Apomorphy-based definition also pinpoints a node, and PhyloCode names prevent effective communication

Acceptable methods of defining taxon (or clade) names in the draft PhyloCode, or so-called phylogenetic nomenclature, are “node based,” “stem based,” and “apomorphy based.” All of them define a clade name by pinpointing a node; whereas node-based and stem-based definitions require two or more taxon “specifiers” to define names, an apomorphy-based definition requires two specifiers of different types; namely, a single-taxon specifier and a character specifier. The taxon specifier in an apomorphy-based definition is completely different from the “type” in the Linnaean system. Taxon (or clade) names in the PhyloCode are characterized in two entirely different manners: One is a name that does not change, either in its orthography or in the contents of the taxon referred to by it (or its meaning) over time; the other is a name that is just like a pure mark and thus has no meaning. Communication through such PhyloCode names is very ineffective or impossible.     

Suggestion for a possible approach to molecular biology

A hypothetical “self-reproducing living molecule” has been recently frequently discussed in the literature. A physical theory of such a molecule is tentatively outlined. The relational, rather than the quantitative, aspects of the process are emphasized. The process of synthesis of such a molecule from its components is considered as a transition of a complex system between two quantum-mechanical states. The requirement that a “living molecule” should be able to multiply only by self-reproduction but not by a formationde novo leads to the conclusion that the above mentioned transition is a forbidden one. A constellation of conditions under which the forbiddenness is lifted by the presence of an already existing “living molecule” is suggested. The outlined mechanism leads to the conclusion that the property of self-reproduction does not so much reside in the self-reproducing molecule itself as in its relations to other molecules of a system.     

The evolution of the human mind and logic--mathematics structures

The evolution of the human mind is discussed based on: (i) the fact that living beings interchange matter, energy and information with their environment, (ii) an ontological interpretation of the "reality" of the quantum world, of which logic-mathematics structures are considered constitutive parts, (iii) recent theories according to which living beings are considered as dynamic complex systems organized by information, and (iv) the fact that the evolution of living beings is guided by information about the environment and by intrinsic information on living systems (auto-organization). Assuming the evolution of vision as a model we observe that the driving forces that directed the evolution of the eyes, as dynamic complex systems, are the information about the environment supplied by sunlight and the intrinsic information-gaining mechanism of living organisms. Thus, there exists a convergence toward a visual system with the greatest ability to obtain light information, like the human eye, and also a divergence that leads to the development of specific qualities in some species. As in the case of vision the evolution of the human mind-brain cannot be a consequence of factors unrelated to the object of its own functioning. The human mind was structured for the acquisition from reality of the logic-mathematics structures that underlie the whole universe and consequently of an internal representation of the external world and of its own self. Thus, these structures are, together with the intrinsic capacity for auto-organization of the human brain, the predominant driving force of the human mind evolution. Both factors are complementary.     

Psychological adaptations for assessing gossip veracity

Evolutionary models of human cooperation are increasingly emphasizing the role of reputation and the requisite truthful “gossiping” about reputation-relevant behavior. If resources were allocated among individuals according to their reputations, competition for resources via competition for “good” reputations would have created incentives for exaggerated or deceptive gossip about oneself and one’s competitors in ancestral societies. Correspondingly, humans should have psychological adaptations to assess gossip veracity. Using social psychological methods, we explored cues of gossip veracity in four experiments. We found that simple reiteration increased gossip veracity, but only for those who found the gossip relatively uninteresting. Multiple sources of gossip increased its veracity, as did the independence of those sources. Information that suggested alternative, benign interpretations of gossip decreased its veracity. Competition between a gossiper and her target decreased gossip veracity. These results provide preliminary evidence for psychological adaptations for assessing gossip veracity, mechanisms that might be used to assess veracity in other domains involving social exchange of information.     

Domaine de la biologie théorique

Summary In order to delimit the field of theoretical biology, the author distinguishes in empirical biology a substructure and a superstructure. Empirical biology cannot be constituted without a minimum of reference to philosophical ideas such as the principle of identity (substructure); having regard to its objective, which is explanation by means of physico-chemical models, it does not easily avoid ontological aspirations. Further, experimental research makes great use of scientific theories. Finally, the elaboration of the empirical data of biology may find its fulfilment in an ontological science, philosophical biology, which is a branch of the philosophy of nature. Philosophical biology, superstructure of experimental biology, is a discipline intermediate between the special sciences of life, defined in an empirical sense, and metaphysics.

