Evolution of the Vertebrate Central Nervous System: Patterns and Processes

AS brains do not fossilize, most proposed phylogenetic sequencesfor central nervous system characters must be based on the patternsof variation of those characters in living organisms. Similarly,hypotheses regarding how brains change through time, and theevolutionary processes that produce these changes, are ultimatelybased on the character patterns recognized. It is critical inthese analyses to distinguish between homologous and homoplasouscharacters if errors in the reconstruction and interpretationof phylogenies are to be minimized. Definitions of homologyand homoplasy are reviewed, as are the concepts that bear ontheir application. Cladistic definitions are adopted, and criteriafor distinguishing homologous from homoplasous characters arediscussed. Analysis of a number of CNS characters that are usuallyassumed to be homologous reveals that homoplasous charactersappear among them. As in other organ systems, homoplasous charactersare actually common. A number of previous hypotheses regardingCNS evolution are reviewed in the context of new data on neuralconnections and their cladistic analysis. Some of these hypothesesmay be falsified by a cladistic treatment of CNS characters,whereas sufficient data do not exist to evaluate others.     

Toward Conceptual Cohesiveness: a Historical Analysis of the Theory and Utility of Ecological Boundaries and Transition Zones

Ecological transition zones are increasingly recognized as systems that play a critical role in controlling or modifying flows of organisms, materials, and energy across landscapes. Many concepts describing transitional areas have been proposed over the years, such as the prevalent and durable ecotone concept. Confusion among ecologists and land managers about transition zone concepts and the isolation of studies that use only one transition concept can hinder unified progress in understanding these key systems. Currently, a movement toward conceptual synthesis under the umbrella concept of ‘ecological boundary’ is underway. Here we examine the history and theoretical baggage of the ecotone, riparian zone, and several other concepts. Subsequently, we present a conceptual cluster analysis, which facilitates a better understanding of the similarities and differences between boundary and transition concepts. We emphasize the hierarchical nature of these concepts: higher-level synthetic concepts can be used in the development of theory, whereas lower-level concepts allow more specificity and the formulation of operational definitions. Finally, we look briefly at the utility and future use of boundary and transition zone concepts.     

Unifying principles of regeneration I: Epimorphosis versus morphallaxis

Because research on regeneration has a long history, some classic definitions and concepts about regeneration which were established in earlier times have been retained without reconsideration for a long time, even though many relevant new findings have accumulated. To clarify the points on which research should be focused on for elucidating the mechanisms of regeneration, we should reconsider such classical definitions and principles of regeneration at the cellular and molecular level. Here, we consider two differing principles of regeneration which have been classically defined as 'epimorphosis' and 'morphallaxis', and propose the abandonment of these classical categories and their replacement by a new unifying principle in order to facilitate regeneration studies.     

Phylogenetic definitions and taxonomic philosophy

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names.     

Core concepts of spatial prioritisation in systematic conservation planning

Systematic conservation planning (SCP) is a field of conservation biology concerned with delivering on‐the‐ground actions that achieve conservation goals. It describes a set of operational models that cover both design and implementation of conservation, with a strong focus on mobilising the collective action typically required to implement conservation. SCP, as it was originally described, was composed of six different stages: collection of data, identification of conservation goals, evaluation of the existing protected area network, design of expansions, implementation of conservation action, and long‐term maintenance of biodiversity in the network. Since then, the operational model has been expanded into several different variants. Conservation actions applied inside SCP include establishment and expansion of reserve networks and allocation of habitat restoration and management. Within the broader context of SCP, there is a fundamental biogeographic‐economic analysis frequently called spatial conservation prioritisation or conservation assessment, which is used for identifying where important areas for biodiversity are and how conservation goals might be achieved efficiently. Here, we review the usage and meaning of the 12 biogeographic‐economic core concepts of SCP: adequacy, complementarity, comprehensiveness, effectiveness, efficiency, flexibility, irreplaceability, replacement cost, representation, representativeness, threat, and vulnerability. Some of the concepts have clear definitions whereas others may have alternative and possibly conflicting definitions. With a comprehensive literature review literature, we elucidate the historical backgrounds of these concepts, the first definitions and usages, alternative later definitions, key applications, and prior reviews. This review reduces linguistic uncertainty in the application of SCP. Since SCP is a global activity with a multitude of different stakeholders involved, it is vital that those involved can speak the same language. Through these concepts, this review serves as a source of information about the historical development of SCP. It provides a comprehensive review for anyone wishing to understand the key concepts of spatial prioritisation within SCP.     

