Perspectives: Towards a language for mapping relationships among taxonomic concepts

Abstract

Taxonomic concepts (sensu Berendsohn) embody the underlying meanings of scientific names as stated in a particular publication, thus offering a new way to resolve semantic ambiguities that result from multiple revisions of a taxonomic name. This paper presents a comprehensive and powerful language for representing the relationships among taxonomic concepts. The language features terms and symbols for concept relationships within a single taxonomic hierarchy, or between two related but independently published hierarchies. Taxonomic concepts pertaining to a single hierarchy are characterised by parent/child relationships, whereas those pertaining to two independent hierarchies may have the following basic relationships: congruence, inclusion (non‐symmetrical, relative to the side of comparison), overlap, and exclusion. The relationships are asserted by specialists who have the option to add or subtract concepts on one or both sides of a relationship equation in order to reconcile differences between non‐congruent taxonomic perspectives. The terms ‘and’, ‘or’ and ‘not’ are available, respectively, to connect multiple simultaneously or alternatively valid relationship assessments, or to explicitly negate the validity of a relationship. The language also permits the decomposition of a relationship according to the intensional (property referencing) and ostensive (member pointing) aspects of the compared taxonomic concepts. Adopting the concept relationship language will facilitate a more precise documentation of similarities and differences in multiple succeeding taxonomic perspectives, thereby preparing the stage for an ontology‐based integration of taxonomic and related biological information.     

Long-Distance Paradox and the Hybrid Nature of Language

Non-adjacent or long-distance dependencies (LDDs) are routinely considered to be a distinctive trait of language, which purportedly locates it higher than other sequentially organized signal systems in terms of structural complexity. This paper argues that particular languages display specific resources (e.g. non-interpretive morphological agreement paradigms) that help the brain system responsible for dealing with LDDs to develop the capacity of acquiring and processing expressions with such a human-typical degree of computational complexity. Independently obtained naturalistic data is discussed and put to the service of the idea that the above-mentioned resources exert their developmental role from the outside, but in compliance with other internal resources, ultimately compounding an integrated developmental system. Parallels with other human and nonhuman developmental phenomena are explored, which point to the conclusion that the developmental system of concern can be assimilated to cases currently been conceptualized as ‘cue-response systems’ or ‘developmental hybrids’ within the ecological-developmental paradigm in theoretical biology. Such a conclusion is used to support the idea that both current externalist and internalist concepts fall short of a correct characterization of language.     

Lethal interactions among vertebrate top predators: a review of concepts,assumptions and terminology

Lethal interactions among large vertebrate predators have long interested researchers because of ecological and conservation issues. Research focusing on lethal interactions among vertebrate top predators has used several terms with a broad sense, and also introduced new terminology. We analysed the published literature with reference to the main underlying concepts and the use of terminology and its ecological context. The most frequently used terms in the literature were ‘predation’, ‘intraguild predation’, ‘interference competition’, and ‘interspecific killing’. Most studies presented evidence of the killing of the victim (77%), but information regarding its consumption was not given in 48% of cases. More than half of the analysed studies (56%) had no solid information on the degree of competition between interacting species. By reviewing definitions and their underlying assumptions, we demonstrate that lethal interactions among large vertebrate predators could be designated using four terms—‘predation’, ‘intraguild predation’, ‘interspecific competitive killing’, and ‘superpredation’—without the need to employ additional terminology that may increase confusion and misuse. For a correct framework of these lethal interactions it is critical to assess if the kill is consumed, if the victim is indeed a competitor of the killer, and if the prey is a high‐order predator. However, these elements of the framework are simultaneously the most common constraints to studies of lethal interactions, since they often require a great effort to obtain. The proper use of terms and concepts is fundamental to understanding the causes behind lethal interactions and, ultimately, what is actually happening in these complex interactions.     

