coalescence is for some pair of genes relative to another pair. Such a measure is in general not equivalent to identity by descent; rather, it approximates a ratio of differences of probabilities of identity by descent. These results are contrasted with some other formulas relating identity, allele frequency, and inbreeding coefficients. Additional assumptions are necessary to obtain most of them, and some of these assumptions are not always correct, for example when there is localized dispersal. Therefore, definitions based on such formulas are not always well-formulated. By contrast, the generic definitions are both well-formulated and more broadly applicable.     

CHARACTER DEFINITIONS AND CHARACTER STATE DELINEATION: THE BETE NOIRE OF PHYLOGENETIC INFERENCE

Abstract— Currently characters are static concepts whose definition and state delineations seldom undergo any scrutiny. Common systematic practice tends to synthesize character slates by combining or dividing observed conditions, a situation most likely due to current theoretical limitations in phylogenetic inference, which tends to ignore problems of multistate characters. This process we refer to as the “synthetic” method for character definition. Character definitions derived for the genera of North American Cochylini (Lepidoptera: Tortricidae) using “synthetic” character states postulated that the cochylines were not monophyletic. The use of cladogram characters and nearest neighbor matrices in uncovering potential flaws in character state delineation is demonstrated. The “synthetic” set of character definitions proved deficient upon such analysis, principally due to its attempt to force highly variable features into a few states. The set of character definitions produced from this analysis is referred to as “reflective” because it does not ignore observed variation. It produces characters with many states and presents problems of setting up transformation series. Three means lor deriving transformations are applied to produce transformation series for the reflective set of character definitions: the unordered outgroup method, morphocline analysis and Transformation Series Analysis (TSA). All three data sets postulated the Cochylini as monophyletic. The three sets of phylogenies were compared. Consensus trees are ambiguous when analysing changes in hierarchy. In order to summarize these results in a manner which does not destroy the phylogenetic structure, positional subtrees, a new means for summarizing multiple solution cladograms, are introduced. It was found that all three sets of transformations produced very different cladograms which in turn were very different from the tree produced by the original, synthetic definitions. The results of each of these methods were assessed for their internal consistency. TSA gave the least contradictory results.     

Aspects of early arthritis. Definition of disease states in early arthritis: remission versus minimal disease activity

With regard to rheumatoid arthritis, remission as currently used in the literature can have two meanings: either a state with persistent absence of clinical and radiological signs of disease activity without being treated for a specific time period, or it may point to a disease state with minimal disease activity during antirheumatic treatment. A risk factor for the first is absence of autoantibodies, with the anti-CCP-antibodies as best predictors, whereas risk factors for achieving a drug-induced state of minimal disease activity are not well defined. These definitions of remission refer to different disease states; therefore, we propose that the term remission is reserved for patients that are not treated with antirheumatic drugs.     

Toward a Locational Definition of State Systems of Settlement

Recent information indicates that urbanism is only one of several options providing the means to consolidate, concentrate, and organize the coercive power necessary for state formation. Central Place Theory (CPT) is a model of urban settlement frequently chosen to approach the broader problem of state formation, but its universal applicability is in doubt. In this paper, spatial and functional definitions of urbanism and other concepts (functional center, functional lattice) related to state systems of settlement are derived using locational analytic approaches other than CPT, and their implications are discussed. A typology of state-level settlements is introduced. Advantages of a locational approach to the investigation of settlement systems are suggested.     

Adverse environmental impact: 30-year search for a definition

Since passage of the Clean Water Act in 1972, there has been a long, unresolved struggle to define a key phrase in Section 316(b) of the act: "adverse environmental impact" (AEI). Section 316(b) requires that the best technology available be used in cooling-water intake structures to minimize AEI due to entrainment and impingement of aquatic organisms. Various attempts were made to evaluate and define AEI, including focused national conferences on impact assessment. Unresolved arguments regarding AEI were reinvigorated following the 1995 Consent Decree requiring EPA to propose new rules to implement Section 316(b). This article reviews and compares eight proposed definitions of AEI. Six of the definitions define AEI as impact expressed at the population or higher level of biological organization. The two remaining definitions are unrelated to populations: a 1% cropping of the near-field organisms and "one fish equals AEI". The latter definition is based on the desire of some stakeholders to define AEI as the loss of any public trust resources. Equating loss of public trust resources with AEI hampers consensus on a definition because a societal-based policy concept (public trust resources) is commingled with science-based definitions based on population effects. We recommend that a population-based definition of AEI be incorporated into Section 316(b) guidance and observe that this will not preclude a state from exercising its law and policy to protect public trust resources.     

