The neutral theory of biodiversity purports that patterns in the distribution and abundance of species do not depend on adaptive differences between species (i.e. niche differentiation) but solely on random fluctuations in population size (“ecological drift”), along with dispersal and speciation. In this framework, the ultimate driver of biodiversity is speciation. However, the original neutral theory made strongly simplifying assumptions about the mechanisms of speciation, which has led to some clearly unrealistic predictions. In response, several recent (...) studies have combined neutral community models with more elaborate speciation models. These efforts have alleviated some of the problems of the earlier approaches, while confirming the general ability of neutral theory to predict empirical patterns of biodiversity. However, the models also show that the mode of speciation can have a strong impact on relative species abundances. Future work should compare these results to diversity patterns arising from non‐neutral modes of speciation, such as adaptive radiations. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the (...) Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

Biologists studying ecology and evolution use the term “population” in many different ways. Yet little philosophical analysis of the concept has been done, either by biologists or philosophers, in contrast to the voluminous literature on the concept of “species.” This is in spite of the fact that “population” is arguably a far more central concept in ecological and evolutionary studies than “species” is. The fact that such a central concept has been employed in so many different ways is (...) potentially problematic for the reason that inconsistent usages (especially when the usage has not been made explicit) might lead to false controversies in which disputants are simply talking past one another. However, the inconsistent usages are not the only, or even the most important reason to examine the concept. If any set of organisms is legitimately called a “population,” selection and drift processes become purely arbitrary, too. Moreover, key ecological variables, such as abundance and distribution, depend on a nonarbitrary way of identifying populations. I sketch the beginnings of a population concept, drawing inspiration from the Ghiselin-Hull individuality thesis, and show why some alternative approaches are nonstarters. (shrink)

Ever since the early decades of this century, there have emerged a number of competing schools of ecology that have attempted to weave the concepts underlying natural resource management and natural-historical traditions into a formal theoretical framework. It was widely believed that the discovery of the fundamental mechanisms underlying ecological phenomena would allow ecologists to articulate mathematically rigorous statements whose validity was not predicated on contingent factors. The formulation of such statements would elevate ecology to the standing of a rigorous (...) scientific discipline on a par with physics. However, there was no agreement as to the fundamental units of ecology. Systems ecologists sought to identify the fundamental organization that tied the physical and biological components of ecosystems into an irreducible unit: the ecosystem was their fundamental unit. Population ecologists sought, instead, to identify the biological mechanisms regulating the abundance and distribution of plant and animal species: to these ecologists, the individual organism was the fundamental unit of ecology, and the physical environment was nothing more than a stage upon which the play of individuals in perennial competition took place. As Joel Hagen has pointed out, the two schools were thus dividied by fundamentally different and irreconcilable assumptions about the nature of ecosystems.Notwithstanding these divisive efforts to elevate the image of ecology, the discipline remained in the shadows of American academia until the mid-1960s, when systems ecologists succeeded in projecting ecology onto the national scene. They did so by seeking closer involvement with practical problems: they argued before Congress that their approach to the theoretical problems of ecology was uniquely suited to the solution of the impending “environmental crisis.” With the establishment of the International Biological Program, they succeeded in attracting unprecedented levels of funding for systems ecology research. Theoretical population ecologists, on the other hand, found themselves consigned to the outer regions of this new institutional landscape. The systems ecologists' successful capture of the limelight and the purse brought the divisions between them and population ecologists into sharper relief — hence the hardening of the division of ecology observed by Hagen.45I have argued that the population biologist Richard Levins, prompted by these institutional developments, sought to challenge the social position of systems ecology, and to assert the intellectual priority of theoretical population ecology. He attempted to do so by articulating a nontrivial and rather carefully thought out classification of ecological models that led to the disqualification of systems analysis as a legitimate approach to the study of ecological phenomena. I have suggested that — ultimately —Levins's case against systems analysis in ecology rested on the view that an aspiration to realism and prediction was incompatible with an interest in theoretical issues, a concern that he equated with the search for generality. He sought to reinforce this argument by exploiting the fact that systems ecologists had staked their future on the provision of technical solutions to the problems of the “environmental crisis”: he associated systems ecologists' aspiration to realism and precision with a concern for practical issues, trading on the widely accepted view that practical imperatives are incompatible with the aims of scientific inquiry.46 These are plausible, but nonetheless questionable, claims which have now become an integral part of ecological knowledge. And finally, I hope to have shown how even the most abstract levels of scientific argument are shaped by political considerations, and how discussions of the conceptual development of modern ecology might benefit from a greater consideration of its historical and social dimensions.47. (shrink)

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining (...) transposon-host interactions. This review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology. (shrink)