Measuring fractional forest canopy element cover and openness – definitions and methodologies revisited

Canopy structural parameters are often used to give adequate representation of vegetated ecosystems for various purposes including primary productivity, climate system, water and carbon gas exchanges, and radiation extinction. Canopy structural parameters are usually described using several pseudo‐synonymous terms, often measuring different components of vegetation canopies. Standardization in the definitions has fallen short, leading to confusion of terms even in standard text books making the comparison of historic measures futile. Here we clarify concepts that have been used for fractional canopy element cover and openness measures. The fractional canopy element cover and openness concepts considered are canopy closure, canopy cover, canopy openness, crown closure, crown completeness, crown cover, crown porosity, site openness and tilt openness. New methodologies are presented to obtain large scale fractional canopy element cover and openness measures using hemispherical photography. The new methodologies and variations in definitions of fractional canopy element cover and openness concepts are demonstrated using photographic measurements in complex topography. The results indicate that both fractional canopy element cover and openness parameters can be estimated with a few point‐based measurements using hemispherical photography. Hemispherical photography is therefore less time, labour and resource intensive, as compared to point based measuring techniques of canopy element cover and openness. Most of the commonly and interchangeably used concepts of fractional canopy element cover and openness measures represent physically different structural properties of a vegetated ecosystem.     

Through the Jungle of Biological Diversity

Biological diversity would apparently seem the most intuitive and easily studied of all the ecological concepts. However, in practice biodiversity has suffered from great number of definitions that vary with the specific needs of the different researchers, thus making it extremely confusing as an ecological concept. In this paper, I shortly review the concept of biodiversity showing that there exists a substantial ambiguity among ecologists as far as biodiversity conceptualization and evaluation is concerned. I conclude that, due to this major disagreement on its very nature, biodiversity may be defined simply as a set of multivariate summary statistics for quantifying different characteristics of community structure.     

Ecological units: definitions and application

Concepts of ecological units, such as population, community, and ecosystem, are at the basis of ecological theory and research and have increasingly become the focus of conservation strategies. Concepts of these units still suffer from inconsistencies and confusions over terminology. The different concepts are treated here together as a common "conceptual cluster," with similar ecological functions (roles) and similar problems in their definition and use. An analysis of the multitude of existing terms and concepts that have been developed for these units reveals that they differ with respect to at least four basic criteria: (i) the questions as to whether they are defined statistically or via a network of interactions; (ii) if their boundaries are drawn by topographical or process-related criteria; (iii) how high the required internal relationships are; and (iv) if they are perceived as "real" entities or abstractions by an observer The various definitions cannot be easily sorted into just a few types, but they can be characterized by several independent criteria. I argue that serious problems arise if the different possibilities of defining ecological units are not recognized and if the concepts are perceived as self-evident. The different concepts of ecological units should be defined and used in a philosophically informed manner I propose a dual approach to the use of ecological units. Generic meanings of the main concepts (especially population, community, and ecosystem) should be retained only as heuristically useful perspectives, while specific and "operational" definitions of the concepts as units should be developed, depending on specific purposes of their use. Some thoughts on the basic requirements for such definitions and the domains of their uses are briefly explained.     

Medical professionalism: one size fits all?