Life With or Without Names

The terms ‘life’, ‘species’ and ‘individuals’ are key concepts in biology. However, theoretical and practical concerns are directly associated with definitions of these terms and their use in researchers’ work. Although the practical implications of employing definition of ‘species’ and ‘individuals’ are often clear, it is surprising how most biologists work in their field of study without adhering to a specific definition of life. In everyday scientific practice, biologists rarely define life. This is somewhat understandable: the majority of biologists accept the standard definition of life without exploring it, but this represents a bad attitude. In this essay, we update the concepts of life, species, and individuals in the light of the new techniques for massive DNA sequencing collectively known as high throughput DNA sequencing (HTS). A re-evaluation of the newest approaches and traditional concepts is required, because in many scientific publications, HTS users apply concepts ambiguously (in particular that of species). However, the absence of clarity is understandable. For most of the last 250 years, from Linnaeus to the most recent researches, identification and classification have been performed applying the same process. On the contrary, through HTS, biologists have become simply identifiers, who construct boundaries around the biological entities and do not examine the taxa at length, resulting in uncertainty in most readers and displeasure in traditional taxonomists. We organised our essay to answer a basic question: can we develop new means to observe living organisms?     

A critique of 'countryside biogeography' as a guide to research in human‐dominated landscapes

Proliferation of redundant terms in ecology and conservation slows progress and creates confusion. ‘Countryside biogeography’ has been promoted as a new framework for conservation in production landscapes, so may offer a replacement for other concepts used by landscape ecologists. We conducted a systematic review to assess whether the 'countryside biogeography' concept provides a distinctive framing for conservation in human‐dominated landscapes relative to existing concepts. We reviewed 147 papers referring to countryside biogeography and 81 papers that did not. These papers were divided into categories representing three levels of use of countryside biogeography concepts (strong, weak, cited only) and two categories that did not use countryside biogeography at all but used similar concepts including fragmentation and matrix. We revealed few distinctions among groups of papers. Countryside biogeography papers made more frequent use of the terms 'ecosystem services', 'intensification' and 'land sparing' compared with non‐countryside biogeography papers. Papers that did not refer to countryside biogeography sampled production areas (e.g. farms) less often, and this related to their focus on habitat specialist species for which patch‐matrix assumptions were reasonable. Countryside biogeography offers a conceptual wrapper rather than a distinctive framework for advancing research in human‐modified landscapes. This and similar wrappers such as ‘conservation biogeography’ and ‘agricultural biogeography’ risk creating confusion among new researchers, and can prevent clear communication about research. To improve communication, we recommend using the suite of well‐established terms already applied to conservation in human‐modified landscapes rather than through an interceding conceptual wrapper.     

Ethnonationalism,ethnic nationalism,and mini‐nationalism: A comparison of Connor,Smith and Snyder

Some terms have been coined to highlight the important relation between nationalism and ethnicity. However, there has been much confusion as to the meaning of such concepts as ‘ethnonationalism’, ‘ethnic nationalism’ and ‘mini‐nationalism’. This article compares the three terms, as used respectively in the works of Walker Connor, Anthony Smith and Louis Snyder. These scholars are selected not only because of their well‐respected position in the study of nationalism but also because their works are representative of each of the three concepts. The comparison finds that since both Connor and Smith emphasized the ethnic dimension of nationalism, their ideas can be presented in one analytical framework. In fact, Connor's ‘ethnonationalism’ and Smith's ‘ethnic nationalism’ overlap with each other. However, Smith's theory of nationalism is comprehensive enough to take care of the fact that the nationalisms of many new states of today's world have no ethnic base at all, whereas Connor's analysis makes no mention of this. In this respect, Smith's model is preferred to that of Connor. Finally, Snyder's ‘mini‐nationalism’ is seen as the least useful concept, since the use of size rather than ethnicity to classify nationalisms does not increase our understanding of the concept.     