Like the rest of the developed world, African nations are now subject to consumerist tendencies of the global economic architecture and activities, which excessively exploit natural resources for profits and are at the centre of what this article describes as ‘disharmony between nature and humanity’. The exploitative nature of consumerist tendencies requires healing and restoration as it leads towards unpredictable and destructive weather patterns in which the relationships between human activity and the environment have created patterns and feedback mechanisms that (...) govern the presence, distribution and abundance of species assemblages. Disharmony is employed to describe the exploitative nature of consumerist tendencies that lead to unpredictable weather patterns. The consequences include climate change and natural disasters such as floods, drought and environmental pollution, which have been severely experienced in Southern Africa recently. This article provides a qualitative literature review on recent religious and ecumenical responses to climate change crisis and draws on the notions of ‘cultural landscapes’ and ‘ecotheology’ to highlight an exploitative relationship, which is characterised by disharmony in the relationship between humanity and nature. This illustration demonstrates how the concept of unity between ‘self and the entire Kosmos’ in African worldview presents a potentially constructive African theology of ecology. Amongst other recommendations, the article proposed that in order for humanity to restore harmony and attain fullness of life – oikodome – with nature the notions of healing, reconciliation, liberation and restoration should be extended to human relations or interactions with nature and all of God’s creation.Contribution: This article represents a contextual and systematic reflection on climate challenges facing the African context within a paradigm in which the intersection of philosophy, religious studies, social sciences, humanities and natural sciences generates an interdisciplinary, multidisciplinary and transdisciplinary contested discourse. (shrink)

While evenness is understood to be maximal if all types (species, genotypes, alleles, etc.) are represented equally (via abundance, biomass, area, etc.), its opposite, maximal unevenness, either remains conceptually in the dark or is conceived as the type distribution that minimizes the applied evenness index. The latter approach, however, frequently leads to conceptual inconsistency due to the fact that the minimizing distribution is not specifiable or is monomorphic. The state of monomorphism, however, is indeterminate in terms (...) of its evenness/unevenness characteristics. Indeed, the semantic indeterminacy also shows up in the observation that monomorphism represents a state of pronounced discontinuity for the established evenness indices. This serious conceptual inconsistency is latent in the widely held idea that evenness is an independent component of diversity. As a consequence, the established evenness indices largely appear as indicators of relative polymorphism rather than as indicators of evenness. In order to arrive at consistent measures of evenness/unevenness, it seems indispensable to determine which states are of maximal unevenness and then to assess the position of a given type distribution between states of maximal evenness and maximal unevenness. Since semantically, unevenness implies inequality among type representations, its maximum is reached if all type representations are equally different. For given number of types, this situation is realized if type representations, when ranked in descending order, show equal differences between adjacent types. We term such distributions “stepladders” as opposed to “plateaus” for uniform distributions. Two approaches to new evenness measures are proposed that reflect different perspectives on the positioning of type distributions between the closest stepladders and the closest plateaus. Their two extremes indicate states of complete evenness and complete unevenness, and the midpoint is postulated to represent the turning point between prevailing evenness and prevailing unevenness. The measures are graphically illustrated by evenness surfaces plotted above frequency simplices for three types, and by transects through evenness surfaces for more types. The approach can be generalized to include variable differences between types (as required in analyses of functional evenness) by simply replacing types with pairs of different types. Pairs, as the new types, can be represented by their abundances, for example, and these can be modified in various ways by the differences between the two types that form the pair. Pair representations thus consist of both the difference between the paired types and their frequency. Omission of pair frequencies leads to conceptual ambiguity. Given this specification of pair representations, their evenness/unevenness can be evaluated using the same indices developed for simple types. Pair evenness then turns out to quantify dispersion evenness. (shrink)

Because of their elementary significance in almost all fields of science, measures of association between two variables or traits are abundant and multiform. One aspect of association that is of considerable interest, especially in population genetics and ecology, seems to be widely ignored. This aspect concerns association between complex traits that show variable and arbitrarily defined state differences. Among such traits are genetic characters controlled by many and potentially polyploid loci, species characteristics, and environmental variables, all of which may (...) be mutually and asymmetrically associated. A concept of directed association of one trait with another is developed here that relies solely on difference measures between the states of a trait. Associations are considered at three levels: between individual states of two variables, between an individual state of one variable and the totality of the other variable, and between two variables. Relations to known concepts of association are identified. In particular, measures at the latter two levels turn out to be interpretable as measures of differentiation. Examples are given for areas of application (search for functional relationships, distribution of variation over populations, genomic associations, spatiogenetic structure). (shrink)

Traditional diversity indices are computed from the abundances of species present and are insensitive to taxonomic differences between species. However, a community in which most species belong to the same genus is intuitively less diverse than another community with a similar number of species distributed more evenly between genera. In this paper, we propose an information-theoretical measure of taxonomic diversity that reflects both the abundances and taxonomic distinctness of the species. Unlike previous measures of taxonomic (...) diversity, such as Rao's quadratic entropy, in this new measure the analyzed taxonomic properties are associated with the single species instead of species pairs. (shrink)

Species’ adaptation to their environments occurs via a range of mechanisms of adaptation. These include genetic adaptations as well as non-traditional inheritance mechanisms such as learned behaviors, niche construction, epigenetics, horizontal gene transfer, and alteration of the composition of a host’s associated microbiome. We propose to supplement these with another modality of eco-evolutionary dynamics: cases in which adaptation to the environment occurs via what may be called a “distributed adaptation,” in which the adaptation is not conferred via something carried (...) by an individual of the adapted species (as with genes, behavior, or associated microbes), but by some structural or compositional aspect of the population. Put differently, the adaptively relevant information cannot be reduced to information possessed by a single individual, whether genetic or otherwise. Rather, the adaptively relevant information is distributed, and is found strictly at the population level. While human culture is presumably such a case, as may be cases found in social insects, we want to suggest that there are other cases that belong to this category and to explore its evolutionary implications. In particular, we discuss the factors that affect whether adaptive information is stored in a distributed way, to what degree, and what kinds of adaptive information are most likely to be found in this modality of adaptation. (shrink)