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Zusammenfassung Um den Bereich der theoretischen Biologie abzugrenzen, unterscheidet der Autor in der positiven Biologie eine “Infrastruktur” und eine “Suprastruktur”. Die positive Biologie kann nicht ohne ein Minimum von Beziehungen zu den philosophischen Begriffen aufgebaut werden, wie z.B. zu dem Prinzip der Identit?t (Infrastruktur); ihrem Ziele nach betrachtet, welches in der Erkl?rung durch physiko-chemische Grundbegriffe besteht, kann sie sich nicht gut den ontologischen Ansprüchen entziehen. Darüber hinaus bedient sich die experimentelle Forschung weitgehend der wissenschaftlichen Theorien. Zum Schluss kann die Bearbeitung der empirischen Erkenntnisse in der Biologie ihre Vollendung in einer ontologischen Wissenschaft, die philosophische Biologie, welche ein Zweig der Philosophie der Natur ist, finden. Die philosophische Biologie, die der experimentellen übergeordnet ist, steht als Disziplin zwischen den besonderen Wissenschaften vom Leben, verstanden im empirischen Sinne, und der Metaphysik.

     

Globalization and Migration: Post-Colonial Dutch Antillean and Aruban Immigrant Political Incorporation in the Netherlands

For much of its colonial history, the Netherlands experienced little contact with its island possessions in the Caribbean. Subsequent Dutch policy was formulated in the shadow of the Netherlands primary concern with its prosperous colony of Indonesia. The 1985 closing of the oil refineries in Aruba and Curacao, Netherlands Antilles and Aruba’s “status aparte” in 1986 triggered a mass migration from those Dutch “overseas countries” to the Netherlands. These recent migrations of thousands of Dutch post-colonial citizens have added to the Dutch reevaluation of its colonial past and debates about its multicultural democratic future.     

Connectivity and information transfer in flow networks: Two magic numbers in ecology?

An ecosystem can be visualized as a graph of certain preassigned trophic compartments; these nodes are then mutually connected through the internal exchanges of material and energy. The mathematical theory of information can be applied to such a graph in order to define two relevant indices: a measure of connectivity (the entropy H of the connections) and a measure of the degree of the “energetic” specialization (the internal transfer of informationI). The computation of these indices in stationary real cases suggests that the observed complexity of ecosystems is conditioned by two competing effects. The first can be interpreted as a “thermodynamical” principle related to the unavoidable irreversibility taking place inside the system, whereas the second can be taken as a “biological” principle concerned with the selection of some particular interactions: those which maximize the information circulating between the compartments.     

From view cells and place cells to cognitive map learning: processing stages of the hippocampal system

 The goal of this paper is to propose a model of the hippocampal system that reconciles the presence of neurons that look like “place cells” with the implication of the hippocampus (Hs) in other cognitive tasks (e.g., complex conditioning acquisition and memory tasks). In the proposed model, “place cells” or “view cells” are learned in the perirhinal and entorhinal cortex. The role of the Hs is not fundamentally dedicated to navigation or map building, the Hs is used to learn, store, and predict transitions between multimodal states. This transition prediction mechanism could be important for novelty detection but, above all, it is crucial to merge planning and sensory–motor functions in a single and coherent system. A neural architecture embedding this model has been successfully tested on an autonomous robot, during navigation and planning in an open environment. Received: 28 June 1999 / Accepted in revised form: 26 April 2001     

Perceive, Co-opt, Modify, and Live! Organism as a Centre of Experience

Organic appearances are largely neglected by contemporary biology; partly because they are regarded as superficial effects of causes concealed beneath the surface. The persuasion that everything what does exist is existent for some immediately non-apparent reasons belongs to a general belief of modern science. All organisms are of the same evolutionary origin and of the same world wherein appearance coincides with existence. In this study, living beings are approached as appearing centers of experience that reflects their evolutionary history. From biohermeneutic point of view the evolution of organisms, interactions between organisms, and their relationships to environment is understood as “evolution of interpretations”. I use simple conceptual framework of perception, semiotic co-option, and modification to explain the evolution of semantic organs, i.e. organs that operate through the meaning that was given to them by an animal interpreter.     