Unpacking the species conundrum: philosophy,practice and a way forward

The history of ecology and evolutionary biology is rife with attempts to define and delimit species. However, there has been confusion between concepts and criteria, which has led to discussion, debate, and conflict, eventually leading to lack of consistency in delimitation. Here, we provide a broad review of species concepts, a clarification of category versus concept, an account of the general lineage concept (GLC), and finally a way forward for species discovery and delimitation. Historically, species were considered as varieties bound together by reproduction. After over 200 years of uncertainty, Mayr attempted to bring coherence to the definition of species through the biological species concept (BSC). This has, however, received much criticism, and the last half century has spawned at least 20 other concepts. A central philosophical problem is that concepts treat species as ‘individuals’ while the criteria for categorization treats them as ‘classes’. While not getting away from this problem entirely, the GLC attempts to provide a framework where lineage divergence is influenced by a number of different factors (and correlated to different traits) which relate to the different species concepts. We also introduce an ‘inclusive’ probabilistic approach for understanding and delimiting species. Finally, we provide a Wallacean (geography related) approach to the Linnaean problem of identifying and delimiting species, particularly for cases of allopatric divergence, and map this to the GLC. Going one step further, we take a morphometric terrain approach to visualizing and understanding differences between lineages. In summary, we argue that while generalized frameworks may work well for concepts of what species are, plurality and ‘inclusive’ probabilistic approaches may work best for delimitation.     

Fish infections associated with the genus Aeromonas: a review of the effects on oxidative status

The aim of this review was to summarize the current knowledge regarding the effects of aeromonosis on fish oxidative status. The bibliographic survey was carried out on the research platforms: Scopus and Science Direct. The keywords ‘Aeromonas’, ‘fish’ and ‘oxidative status’ (or ‘oxidative stress’, ‘oxidative damage’ and similar terms) were used. Scientific papers and short communications were considered. Studies involving fish aeromonosis and enzymatic or non-enzymatic markers of oxidative status were selected. The results of antioxidant enzymes activities/expressions after infection lack consistency, suggesting that these findings should be interpreted with caution. Most of the analysed studies pointed to an increase in reactive oxygen species, malondialdehyde and protein carbonylation levels, indicating possible oxidative damage caused by the infection. Thus, these three biomarkers are excellent indicators of oxidative stress during infection. Regarding respiratory burst activity, several studies have indicated increased activity, but other studies have indicated unchanged activity after infection. Nitric oxide levels also increased after infection in most studies. Therefore, it is suggested that the fish’s immune system tries to fight a bacterial infection by releasing reactive oxygen and nitrogen species.     

The use of natural language to communicate the perception of vibrotactile stimuli

This study explores the subjective use of adjectives to verbally communicate vibrotactile stimulation across multiple frequencies. In total, nine different vibrotactile stimulus frequencies (10–300?Hz) were utilized, and subjective evaluation methods, which involved adjectives, were used to assess the sensory representations of the participants (18 healthy male participants; mean age, 22.9 years; standard deviation, 3.5). Sensory terms such as ‘slow,’ ‘protruding,’ and ‘thick’ were used as representative expressions to describe low-frequency (10–100?Hz) vibrotactile stimulations, while ‘fast,’ ‘shallow,’ and ‘tickly’ were used to describe high-frequency (225–300?Hz) vibrotactile stimulations. At the frequencies of 150 and 200?Hz, no characteristic word was found because there was no difference in subjective evaluation scores from other low or high frequencies. The results suggest that vibrotactile stimulation at different frequencies induce diverse sensory representations, owing to not only the motion and shape of the stimuli but also the subjective responses of the perceivers. The results of this study could be utilized in developing affective haptic devices in the future.     

Methodological problems in evolutionary biology II. Appraisal of arguments against adaptationism

Methodological analysis shows that the concepts of fitness and adaptation are more complex than the literature suggests. Various arguments against ‘adaptationism’ are inadequate since they are couched in terms of unduly simplistic notions.     

Roadwork: expertise at work building roads in the Maldives

This article engages critically with concepts of ‘skill’, ‘expertise’, and ‘capacity’ as they operate as markers of distinction and domination and shape migratory labour relations among road construction workers from across South Asia in the Maldives archipelago. The article examines roadwork at three levels: the professional biographies leading to ‘flexible specialization’ rather than technical expertise amongst Maldivian managers; the technical expertise and social incorporation of ‘skilled’ Sri Lankan supervisors; and the key material expertise of ‘non-skilled’ Bangladeshi labourers in precarious employment. Whilst discussions of South Asian labour migration have been dominated by caste and class, this article argues that it is important to consider how the cultural production and understanding of concepts such as ‘expertise’, ‘capacity’, and ‘exposure’ at worksites can (also) become distinguishing factors in (hierarchical) migratory labour relations.     