In the final analysis, sustainable agriculture must derive from applied ecology, especially the principle of the regulation of the abundance and distribution of species (and, secondarily, their activities) in space and time. Interspecific competition in natural ecosystems has its counterparts in agriculture, designed to divert greater amounts of energy, nutrients, and water into crops. Whereas natural ecosystems select for a diversity of species in communities, recent agriculture has minimized diversity in favour of vulnerable monocultures. Such systems (...) show intrinsically less stability and resilience to perturbations. Some kinds of crop rotation resemble ecological succession in that one crop prepares the land for successive crop production. Such rotations enhance soil organic processes such as decomposition and material cycling, build a nutrient capital to sustain later crop growth, and reduce the intensity of pest buildup. Species in natural communities occur at discrete points along the r-K continuum of reproductive maturity. Clearing forested land for agriculture, rotational burning practices, and replacing perennial grassland communities by cereal monocultures moves the agricultural community towards the r extreme. Plant breeders select for varieties which yield at an earlier age and lower plant biomass, effectively moving a variety towards the r type. Features of more natural landscapes, such as hedgerows, may act as physical and biological adjuncts to agricultural production. They should exist as networks in agricultural lands to be most effective. Soil is of major importance in agroecosystems, and maintaining, deliberately, its vitality and resilience to agricultural perturbations is the very basis of sustainable land use. (shrink)

Ecology is the study of the interactions of organisms and their environments. The methods of ecology fall roughly into three categories: descriptive surveys of patterns of species and resource distribution and abundance, theoretical modeling, and experimental manipulations. Ecological systems are “open” systems, and patterns and processes are products of a huge number of interacting forces. Ecology and the environmental sciences have made enormous advances since the mid-twentieth century in the understanding of ecological systems, as well as in (...) the human impact on the environment. Theory in ecology usually centers on the development of models. Environmental outcomes are uncertain and when making decisions under uncertainty, there are a variety of options available. One option is to carry out a cost benefit analysis based upon expected utilities and other is to adopt the precautionary principle. Uncertainty and under determination of theory by evidence is a fact of life in science. (shrink)

Traditional diversity measures such as the Shannon entropy are generally computed from the species' relative abundance vector of a given community to the exclusion of species' absolute abundances. In this paper, I first mention some examples where the total information content associated with a given community may be more adequate than Shannon's average information content for a better understanding of ecosystem functioning. Next, I propose a parametric measure of statistical information that contains both Shannon's entropy and total (...) information content as special cases of this more general function. (shrink)

The science of animal consciousness investigates (i) which animal species are conscious (the distribution question) and (ii) how conscious experience differs in detail between species (the quality question). We propose a framework which clearly distinguishes both questions and tackles both of them. This two-tier account distinguishes consciousness along ten dimensions and suggests cognitive capacities which serve as distinct operationalizations for each dimension. The two-tier account achieves three valuable aims: First, it separates strong and weak indicators of the (...) presence of consciousness. Second, these indicators include not only different specific contents but also differences in the way particular contents are processed (by processes of learning, reasoning or abstraction). Third, evidence of consciousness from each dimension can be combined to derive the distinctive multi-dimensional consciousness profile of various species. Thus, the two-tier account shows how the kind of conscious experience of different species can be systematically compared. (shrink)

The mass extinction visited upon us by capitalism involves many kinds of devastation. Here I clarify the grounds for assessing the most obvious of these harms, i.e., decimation of species diversity. The thesis that variety among species has intrinsic value motivates, and in turn follows from, the “variable value view” (VVV) of abundance within any given species. In contrast, standard axiologies have no place for the intrinsic value of species diversity. I show that the VVV (...) provides a better justification than the latter do, of the way in which a widely-used empirical indicator summarizes the overall state of life on Earth. These considerations favor ecocentric value theory – which ascribes intrinsic value to properties of ecological wholes, like species diversity, that do not supervene on the well-being of their constituent organisms – over its main competitors. I conclude by widening the focus from wild nature alone to the biosphere comprising both wilderness and the domesticated realm. This broadened perspective helps to link the science and ethics of biodiversity with the political struggle to extract ourselves from the moral abyss of mass extinction. (shrink)