An ant’s eye view of culture: propagation of new traditions through triggering dormant behavioural patterns

We consider a previously unknown way of propagation of behavioural traditions in animal communities using hunting in ants as an example. We experimentally revealed that common litter dwelling ants Myrmica rubra effectively hunt jumping prey and the way the hunting behavioural pattern is distributed within ant colonies is rather sophisticated. Comparison of our results with those obtained on vertebrates enables us to suggest that “distributed social learning” plays an important role in spreading new traditions in animal communities: initial performances by a few carriers of an “at once and entirely” available behavioural pattern propagate this pattern among specimens which have only dormant “sketches” of it. Spread of these behaviours in populations is based on relatively simple forms of social learning such as social facilitation which underlies species’ predisposition to learn certain sequences of behavioural acts. To be triggered, carriers of dormant “sketches” of a relevant behavioural pattern should encounter performances of this pattern with sufficient frequency. We call this strategy triggering of dormant behavioural patterns. Integration of behaviour thus takes place not only at the individual level but at the population level as well.     

Does the Segregation of Evolution in Biology Textbooks and Introductory Courses Reinforce Students’ Faulty Mental Models of Biology and Evolution?

The well-established finding that substantial confusion and misconceptions about evolution and natural selection persist after college instruction suggests that these courses neither foster accurate mental models of evolution’s mechanisms nor instill an appreciation of evolution’s centrality to an understanding of the living world. Our essay explores the roles that introductory biology courses and textbooks may play in reinforcing undergraduates’ pre-existing, faulty mental models of the place of evolution in the biological sciences. Our content analyses of the three best-selling introductory biology textbooks for majors revealed the conceptual segregation of evolutionary information. The vast majority of the evolutionary terms and concepts in each book were isolated in sections about evolution and diversity, while remarkably few were employed in other sections of the books. Standardizing the data by number of pages per unit did not alter this pattern. Students may fail to grasp that evolution is the unifying theme of biology because introductory courses and textbooks reinforce such isolation. Two goals are central to resolving this problem: the desegregation of evolution as separate “units” or chapters and the active integration of evolutionary concepts at all levels and across all domains of introductory biology.     

“Not <Emphasis Type="Italic">Here</Emphasis>”: Making the Spaces and Subjects of “Global Health” in Botswana

This essay argues that what makes “global health” “global” has more to do with configurations of space and time, and the claims to expertise and moral stances these configurations make possible, than with the geographical distribution of medical experts or the universal, if also uneven, distribution of threats to health. Drawing on a study of public–private partnerships supporting Botswana’s HIV/AIDS treatment program, this essay demonstrates ethnographically the processes by which “global health” and its quintessential spaces, namely “resource-limited” or “resource-poor settings,” are constituted, reinforced, and contested in the context of medical education and medical practice in Botswana’s largest hospital. Using Silverstein’s work on orders of indexicality, I argue that the terms of “global health” are best understood as chronotopic, and demonstrate how actors orient themselves and others spatio-temporally, morally, and professionally by using or refuting those terms. I conclude by arguing that taking “global health” on its own terms obscures the powerful forces by which it becomes intelligible. At stake are the frames within which medical anthropologists understand their objects of study, as well as the potential for the spaces of “global health” intervention to expand ever outward as American medical personnel attempt to calibrate their experiences to their expectations.     

Reproductive Politics,Biopolitics and Auto-immunity: From Foucault to Esposito

The contingent cultural, epistemological and ontological status of biology is highlighted by changes in attitudes towards reproductive politics in the history of feminist movements. Consider, for example, the American, British, and numerous European instances of feminist sympathy for eugenics at the turn of the century. This amounted to a specific formation of the role, in late nineteenth and early twentieth century feminisms, of concepts of biological risk and defence, which were transformed into the justificatory language of rights claims. In this context, one can ask how reproductive politics are to be fitted into the paradoxical relationship between biopolitics and thanatopolitics discussed by Michel Foucault and more recently by Roberto Esposito. In this context, “reproductive life,” can be thought of arising at the intersection of thanapolitics and biopolitics as these relate to women’s bodies. Revisiting Foucault and Esposito in the light of reproductive politics also allows a reconsideration of the paradoxical feminist aims involved in defending individual rights by reference to overall biopolitical interest and futurity.     