A number of medical specialties have recently developed their own specialty-specific charters. This proliferation of charters is representative of an unease about medical professionalism that has arisen not just from increasing medical specialization, but also from evolving needs as physicians progress through their careers. The development of such specialty-specific definitions of professionalism is undesirable: all specialties should adhere to the same basic principles. These charters and "definitions" should be incorporated into a formal developmental model, derived from needs assessments from the level of medical school through the level of specialization. Such a model would provide physicians with more concrete guidance regarding professional behavior at each stage of their careers, address unmet needs in neglected areas such as mid- and late career, and help alleviate the tension associated with expressing these ideas. Incorporating concepts derived from more classic models of development may create opportunities to address the teaching of values and identify barriers to success.     

Comparison of definitions of the lag phase and the exponential phase in bacterial growth.

Different definitions for the lag time and of the duration of the exponential phase can be used to calculate these quantities from growth models. The conventional definitions were compared with newly proposed definitions. It appeared to be possible to derive values for the lag time and the duration of the exponential phase from the growth models and differences between the various definitions could be quantified. All the different values can be calculated from the growth parameters microm, lambda and alpha. Therefore, it appeared to be unnecessary to use complicated mathematical equations; simple equations were adequate. For the Gompertz model the conventional definition of the lag time did not differ appreciably from the newly proposed definition. The end-point of the exponential phase and thus the duration of the exponential phase differed considerably for the two definitions. For the logistic model the two definitions lead to considerable differences for all quantities. It is recommended that the conventional definition is used for calculating the lag time. For the duration of the exponential phase it is recommended that the new definition is used. The value can be calculated, however, directly from the conventional growth parameters.     

Intrinsically disordered proteins from A to Z

The ideas that proteins might possess specific functions without being uniquely folded into rigid 3D-structures and that these floppy polypeptides might constitute a noticeable part of any given proteome would have been considered as a preposterous fiction 15 or even 10 years ago. The situation has changed recently, and the existence of functional yet intrinsically disordered proteins and regions has become accepted by a significant number of protein scientists. These fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting and attractive targets for modern protein research. This review summarizes some of the major discoveries and breakthroughs in the field of intrinsic disorder by representing related concepts and definitions.     

浅谈传粉生物学中几个术语的含义及其中文译名

准确理解外来的专业术语并给予合适的中文译名,不仅有助于推动学科的发展,而且有利于同行之间的交流。传粉生物学是近年来在我国迅速发展的一个生态学与进化生物学的分支领域。本文讨论了该学科中的几个重要术语的含义和它们的中文译名,建议将pollen discounting和seed discounting译为“花粉折损”和“种子折损”,herkogamy译为 “雌雄异位”,trade-off译为“权衡”。     

Comparison of definitions of the lag phase and the exponential phase in bacterial growth

M.H. ZWIETERING, F.M. ROMBOUTS AND K. VAN 'T RIET. 1992. Different definitions of the lag time and of the duration of the exponential phase can be used to calculate these quantities from growth models. The conventional definitions were compared with newly proposed definitions. It appeared to be possible to derive values for the lag time and the duration of the exponential phase from the growth models, and differences between the various definitions could be quantified. All the different values can be calculated from the growth parameters μ _m , and a. Therefore, it appeared to be unnecessary to use complicated mathematical equations: simple equations were adequate. For the Gompertz model the conventional definition of the lag time did not differ appreciably from the newly proposed definition. The end-point of the exponential phase and thus the duration of the exponential phase differed considerably for the two definitions. For the logistic model the two definitions lead to considerable differences for all quantities. It is recommended that the conventional definition is used for calculating the lag time. For the duration of the exponential phase it is recommended that the new definition is used. The value can be calculated, however, directly from the conventional growth parameters.     