By the 1840s and 1850s biogeographical theory had polarized into two opposing views — both of which had their origins in the sixteenth or seventeenth centuries. At issue in this polarization was the question of God's involvement with His creation. At one end of the spectrum were Sclater, Agassiz, Kirby, and others who saw a neatly designed world in which geographical distributions were planned and executed by the hand of God at creation. For most of these naturalists, organisms were created (...) en masse within the regions they now occupy. Disjunct distributions were proof to them that God had indeed created species in situ as many individuals. These naturalists hoped to reveal God's biogeographical plan by discovering His regions of creation. They had hoped to demonstrate a neatly devised set of regions of creation which might be applicable to all creatures, but in attempting to do so, they arrived at conflicting sets of delineations — thus helping to undermine their conceptions of nature in which design (both idealist and utilitarian) played an important part.93At the other end of the biogeographical spectrum were the theoretical ideas of Prichard and Lyell, who viewed a more remote God — one who allowed His creation to be shaped and modified by secondary laws. Lyell in particular wished to leave considerations of design aside, hoping to demonstrate that the shape of the present creation is due to natural laws. Prichard and Lyell saw God's role in the creation of species (and distributions) as being extremely limited. In fact, the regions of creation seen today are in actuality only natural artifacts produced by migrations and barriers. They saw distributions being in constant flux, as was the rest of nature.Those supporting the views of Prichard and Lyell spent a great deal of effort in attempting to remove a major obstacle in their paths — disjunct distributions. If disjunct distributions were indeed the products of separate creative acts, as Sclater and others claimed, then the arguments of Prichard and Lyell would be negated. For if the creation of a species was shown to be the product of multiple creations, then what was the need of migrations and dispersal mechanisms? Also at stake, of course, was the concept of species based upon generation. Darwin was well aware that if the supernatural implications of disjunct distributions could not be refuted, then his evolutionary system — founded upon a species concept based on descent — would be in peril.94A further barrier to the acceptance of the Prichard/Lyell view was the fact that those sympathetic to a nonsupernatural explanation of disjunct distributions could not agree upon a natural explanation for those anomalies, and an internal debate between naturalists within this group raged for decades.95By 1859 a biogeographical stalemate had occurred. Sclater and others, supporting their static view of nature, continued to look for regions of creation, pointing to disjunct distributions in support of their arguments, while those favorable to the views of Prichard and Lyell continued to search for natural explanations for such biogeographical anomalies.The key needed to resolve the biogeographical debate was a credible theory for species origins. By 1858 there were essentially three options for British naturalists: supernatural creation, Lamarckian transmutation, or natural creation. A few British naturalists grasped at these straws, but most workers preferred the option of remaining silent until a more viable explanation for the origin and distribution of species could be advanced.96 And not until the publication of Darwin's theory did that explanation become available. (shrink)

Explains Aristotle's views on the possibility of continuous variation between biological species. While the Porphyrean/Linnean classification of species by a tree suggests species are distributed discretely, Aristotle admitted continuous variation between species among lower life forms.

ORIGIN OF SPECIES. INTRODUCTION. When on board HMS 'Beagle,' as naturalist, I was ranch struck with certain facts in the distribution of the organic beings ...

Plant and animal species are information-processing entities of such complexity, integration, and adaptive competence that it may be scientifically fruitful to consider them intelligent. The possibility arises from the analogy between learning and evolution, and from recent developments in evolutionary science, psychology and cognitive science. Species are now described as spatiotemporally localized individuals in an expanded hierarchy of biological entities. Intentional and cognitive abilities are now ascribed to animal, human, and artificial intelligence systems that process information adaptively, and (...) that manifest problem-solving abilities. The structural and functional similarities between such systems and species are extensive, although they “are usually obscured by population-genetic metaphors that have nonetheless contributed much to our understanding of evolution.In this target article, I use Sewall Wright's notion of the “adaptive landscape” to compare the performances of evolving species to those of intelligent organisms. With regard to their adaptive achievements and the kinds of processes by which they are achieved, biological species compare very favorably to intelligent animals by virtue of interactions between populations and their environments, between ontogeny and phylogeny, and between natural, interdemic, organic, and species selection. Addressing the question of whether species are intelligent could help to refine our ideas about species, evolution, and intelligence, and could open new lines of empirical and theoretical inquiry in many disciplines. (shrink)

Although there exist advantages to group-living in comparison to a solitary lifestyle, costs and gains of group-living may be unequally distributed among group members. Predation risk, vigilance levels and food intake may be unevenly distributed across group spatial geometry and certain within-group spatial positions may be more or less advantageous depending on the spatial distribution of these factors. In species characterized with dominance hierarchy, high-ranking individuals are commonly observed in advantageous spatial position. However, in complex social systems, individuals (...) can develop affiliative relationships that may balance the effect of dominance relationships in individual's spatial distribution. The objective of the present study is to investigate how the group spatial distribution of a semi-free ranging colony of Mandrills relates to its social organization. Using spatial observations in an area surrounding the feeding zone, we tested the three following hypothesis: (1) does dominance hierarchy explain being observed in proximity or far from a food patch? (2) Do affiliative associations also explain being observed in proximity or far from a food patch? (3) Do the differences in rank in the group hierarchy explain being co-observed in proximity of a food patch? Our results showed that high-ranking individuals were more observed in proximity of the feeding zone while low-ranking individuals were more observed at the boundaries of the observation area. Furthermore, we observed that affiliative relationships were also associated with individual spatial distributions and explain more of the total variance of the spatial distribution in comparison with dominance hierarchy. Finally, we found that individuals observed at a same moment in proximity of the feeding zone were more likely to be distant in the hierarchy while controlling for maternal kinship, age and sex similarity. This study brings some elements about how affiliative networks and dominance hierarchy are related to spatial positions in primates. (shrink)

Charles Darwin's On the Origin of Species is unquestionably one of the chief landmarks in biology. The Origin (as it is widely known) was literally only an abstract of the manuscript Darwin had originally intended to complete and publish as the formal presentation of his views on evolution. Compared with the Origin, his original long manuscript work on Natural Selection, which is presented here and made available for the first time in printed form, has more abundant examples and illustrations (...) of Darwin's argument, plus an extensive citation of sources. (shrink)