A neutral terminology to define 'invasive' species

The use of simple terms to articulate ecological concepts can confuse ideological debates and undermine management efforts. This problem is particularly acute in studies of nonindigenous species, which alternatively have been called ‘exotic’, ‘introduced’, ‘invasive’ and ‘naturalised’, among others. Attempts to redefine commonly used terminology have proven difficult because authors are often partial to particular definitions. In an attempt to form a consensus on invasion terminology, we synthesize an invasional framework based on current models that break the invasion process into a series of consecutive, obligatory stages. Unlike previous efforts, we propose a neutral terminology based on this framework. This ‘stage‐based’ terminology can be used to supplement terms with ambiguous meanings (e.g. invasive, introduced, naturalized, weedy, etc.), and thereby improve clarity of future studies. This approach is based on the concept of ‘propagule pressure’ and has the additional benefit of identifying factors affecting the success of species at each stage. Under this framework, invasions can be more objectively understood as biogeographical, rather than taxonomic, phenomena; and author preferences in the use of existing terminology can be addressed. An example of this recommended protocol might be: ‘We examined distribution data to contrast the characteristics of invasive species (stages IVa and V) and noninvasive species (stages III and IVb)’.     

Understanding Power in Indigenous Protected Areas: the Case of the Tla-o-qui-aht Tribal Parks

This article draws on concepts of power from political ecology and political sociology to describe the ways that the Tla-o-qui-aht First Nation (a Canadian indigenous people) have attempted to realize their goals under the broad rubric of their Tribal Parks initiative. Like some other Indigenous peoples’ and Community Conserved territories and Areas (ICCAs), the Tribal Parks example features de facto legal pluralism, lack of clear tenure and/or legal recognition, oppositional and/or cooperative relationships with other actors, and situations where local actors are influenced by intersecting global discourses on conservation and indigenous rights and culture. Globally, ICCAs are a form of protected area and are potentially critical in terms of meeting ambitious global protected area targets as well in addressing issues related to the rights and well-being of indigenous peoples. As such, understanding the ‘customary law or other effective means’, or the dynamics of power through which indigenous groups are able (or not) to realize their protected area goals is of global significance. This article illuminates the contours of power through two specific Tribal Parks case studies: the first involves contestations over industrial logging, while the second focuses on the establishment and implementation of what came to be called an ‘ecosystem services fee’ paid by ecotourism outfitters operating within a Tribal Park. Results highlight that the Tla-o-qui-aht have drawn power from different sources and exercised it by different means including turning to the Courts in a context of legal uncertainty, protest and direct action coupled with appeals to public opinion, developing and drawing on relationships with both local and non-local interests, and by strategically ‘tapping into’ prominent discourses.     

Biological aspects of Bemisia tabaci biotype B and the chemical causes of resistance in soybean genotypes

In Brazil, the silverleaf whitefly (SLW), Bemisia tabaci biotype B, is a serious soybean pest. SLW management is difficult and new control strategies, such as host–plant resistance, are required. Herein, we aimed to evaluate the biology of SLW, from eggs to adults, on seven soybean cultivars. The emergence of adult insects was monitored daily. Defense-related compounds were identified and quantified from the V3 to the V8 stages in SLW-infested and non-infested plants. The rates of emergence of SLW adults were lower in cultivars ‘IAC 17,’ ‘IAC 19’, and ‘IAC 24’ compared with the susceptible cultivar ‘IAC Holambra Stwart’. Rutin, genistin, genistein, and salicylic acid were identified and quantified in plant extracts. The rutin, genistin, and genistein levels decreased after SLW infestation. Rutin concentrations increased in infested plants of ‘IAC 17’ (V6) and ‘IAC 19’ (from V5 to V8). ‘Barreiras’ showed the highest genistein content in non-infested plants; from V5 growth stage, it was not detected in cultivars Doko (infested), Vencedora, ‘IAC 17’, and ‘IAC 24’ (non-infested). High levels of salicylic acid were observed in ‘IAC ‘19’-infested plants (at V3 and V5). The results suggest that rutin can be related to SLW adults’ emergence only when the feeding source was ‘IAC 19’. Consequently, further studies are needed to access the associated gene expressions and the effect of other secondary metabolites, mainly volatile compounds from SA pathway, including its consequences on feeding preference and mostly in relation to IAC cultivars.     