Mathematical biology of social behavior

When an individual grows up in a society, he learns certain behavior patterns which are “accepted” by that society. He may in general have a tendency toward behavior patterns other than those which are “accepted” by the society. This tendency toward such unaccepted behavior may be due to a process of cerebration which results in doubt as to the “correctness” of the accepted behavior. Thus, on the one hand, the individual learns to follow the accepted rules almost automatically; on the other hand, he may tend to consciously break those rules. Using a neural circuit, suggested by H. D. Landahl in his theory of learning, a neurobiophysical interpretation of the above situation is outlined. Mathematical expressions are derived which describe the social behavior of an individual as a function of his age, social status, and some neurobiophysical parameters.     

Source-sink landscape theory and its ecological significance

Exploring the relationships between landscape pattern and ecological processes is the key topic of landscape ecology, for which, a large number of indices as well as landscape pattern analysis model were developed. However, one problem faced by landscape ecologists is that it is hard to link the landscape indices with a specific ecological process. Linking landscape pattern and ecological processes has become a challenge for landscape ecologists. “Source” and “sink” are common concepts used in air pollution research, by which the movement direction and pattern of different pollutants in air can be clearly identified. In fact, for any ecological process, the research can be considered as a balance between the source and the sink in space. Thus, the concepts of “source” and “sink” could be implemented to the research of landscape pattern and ecological processes. In this paper, a theory of sourcesink landscape was proposed, which include: (1) In the research of landscape pattern and ecological process, all landscape types can be divided into two groups, “source” landscape and “sink” landscape. “Source” landscape contributes positively to the ecological process, while “sink” landscape is unhelpful to the ecological process. (2) Both landscapes are recognized with regard to the specific ecological process. “Source” landscape in a target ecological process may change into a “sink” landscape as in another ecological process. Therefore, the ecological process should be determined before “source” or “sink” landscape were defined. (3) The key point to distinguish “source” landscape from “sink” landscape is to quantify the effect of landscape on ecological process. The positive effect is made by “source” landscape, and the negative effect by “sink” landscape. (4) For the same ecological process, the contribution of “source” landscapes may vary, and it is the same to the “sink” landscapes. It is required to determine the weight of each landscape type on ecological processes. (5) The sourcesink principle can be applied to non-point source pollution control, biologic diversity protection, urban heat island effect mitigation, etc. However, the landscape evaluation models need to be calibrated respectively, because different ecological processes correspond with different source-sink landscapes and evaluation models for the different study areas. This theory is helpful to further study landscape pattern and ecological process, and offers a basis for new landscape index design. __________ Translated from Acta Ecologica Sinica, 2006, 26(5): 1444–1449 [译自: 生态学报]     

Quantitatively defining the conservation status of Natura 2000 forest habitats and improving management options for enhancing biodiversity

The main goal of Natura 2000 network is to guarantee the favourable conservation status of habitats and species ensuring European biodiversity. As a result, certain forest areas have been included in this network listed as 9230-Quercus pyrenaica habitat and 9340-Quercus ilex subsp. rotundifolia forest habitat. These areas were previously used for firewood extraction or livestock grazing and browsing. Nowadays these habitats are coppice forests with asexual regeneration, which is far from the desired conservation status. Traditional timber harvesting plans do not take account of the new objectives required for these Natura sites, which attempt to ensure biodiversity and recreational uses instead of simply focusing on timber production. This paper proposes a flexible methodology (applied to the study area “Dehesa Boyal” in ávila, Spain) for managing Natura 2000 forest sites by stands for sustainable forest management and the new requirements. The methodology has two phases. The first, “Division of the forest area into stands”, defines homogeneous patches of vegetation distinct in species composition, physiognomic structure and future management. The second, “Conservation status assessment of stands”, quantifies the conservation status of each previously classified stand considering a series of factors such as: functional health, restoration, floral richness and structure. A total value integrating the conservation status of stands is then calculated for the habitat. Both phases use Geographic Information System tools for managing information and visualizing results. The proposed methodology provides forest managers with a good knowledge of the territory and subsequently enables them to take appropriate conservation measures to maintain biodiversity.     