The species problem is often described as the abundance of conflicting definitions of _species_, such as the biological species concept and phylogenetic species concepts. But biologists understand the notion of species in a non-definitional as well as a definitional way. In this article I argue that when they understand _species_ without a definition in their mind, their understanding is often mediated by the notion of _good species_, or prototypical species, as the idea of ``prototype'' (...) is explicated in cognitive psychology. This distinction helps us make sense of several puzzling phenomena regarding biologists' dealing with species, such as the fact that in everyday research biologists often behave as if the species problem is solved, while they should be fully aware that it is not. I also briefly discuss implications of this finding, including that some extant attempts to answer what the nature of species is have an inadequate assumption about how the notion of species is represented in biologists' minds. (shrink)

I want to make plausible the following claim:Analyzing scientific inquiry as a species of socially distributed cognition has a variety of advantages for science studies, among them the prospects of bringing together philosophy and sociology of science. This is not a particularly novel claim, but one that faces major obstacles. I will retrace some of the major steps that have been made in the pursuit of a distributed cognition approach to science studies, paying special attention to the promise that (...) such an approach holds out for bridging the rift between philosophy and the social studies of science. (shrink)

Amine acetylation is a diverse topic with importance to the regulation of several physiological processes as well as the metabolism of drugs and environmental chemicals. Arylalkylamine N‐acetyltransferase is widely distributed in several species, where this enzyme plays an important role in the seasonal regulation of reproduction and photoperiodism in vertebrates through the pathway of melatonin formation. In insects, this enzyme is involved in monoamine neurotransmitter inactivation and the formation of catecholamine intermediates necessary for sclerotization of the insect cuticle.

Recent work in viral genomics has shown that bacteriophages exhibit a high degree of mosaicism, which is most likely due to a long history of prolific horizontal gene transfer (HGT). Given these findings, we argue that each of the most plausible attempts to properly classify bacteriophages into distinct species fail. Mayr's biological species concept fails because there is no useful viral analog to sexual reproduction. Phenetic species concepts fail because they obscure the mosaicism and the rich reticulated (...) viral histories. Phylogenetic species concepts, even when extended to take into account reticulation, fail because there is no non-arbitrary distinction between recombination events that create a new viral species and those that do not. There is good reason to think that bacteriophages, arguably the Earth's most abundant biological agent, evolve without forming species.1. Introduction2. The Biology of Viruses2.1. Bacteriophage life cycles2.2. Mechanisms of HGT3. The Species Problem and Species Concepts3.1. Phenetic species concepts3.2. The biological species concept3.3. Phylogenetic species concepts3.4. The ecological species concept3.5. Homeostatic property cluster species4. Viruses and Species Taxonomy5. Reticular Phylogenies6. Conclusion. (shrink)

The endangered species Tokudaia osimensis has the unique chromosome constitution of 2n = 25, with an XO/XO sex chromosome configuration (2n = 25; XO). There is urgency to preserve this species and to elucidate the regulator(s) that can discriminate the males and females arising from the indistinguishable sex chromosome constitution. However, it is not realistic to examine this rare animal species by sacrificing individuals. Recently, true naïve induced pluripotent stem cells were successfully generated from a female T. (...) osimensis, and the sexual plasticity of its germ cells was elucidated. This achievement constitutes the basis of an attractive research area, including embryonic fate determination, sex determination, and factor(s) that can replace the Y chromosome. In this essay, concrete strategies to conserve rare animal species and to reveal their specific characteristics using other compatible and abundant animals are proposed. -/- . (shrink)

We have demonstrated, using the Cantor dust method, that the statistical distribution of appearance and disappearance of rodents species (Arvicolid rodent radiation in Europe) follows power laws strengthening the evidence for a fractal structure set. Self-similar laws have been used as model for the description of a huge number of biological systems. With Nottale we have shown that log-periodic behaviors of acceleration or deceleration can be applied to branching macroevolution, to the time sequences of major evolutionary leaps (global (...) life tree, sauropod and theropod dinosaurs postural structures, North American fossil equids, rodents, primates and echinoderms clades and human ontogeny). The Scale-Relativity Theory has others biological applications from linear with fractal behavior to non-linear and from classical mechanics to quantum mechanics. (shrink)

People living in rural areas make up 20 percent of the U.S. population, but only 9 percent of physicians practice there. This uneven distribution is significant because rural areas have higher percentages of people in poverty, elderly people, people lacking health insurance coverage, and people with chronic diseases. As a way of ameliorating these disparities, e-health initiatives are being implemented. But the rural e-health movement raises its own set of distributive justice concerns about the digital divide. Moreover, even if (...) the digital divide is overcome, e-health services may be of an inferior quality compared to face-to-face medical encounters. In this paper, I argue that before we can fully understand the distributive justice implications of e-health, we must first understand what distributive justice means. I argue that five elements—fairness, quality, accessibility, availability, and efficiency—constitute a general conception of justice and that all of these elements must be considered when evaluating e-health for rural health profession shortage areas. In doing so, it may be necessary to make important tradeoffs among these elements. I then examine the development of e-health programs in light of Rawls’s principle of equal opportunity and Daniels’s notion of species-typical functioning. I conclude that in the context of e-health, Rawls’s principle should be expanded to include geography as a prima facie morally relevant criterion for allocating healthcare benefits. I also conclude that Daniels’s notion of species-typical functioning provides grounds for thinking of health and some healthcare services as special goods. (shrink)