The more you introduce the more you get: the role of colonization pressure and propagule pressure in invasion ecology

Aim  We argue that 'propagule pressure', a key term in invasion biology, has been attributed at least three distinct definitions (with usage of a related term causing additional confusion). All of the definitions refer to fundamental concepts within the invasion process, with the result that the distinct importance of these different concepts has been at best diluted, and at worst lost.
Location  Global.
Methods  We reviewed pertinent literature on propagule pressure to resolve confusion about different uses of the term 'propagule pressure' and we introduced a new term for one variant, colonization pressure. We conducted a computer simulation whereby the introduction of species is represented as a simple sampling process to elucidate the relationship between propagule and colonization pressure.
Results  We defined colonization pressure as the number of species introduced or released to a single location, some of which will go on to establish a self-sustaining population and some of which will not. We subsequently argued that colonization pressure should serve as a null hypothesis for understanding temporal or spatial differences in exotic species richness, as the more species that are introduced, the more we should expect to establish. Finally, using a simple simulation, we showed that propagule pressure is related to colonization pressure, but in a non-linear manner.
Main conclusion  We suggest that the nature of the relationship between propagule pressure and colonization pressure, as well as the efficacy of various proxy measures of each, require more detailed exploration if invasion ecology is to continue to develop into a more predictive science.     

Defining Life: Synthesis and Conclusions

The first part of the paper offers philosophical landmarks on the general issue of defining life. §1 defends that the recognition of “life” has always been and remains primarily an intuitive process, for the scientist as for the layperson. However we should not expect, then, to be able to draw a definition from this original experience, because our cognitive apparatus has not been primarily designed for this. §2 is about definitions in general. Two kinds of definition should be carefully distinguished: lexical definitions (based upon current uses of a word), and stipulative or legislative definitions, which deliberately assign a meaning to a word, for the purpose of clarifying scientific or philosophical arguments. The present volume provides examples of these two kinds of definitions. §3 examines three traditional philosophical definitions of life, all of which have been elaborated prior to the emergence of biology as a specific scientific discipline: life as animation (Aristotle), life as mechanism, and life as organization (Kant). All three concepts constitute a common heritage that structures in depth a good deal of our cultural intuitions and vocabulary any time we try to think about “life”. The present volume offers examples of these three concepts in contemporary scientific discourse. The second part of the paper proposes a synthesis of the major debates developed in this volume. Three major questions have been discussed. A first issue (§4) is whether we should define life or not, and why. Most authors are skeptical about the possibility of defining life in a strong way, although all admit that criteria are useful in contexts such as exobiology, artificial life and the origins of life. §5 examines the possible kinds of definitions of life presented in the volume. Those authors who have explicitly defended that a definition of life is needed, can be classified into two categories. The first category (or standard view) refers to two conditions: individual self-maintenance and the open-ended evolution of a collection of similar entities. The other category refuse to include reproduction and evolution, and take a sort of psychic view of the living. §6 examines the relationship between the question of the definition of life and that of the origins of life. There is a close parallel between the general conceptions of the origins of life and the definitions of life.     

The Indignity of Relative Concepts of Animal Dignity: A Qualitative Study of People Working with Nonhuman Animals

The Swiss animal welfare legislation is considered to be one of the strictest such laws worldwide. One unique feature is the inclusion of the concept of “dignity of the creature” and, more precisely, animal dignity. We interviewed 19 people from Switzerland and Germany about their concepts of animal dignity. Thereby, we investigated whether the very specific concept of the Swiss law is reflected in the minds of those who work with nonhuman animals on a daily basis. The results of our qualitative interviews revealed an awareness of the legal term among Swiss interviewees, but their personal concepts of animal dignity were not based on or similar to the legal definitions. The interviewed participants presented a broad range of concepts, including: similarities to human dignity, replacing concepts such as respect or integrity, and context-dependent, contingent forms of dignity. The applicability or usefulness of animal dignity was questioned by several participants; many judged it to be confusing or difficult. Therefore, we conclude by discussing animal integrity as an alternative concept that reflects the interviewees’ ideas of treating nonhuman animals in a respectful and appropriate way, and at the same time does not have the strongly metaphysical connotations of a concept such as human dignity.