THE NEW PARADIGM OF RECOVERY FROM SCHIZOPHRENIA: CULTURAL CONUNDRUMS OF IMPROVEMENT WITHOUT CURE

This article is a qualitative investigation of the subjective experience of recovery from the perspective of persons living with schizophrenia-related disorders. An NIMH-sponsored ethnographic study of community outpatient clinics was completed for 90 persons taking second-generation antipsychotic medications. Research diagnostic criteria and clinical ratings were obtained in tandem with an anthropologically developed Subjective Experience of Medication Interview (SEMI) that elicits narrative data on everyday life and activities, medication and treatment, management of symptoms, expectations concerning recovery, and stigma. Ethnographic observations from diverse settings (clinics, public transportation, restaurants, homes) were also obtained. The primary findings are that recovery was experienced in relation to low levels of symptoms, the need to take medications to avoid hospitalization or psychotic episodes, and personal agency to struggle against the effects of illness. The majority of participants articulated their sense of illness recovery and expectation that their lives would improve. Improvement and recovery is an incremental, yet definitively discernable subjective process. Several problems were identified as part of this process surrounding cultural conflicts that generate the experience of ambivalence analyzed here as the “paradox of recovery without cure,” irreconcilable “catch-22” dilemmas involving sacrifice (e.g., one must be “fat” or be “crazy”), and substantial stigma despite improvement in illness and everyday life experience.     

Interactive Bodies: The Semiosis of Architectural Forms

In this paper architectural forms are presented as symbolic forms issued from the complex semiosis that characterises human cognition (Ferreira (2007, 2010)). Being semiotic objects, these symbolic forms are, consequently, context- dependent_they emerge and have meaning, i.e., they are assigned a functional and/or aesthetic value, in particular physical, social and cultural frameworks. As it happens with all semiotic objects, architectural forms, whatever their nature, are not static but highly interactive. In fact, they act as agents of specific semiotic processes, engaged in a permanent dialectic relationship with the environment they are embedded in. From this dialectics important physical, social, cultural and economic changes frequently arise, redefining this way the original framework for decades to come. As Pallasmaa (2009) points out: “Architecture is existentially rooted, and it expresses fundamental existential experiences, the complex condensation of how it feels to be human being in this world. Architecture grounds and frames existence and creates specific horizons of perception, understanding and identity.” Architecture happens in the context of particular landscapes both natural and man-made, individuating spaces, assigning them an identity, turning the frequently undifferentiated physical environment into “locus”, “place”, “site”, “ort”, definitely contributing to the definition of the mental map that individual minds are able to share collectively. The fundamental role played by architectural forms in the definition of “place” and identity and in the shaping or reshaping of a physical, social and cultural environment is analysed in this paper through a case study that observes the consequences of this dynamics in the development of the social and cultural tissue of a particular city.     

Study on high-temperature-resistant and high-yield <Emphasis Type="Italic">Laminaria</Emphasis> variety “Rongfu”

Hybridization of gametophytes, continuous self-crossing and targeted selection were utilized to breed a new Laminaria variety. After five-generation selection breeding, the new variety “Rongfu” was obtained. Its male parent “Yuanza No.10” was the high-yield cultivation variety, and its female parent was variety “Fujian” which could tolerate relatively high seawater temperature. “Yuanza No.10” and “Fujian” were different but complement in their morphological characteristics and biological habits. Variety “Rongfu” was bred through their hybridization which exhibited high-yield potential and high seawater temperature tolerance. The results of traits evaluation in consecutive years showed that “Rongfu” attained higher yields by 24–27% compared to the control (widely used commercial variety) and also contained considerable amounts of iodine, mannitol, and algin. When seawater temperature was 18–21°C, the blade growth of “Rongfu” was maintained and tissue loss by abrasion was significantly lower than the control. Since the adoption of variety “Rongfu” in 2001, its cultivation areas have been extended to Shandong, Fujian and Guangdong province and have reached 14,133 ha currently, i.e., almost one-tenth of the total cultivation areas of Laminaria in China. The results of Random Amplified Polymorphic DNA analysis showed that the relationship between “Rongfu” and other cultivation varieties in China was very close.