Summary The common view has been that Darwin regarded species as artificial and arbitrary constructions of taxonomists, not as distinct natural units. However, in his transmutation notebooks he clearly subscribed to the reality of species, on the basis of the criterion of non-interbreeding. A consequence of this biological species concept was his identification of the acquisition of reproductive isolation as the mark of the completion of speciation. He developed in the notebooks a theory of geographic speciation on (...) the grounds of (a) an empirical correlation between barriers and the geographical distributions of allied species, (b) the analogy of artificial isolation in the formation of new domesticated varieties, and (c) the logical consequence of blending inheritance. A brief discussion of Darwin's species concept in later writings concludes the paper. (shrink)

College of Medicine, University of South Alabama Mobile, AL 36688-0002, USA wbp501{at}jaguar1.usouthal.edu ' + u + '@' + d + ' '//--> Abstract Recent work in viral genomics has shown that bacteriophages exhibit a high degree of mosaicism, which is most likely due to a long history of prolific horizontal gene transfer (HGT). Given these findings, we argue that each of the most plausible attempts to properly classify bacteriophages into distinct species fail. Mayr's biological species concept fails because (...) there is no useful viral analog to sexual reproduction. Phenetic species concepts fail because they obscure the mosaicism and the rich reticulated viral histories. Phylogenetic species concepts, even when extended to take into account reticulation, fail because there is no non-arbitrary distinction between recombination events that create a new viral species and those that do not. There is good reason to think that bacteriophages, arguably the Earth's most abundant biological agent, evolve without forming species. Introduction The Biology of Viruses 2.1 Bacteriophage life cycles 2.2 Mechanisms of HGT The Species Problem and Species Concepts 3.1 Phenetic species concepts 3.2 The biological species concept 3.3 Phylogenetic species concepts 3.4 The ecological species concept 3.5 Homeostatic property cluster species Viruses and Species Taxonomy Reticular Phylogenies Conclusion CiteULike Connotea Del.icio.us What's this? (shrink)

The Shannon information function (H) has been extensively used in ecology as a statistic of species diversity. Yet, the use of Shannon diversity index has also been criticized, mainly because of its ambiguous ecological interpretation and because of its relatively great sensitivity to the relative abundances of species in the community. In my opinion, the major shortcoming of the traditional perspective (on the possible relation of species diversity with information theory) is that species need for an (...) external receiver (the scientist or ecologist) to exist and transmit information. Because organisms are self-catalized replicating structures that can transmit genotypic information to offspring, it should be evident that any single species has two possible states or alternatives: to be or not to be. In other words, species have no need for an external receiver since they are their own receivers. Therefore, the amount of biological information (at the species scale) in a community with one only species would be species, and not bits as in the traditional perspective. Moreover, species diversity appears to be a monotonic increasing function of (or S) when all species are equally probable (S being species richness), and not a function of as in the traditional perspective. To avoid the noted shortcoming, we could use 2H (instead of H) for calculating species diversity and species evenness (= 2H/S). However, owing to the relatively great sensitivity of H to the relative abundances of species in the community, the value of species dominance (= 1 − 2H/S) is unreasonably high when differences between dominant and subordinate species are considerable, thereby lowering the value of species evenness and diversity. This unsatisfactory behaviour is even more evident for Simpson index and related algorithms. I propose the use of other statistics for a better analysis of community structure, their relationship being: species evenness + species dominance = 1; species diversity × species uniformity = 1; and species diversity = species richness × species evenness. (shrink)

In this paper I discuss what triage is and how it might be applied to the preservation of endangered species. I compare the suggested application oftriage to endangered species with its application to wartime military practice, distribution of food aid, and human population control to show that the situation of endangered species is not analogous to these other suggested uses. I argue that, as far as species preservation is concemed, triage starts with the wrong norms (...) and values: it is “human chauvinistic,” giving primacy to economic, political, and sociocultural aspects that emphasize human interests without recognizing the connection between the survival of other species and the survival of humans. (shrink)

This paper analyzes community ecologist Charles Elton’s ideas on animal communities, and situates them with respect to the classical opposition between organicist–holistic and individualistic–reductionist ecological views drawn by many historians of ecology. It is argued that Elton espoused a moderate ecological holism, which drew a middle way between the stricter ecological holism advocated by organicist ecologists and the merely aggregationist views advocated by some of their opponents. It is also argued that Elton’s moderate ecological holism resonated with his preference for (...) analogies between ecological communities and human societies over more common ones between communities and individual organisms. I discuss, on the one hand, how the functionalist-interactionist approach to community ecology introduced by Elton entailed a view of ecological communities as more or less self-maintaining functionally organized wholes, and how his ideas on this matter were incorporated into their views by organicist ecologists Frederic Clements, Victor Shelford, and Warder C. Allee et al. On the other hand, I identify some important divergences between Elton’s ecological ideas and those of organicist ecologists. Specifically, I show how Elton’s ideas on species distribution, animal migrations, and ecological succession entailed a view of animal communities as exhibiting a weaker degree of part-whole integration than that attributed to them by Clements and Shelford; and how Elton’s mixed stance on the balance of nature idea and his associated views on community stability attributed to communities a weaker form of self-regulation than that attributed to them by Allee et al. (shrink)