Definitions of pathogenicity and virulence in invertebrate pathology

Accurate definition and usage of terminology are critical to effective communication in science. In a recently published article, the clarity and consistency of the terms pathogenicity and virulence as used in invertebrate pathology were called into question, and a revision of these terms was proposed. Our objective was to examine definitions of pathogenicity and virulence and their use in invertebrate pathology, and respond to this article. Although usage of the terms pathogenicity and virulence varies, we found considerable consistency in the published definitions of these terms in the invertebrate pathology literature throughout the history of the discipline, as well as among related disciplines such as medicine and microbiology. We did not find the established definitions to be lacking in clarity or utility. Therefore, we recommend that the definition and use of these terms adhere to precedence. Specifically, pathogenicity is the quality or state of being pathogenic, the potential ability to produce disease, whereas virulence is the disease producing power of an organism, the degree of pathogenicity within a group or species. Pathogenicity is a qualitative term, an “all-or-none” concept, whereas virulence is a term that quantifies pathogenicity.     

Propositions for a character-state-based biological taxonomy

A new procedure for defining taxa upon a single character state is developed. It is centred on the designation of two specimens, belonging to two distinct species, exhibiting the same given character state, as type material, and referred to as ‘cladotypes’. A taxon name/definition designates a monophyletic group until one of the following assumptions is falsified: (1) the character state typified by cladotypes is homologous in individuals that are designated as cladotypes, and (2) cohesion mechanisms isolated individuals exhibiting the type‐character‐state from those that do not. A taxon defined by a character state that is found to be a combination of several character states is to be redefined upon a character state shared by its cladotypes. If several character states are available, the character state that makes the taxon the least inclusive taxon including cladotypic species (i.e., species to which belong cladotypes) is to be preferred. Taxon names designate obsolete phylogenetic hypotheses if the first assumption is falsified (such names are to be kept for this purpose, i.e., they are not to be recycled in another definition). Rules governing adaptation of previously erected names are proposed. Main cases of taxa synonymy involve definitions based on different pairs of cladotypes but referring to the same type‐character‐state; and definitions based on the same character‐state initially hypothesised as acquired by convergence in cladotypic species pairs, but later demonstrated as originating from a unique ancestor. Taxa could be synonyms if a permanent splitting event did not segregate individuals exhibiting a new character state, qualified as type‐character‐state, from individuals already assigned to a previously erected taxon. This procedure accommodates potentially any species concept, but is not tied to any; it is an extension of the composite species concept. Species are treated in a different way than other taxa: they are defined as sets of individuals belonging to the same evolving (segments of) metapopulation lineages as a holotype specimen, and do not need a defining character state.     

Evolutionary stasis, constraint and other terminology describing evolutionary patterns

Current use of terms to describe evolutionary patterns is vague and inconsistent. In this paper, logical definitions of terms that describe specific evolutionary patterns are proposed. Evolutionary inertia is defined in a manner analogous to inertia in physics. A character in a static state of evolutionary inertia represents evolutionary stasis while a character showing consistent directional evolutionary change represents evolutionary thrust. I argue that evolutionary stasis should serve as the null hypothesis in all character evolution studies. Deviations from this null model consistent with alternative hypotheses (e.g. random drift, adaptation) can then give us insight into evolutionary processes. Failure to reject a null hypothesis of evolutionary stasis should not be used as a serious explanation of data. The term evolutionary constraint is appropriate only when a selective advantage for a character state transition is established but this transition is prevented by specific, identified factors. One type of evolutionary constraint discussed is evolutionary momentum. A final pattern of evolutionary change discussed is closely related to evolutionary thrust and is referred to as evolutionary acceleration. I provide examples of how this set of definitions can improve our ability to communicate interpretations of evolutionary patterns.     

Beneficial regulation of procedure in editing stratigraphy

In the present state of development of stratigraphy and of international time-correlation, it is important for the editor (a) to encourage discipline in certain data-handling matters, (b) to advise adherence to IUGS decisions on scale definitions, and (c) to allow considerable freedom in matters of correlation method, subject only to normal requirements of clear honest presentation and the statement of confidence and other limitations.     

Intrinsic Brain Connectivity Related to Age in Young and Middle Aged Adults

Age-related variations in resting state connectivity of the human brain were examined from young adulthood through middle age. A voxel-based network measure, degree, was used to assess age-related differences in tissue connectivity throughout the brain. Increases in connectivity with age were found in paralimbic cortical and subcortical regions. Decreases in connectivity were found in cortical regions, including visual areas and the default mode network. These findings differ from those of recent developmental studies examining earlier growth trajectories, and are consistent with known changes in cognitive function and emotional processing during mature aging. The results support and extend previous findings that relied on a priori definitions of regions of interest for their analyses. This approach of applying a voxel-based measure to examine the functional connectivity of individual tissue elements over time, without the need for a priori region of interest definitions, provides an important new tool in brain science.     