Pitch the niche – taking responsibility for the concepts we use in ecology and species distribution modelling

In a discussion it is often easier to staunchly reject or offer resolute support for an idea. This third paper on the niche concept aims to develop a balanced argument by exploring general principles for determining an appropriate level for pitching the niche concept that will guide better use and less abuse of niche concepts. To do this we first have to accept that niche concepts are not necessarily essential for ecology. Rather than to improve niche concepts, our aim should then be to pitch the niche in terms of ecology. This aim helps us develop an ‘ultimate goal of the niche’ by which we can evaluate the concepts we use. For species distribution modelling, there has been a focus on the niche as an equilibrium outcome that perhaps has less relevance for disequilibrium situations (e.g. climate change projections). As is the case for much of ecology, more causal explanations of species' distributions use alternative terminologies and less frequently use the word ‘niche’. We suggest that niche concepts that are better aligned with the rest of ecology could arise from taking more responsibility for our own implementations, and by explaining our models with terms other than niche. A general, holistic niche concept promotes this view and promotes practical thinking about what we are modelling and how we interpret those models, which in turn should help inspire and support innovative modelling approaches in species distribution modelling.     

‘Agent Plus’ and ‘Practical Reasoner’: A Comparative Study of the Ethical Person

This paper explores an understanding of the person in terms of practical reason. Based on my fieldwork among the Jenu Kurumba and on ethnographic data on four other communities, I analyse how these five communities conceptualise the ethical person. To understand these concepts, I consult studies of an anthropology of ethics concerned with practical reason. Additionally I draw on Charles Taylor's concept of the ‘agent plus’ and Alasdair MacIntyre's notion of the ‘practical reasoner’. I argue that both Neo-Aristotelian notions are fundamentally important for understanding the concepts of the ethical person among the five cultural formations investigated in this paper.     

Lifeness signatures and the roots of the tree of life

Do trees of life have roots? What do these roots look like? In this contribution, I argue that research on the origins of life might offer glimpses on the topology of these very roots. More specifically, I argue (1) that the roots of the tree of life go well below the level of the commonly mentioned ‘ancestral organisms’ down into the level of much simpler, minimally living entities that might be referred to as ‘protoliving systems’, and (2) that further below, a system of roots gradually dissolves into non-living matter along several functional dimensions. In between non-living and living matter, one finds physico-chemical systems that I propose to characterize by a ‘lifeness signature’. In turn, this ‘lifeness signature’ might also account for a diverse range of biochemical entities that are found to be ‘less-than-living’ yet ‘more-than-non-living’.     

Coping with ethnicity in South Asia: Bangladesh,Punjab and Kashmir compared

In the anthropological and sociological studies of India the terms ‘tribe’ and ‘caste’, have been in use for almost two hundred years. The related notions of ‘tribalism’ and ‘casteism’ were brought in to replace a static (structural) by a dynamic (organizational, processual) approach. Since the 1970s, ‘ethnic group’ and ‘ethnicity’ have gained currency. After defining the terms, three cases of ethnicity are examined, namely East Bengali Muslim, Punjabi Sikh and Kashmiri Muslim. It is argued that, while the first is a success story, the second seems more like a retreat at present, and the third is at best nascent. The reasons for this difference are explored. Ethnicity, it is argued, is not only characterization of identity, but also a set of strategies to establish a new state. This objective is opposed by competing ethnic groups and the existing state. Ethnic movements therefore involve violence and their outcome is dependent upon a variety of factors and therefore contingent.