This article explores protection efforts that have arisen in the New York City metropolitan area around the monk parakeet, a nonnative bird that has achieved a broad distribution outside its native habitat range. In some urban regions in which populations are established, controversy has developed around the parakeets’ use of utility infrastructure and potential impacts on native species and agricultural crops. This case provides an opportunity to explore animal protection rhetoric about nonnative species, an understudied topic, considering (...) the great extent to which species have become established in ecosystems outside their natural ranges and the persistence of public affinity for nonnative plants and wildlife. This article identifies four major frames through which advocates have delivered the birds to public and legal audiences and considers how they have mobilized and handled notions of “nonnative-ness” in their advocacy work. (shrink)

In this paper I discuss what triage is and how it might be applied to the preservation of endangered species. I compare the suggested application oftriage to endangered species with its application to wartime military practice, distribution of food aid, and human population control to show that the situation of endangered species is not analogous to these other suggested uses. I argue that, as far as species preservation is concemed, triage starts with the wrong norms (...) and values: it is “human chauvinistic,” giving primacy to economic, political, and sociocultural aspects that emphasize human interests without recognizing the connection between the survival of other species and the survival of humans. (shrink)

Alzheimer's disease is characterized by amyloid-beta peptide -loaded plaques in the brain. Abeta is a cleavage fragment of amyloid-beta protein precursor and over production of APP may lead to amyloidogenesis. The regulatory region of the APP gene contains consensus sites recognized by the transcription factor, specificity protein 1 , which has been shown to be required for the regulation of APP and Abeta. To understand the role of SP1 in APP biogenesis, herein we have characterized the relative distribution and (...) localization of SP1, APP, and Abeta in various brain regions of rodent and primate models using immunohistochemistry. We observed that overall distribution and cellular localization of SP1, APP, and Abeta are similar and neuronal in origin. Their distribution is abundant in various layers of neocortex, but restricted to the Purkinje cell layer of the cerebellum, and the pyramidal cell layer of hippocampus. These findings suggest that overproduction of Abeta in vivo may be associated with transcriptional pathways involving SP1 and the APP gene. (shrink)

An individual-based approach is used to describe population dynamics. Two kinds of models have been constructed with different distributions illustrating individual variability. In both models, the growth rate of an individual and its final body weight at the end of the growth period, which determines the number of offspring, are functions of the amount of resources assimilated by an individual. In the model with a symmetric distribution, the half saturation constant in the Michaelis–Menten function describing the relationship between the (...) growth of individuals and the amount of resources has a normal distribution. In the model with an asymmetric distribution, resources are not equally partitioned among individuals. The individual who acquired more resources in the past, will acquire more resources in the future. A single population comprising identical individuals has a very short extinction time. If individuals differ in the amount of food assimilated, this time significantly increases irrespectively of the type of model describing population dynamics. Individuals of two populations of competing species use common resources. For larger differences in individual variability, the more variable species will have a longer extinction time and will exclude less variable species. Both populations can also coexist when their variabilities are equal or even when they are slightly different, in the latter case under the condition of high variability of both species. These conclusions have a deterministic nature in the case of the model with the asymmetric distribution—repeated simulations give the same results. In the case of the model with the symmetric distribution, these conclusions are of a statistical nature—if we repeat the simulation many times, then the more variable species will have a longer extinction time more frequently, but some results will happen when the less variable species has a longer extinction time. Additionally, in the model with the asymmetric distribution, the result of competition will depend on the way of the introduction of variability into the model. If the higher variability is due to an increase in the proportion of individuals with a low assimilation of resources, it can produce a longer extinction time of the less variable species. (shrink)

This special issue is a refreshing contrast to the intuitively influential notion of language as an internal system. This internal approach to language is going strong in some segments of the cognitive sciences. As an assumption, internalism drives much empirical work on language, and it is the basis of prominent theories of language – its nature (e.g. an internalised computational system), its evolution (e.g. a single still-unknown mutation), and its function (e.g. thinking, not communication). -/- Radical fundamentalist versions of these (...) theories are no longer in the main stream, however, despite the attention they may garner by forceful exposition (e.g. Chomsky 2011a). A fuller canvassing of the cognitive sciences – obviously outside the scope of the current presentation – would probably reveal that most researchers, even those who study aspects of language isolated in individual participants, would allow for an intrinsic social characteristic to language. I would go so far as to guess that they would place this social character on explanatory par with other structural or information-processing features that are studied in the lab. And despite what is averred by Chomsky (2011a), this social character in human cognition has been proposed in many domains, from vision (Balcetis & Lassiter 2010) to memory (Barnier et al. 2008). Humans are intrinsically social in a way that distinguishes them from any other primate species, and this sociality seems to be weaved into many cognitive processes (Castiello et al. 2010; Tomasello 2009). -/- But “social” is not the same thing as “distributed,” by the content of this issue. The latter may subsume the former. The distributed approach discussed in this special issue is not “simply” social – it does not just propose an added static feature of any synchronic language context (as noted in Jennings & Thompson this issue). The approach instead regards this social characteristic as just one part of a broader dynamic distributed process that constitutes language, through different kinds of inter-individual coordination at many levels of spatial and temporal scale (Cowley this issue; Fusaroli & Tylén this issue). (shrink)