Characterizing gene family evolution

Gene families are widely used in comparative genomics, molecular evolution, and in systematics. However, they are constructed in different manners, their data analyzed and interpreted differently, with different underlying assumptions, leading to sometimes divergent conclusions. In systematics, concepts like monophyly and the dichotomy between homoplasy and homology have been central to the analysis of phylogenies. We critique the traditional use of such concepts as applied to gene families and give examples of incorrect inferences they may lead to. Operational definitions that have emerged within functional genomics are contrasted with the common formal definitions derived from systematics. Lastly, we question the utility of layers of homology and the meaning of homology at the character state level in the context of sequence evolution. From this, we move forward to present an idealized strategy for characterizing gene family evolution for both systematic and functional purposes, including recent methodological improvements.     

Does Biology Need an Organism Concept?

Among biologists, there is no general agreement on exactly what entities qualify as ‘organisms’. Instead, there are multiple competing organism concepts and definitions. While some authors think this is a problem that should be corrected, others have suggested that biology does not actually need an organism concept. We argue that the organism concept is central to biology and should not be abandoned. Both organism concepts and operational definitions are useful. We review criteria used for recognizing organisms and conclude that they are not categorical but rather continuously variable. Different organism concepts are useful for addressing different questions, and it is important to be explicit about which is being used. Finally, we examine the origins of the derived state of organismality, and suggest that it may result from positive feedback between natural selection and functional integration in biological entities.     

Resolving current disagreements and ambiguities in the terminology of animal communication

Communication is central to most interactions between organisms. There is currently considerable controversy about the evolution, function and even about the most basic definition of communication. The controversy is linked to definitional ambiguities and disagreements. Here we discuss how some recent disagreements can be resolved and offer a clear set of definitions. Central to our approach is a definition of communication as being a trade between one organism (the informer) and another (the perceiver). The informer exerts influence on the perceiver through the communication process, and the perceiver experiences a change in its informational state (that is, gains information) as a consequence of detecting the communication. We define both influence and information explicitly and delineate between signalling, deceptive communication, and situations where perceivers respond to cues rather than signals. We demonstrate how our definitions allow resolution of conflicts arising in recent publications on the definitions on communication and related terms.     

The tracheid-vessel element transition in angiosperms involves multiple independent features: cladistic consequences

Current definitions of tracheids and vessel elements are overly simple. These definitions are based on light microscope studies and have not incorporated information gained with scanning electron microscopy (SEM) or transmission electron microscopy (TEM). Current definitions are based primarily on angiosperms, especially eudicots, and were devised before many basal angiosperms were carefully studied. When all sources of information are taken into account, one can recognize changes in six characters in the evolution of tracheids into vessel elements in angiosperms (or vice versa) as well as in other groups of vascular plants. There is an appreciable number of taxa in which all criteria for vessel origin are not met, and thus incipient vessels are present. At the very least, vessel presence or absence should not be treated as a single binary character state change in construction of cladistic matrices. Increase in conductive area of an end wall by means of lysis of progressively greater areas of pit membrane and increase in pit area on the end wall (as compared to pit area on equivalent portions of lateral walls) are considered the most important usable criteria for recognizing intermediacy between tracheids and vessel elements. Primitive character states in vessel elements are briefly discussed to differentiate them from changes in character states that can be regarded as intermediate between tracheids and vessel elements.     

What are definitions of life good for? Transdisciplinary and other definitions in astrobiology

The attempt to define life has gained new momentum in the wake of novel fields such as synthetic biology, astrobiology, and artificial life. In a series of articles, Cleland, Chyba, and Machery claim that definitions of life seek to provide necessary and sufficient conditions for applying the concept of life—something that such definitions cannot, and should not do. We argue that this criticism is largely unwarranted. Cleland, Chyba, and Machery approach definitions of life as classifying devices, thereby neglecting their other epistemic roles. We identify within the discussions of the nature and origin of life three other types of definitions: theoretical, transdisciplinary, and diagnostic definitions. The primary aim of these definitions is not to distinguish life from nonlife, although they can also be used for classificatory purposes. We focus on the definitions of life within the budding field of astrobiology, paying particular attention to transdisciplinary definitions, and diagnostic definitions in the search for biosignatures from other planets.     

Critical analysis of objections against the biological molecular energy machines.

In the past, two important objections against McClare's idea of biological molecular energy machines were raised. One of the criticisms was concerned with the origin of energy gained in ATP cleavage and with an interpretation of McClare's "excited vibrational state." The former argument reveals a failure of the critics to comprehend McClare's approach. As to the excited vibrational state, it can be identified with nonequilibrium conformational states of the unit rather than with a single vibrational mode. The other criticism based on Brillouin's energy cost of measurement argued that reversible operation of biological molecular energy machines would be virtually impossible. Using propagation velocities of deformations of the unit's structure (instead of velocity of light), the objections against reversibility are invalidated even in the framework of the critic's approach. McClare's idea and relevant definitions are thus physically correct.