This paper distinguishes four recognisably different geographical processes in principle causing species to die out. One of these processes, the one we dub “range eclipse”, holds that one range expands at the expense of another one, thereby usurping it. Channell and Lomolino (2000a, Journal of Biogeography 27: 169–179; 2000b, Nature 403: 84–87; see also Lomolino and Channell, 1995, Journal of Mammalogy 76: 335–347) measured the course of this process in terms of the proportion of the total range remaining in (...) its original centre, thereby essentially assuming a homogeneous distribution of animals over the range. However, part of their measure seems mistaken. By giving a general, analytical formulation of eclipsing ranges, we estimate the exact course of this process. Also, our formulation does not partition a range into two spatially equal parts, its core and its edge, but it assumes continuity. For applying this model to data on the time evolution of species, individual time series should be available for each of them. For practical purposes we give an alternative way of plotting and interpreting such time series. Our approach, being more sensitive than Channell and Lomolino’s, gives a less optimistic indication of range eclipses than theirs once these have started. (shrink)

This thesis lies in the overlap of environmental political theory and environmental ethics. More specifically, it focuses on the intersection between distributive ecological justice (justice to nature), and environmental justice (distributing environmental goods between humans). Against the backdrop of the current sixth extinction crisis, I address the question of what constitutes a just usage of ecological space. I define ecological space as encompassing environmental resources, benefits provided by ecosystems and physical spaces and when considering its just usage I not only (...) take into account claims to ecological space held by other humans but also the demands of justice with regards to nonhuman living beings such as animals and plants. In order to address my overall research question, I look at three areas of inquiry in particular. My first area of concern is questions around how environmental justice can be made compatible with a theory of ecological justice. Here I defend a specific definition of ecological space and provide a critique of theories of justice that are based on the view that humanity has an original ownership of the Earth. Secondly, I defend a biocentric approach to distributive ecological justice based on all living beings constituting together a community of fate, and I additionally clarify the relationship between justice and biodiversity loss. Lastly, considering that the current situation of life on Earth does not resemble the circumstance of moderate scarcity where all needs could theoretically be met (as usually assumed by the most influential theories of justice), I inquire into how demands of environmental and ecological justice differ in different circumstances of scarcity, and what could be considered a just compromise between these two domains of justice. I then apply these last considerations to the Half-Earth proposal for creating large protected areas for nonhuman species, which has been advocated by E. O. Wilson and other ecologists as a means to slow the current rate of anthropogenic species extinctions. In essence, the Half-Earth proposal might be ambitious, but I argue there are good reasons to consider it as one building block of a (distributively) just future for life on Earth. (shrink)

A review of data concerning the uneven distribution of phobias suggests that nonassociative, ethological models can account for most of tile important findings that cannot be attributed to expectancy biases. The origin of a variety of fears that appear in fixed developmental patterns across divergent cultures and species can best be explained by biological models.

Weismann's ideas on species transmutation were first expressed in his famous debate with Moritz Wagner on the mechanism of speciation. Wagner suggested that the isolation of a colony from its original source is a preliminary and necessary factor for speciation. Weismann accepted a secondary, facilitating role for isolation, but argued that natural and sexual selection are the primary driving forces of species transmutation, and are always necessary and often sufficient causes for its occurrence. The debate with Wagner, which (...) occurred between 1868 and 1872 within the framework of Darwin's discussions of geographical distribution, was Weismann's first public battle over the mechanism of evolution. This paper, which offers the first comprehensive analysis of this debate, extends previous analyses and throws light on the underlying beliefs and motivations of these early evolutionists, focusing mainly on Weismann's views and showing his commitment to what he later called "the all sufficiency of Natural Selection." It led to the crystallization of his ideas on the central and essential role of selection, both natural and sexual, in all processes of evolution, and, already at this early stage in his theoretical thinking, was coupled with sophisticated and nuanced approach to biological organization. The paper also discusses Ernst Mayr's analysis of the debate and highlights aspects of Weismann's views that were overlooked by Mayr and were peripheral to the discussions of other historians of biology. (shrink)

We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (Bassaricyon gabbii), (...) lowland species with eastern, cis-Andean (Bassaricyon alleni) and western, trans-Andean (Bassaricyon medius) distributions, and a species endemic to cloud forests in the Andes. The oldest evolutionary divergence in the genus is between this last species, endemic to the Andes of Colombia and Ecuador, and all other species, which occur in lower elevation habitats. Surprisingly, this Andean endemic species, which we call the Olinguito, has never been previously described; it represents a new species in the order Carnivora and is the smallest living member of the family Procyonidae. We report on the biology of this new species based on information from museum specimens, niche modeling, and fieldwork in western Ecuador, and describe four Olinguito subspecies based on morphological distinctions across different regions of the Northern Andes. (shrink)

We construct a family $\fancyscript{F}$ , indexed by five integer parameters, of finite monogenerated left-distributive (LD) groupoids with the property that every finite monogenerated LD groupoid is a quotient of a member of $\fancyscript{F}$ . The combinatorial abundance of finite monogenerated LD groupoids is encoded in the congruence lattices of the groupoids $\fancyscript{F}$ , which we show to be extremely large.