Can't see the colony for the bees: behavioural perspectives of biological individuality

The question ‘what is an individual’ does not often arise in studies within the field of behavioural ecology. Generally behavioural ecologists do not think about what makes an individual because they tend to use intuitive working concepts of individuality. Rarely do they explicitly mention how individuality affects their experimental design and interpretation of results. By contrast, the concept of individuality continues to intrigue philosophers of biology. It is interesting that while philosophers of biology debate definitions of individuality, biologists generally use the concept of individuality every day without much thought. Here we review the philosophical approaches to defining biological individuality, and illustrate how the biological individuality concepts used by biologists are affected by their study question and choice of organism. We clarify the behavioural perspective of biological individuality by introducing the concept of the behavioural individual. The notion of the behavioural individual is particularly interesting when explored in less‐conventional study organisms. By including less‐conventional organisms, it becomes clear why the concept of biological individuality is usually intuitive in behavioural ecology.     

Ecological units: definitions and application

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

The relativity of Darwinian populations and the ecology of endosymbiosis

If there is a single discipline of science calling the basic concepts of biology into question, it is without doubt microbiology. Indeed, developments in microbiology have recently forced us to rethink such fundamental concepts as the organism, individual, and genome. In this paper I show how microorganisms are changing our understanding of natural aggregations and develop the concept of a Darwinian population to embrace these discoveries. I start by showing that it is hard to set the boundaries of a Darwinian population, and I suggest thinking of a Darwinian population as a relative property of a Darwinian individual. Then I argue, in contrast to the commonly held view, that Darwinian populations are multispecies units, and that in order to accept the multispecies account of Darwinian populations we have to separate fitness from natural selection. Finally, I show how all these ideas provide a theoretical framework leading to a more precise understanding of the ecology of endosymbiosis than is afforded by poetic metaphors such as ‘slavery’.     

The Work of Indebtedness: The Traumatic Present of Late Capitalist Chile

In political and biomedical discourses, "posttraumatic stress disorder" has become a set of organizing concepts for trauma and traumatic memory. These concepts, however, are predicated on an understanding of traumatic memory as a discrete etiological event that, when reexperienced, is productive of symptoms. In this essay, I explore alternative framings of trauma that arise out of historical changes in political economic language and from experiences of monetary, historical, and affective indebtedness in Santiago, Chile. This ethnographic research is based in an historically leftist población (poor urban sector) and follows the interwoven narratives of a formerly exiled communist militant and her adopted daughter. Throughout this essay, I describe the mother's attempts to inhabit an untimely language of socialist politics and the daughter's rejection of both this language and her mother's pain. I elaborate on how these attempts are products of and productive of monetary and intersubjective indebtedness in a neoliberal present. By describing the differing historical languages inhabited by these subjects, I attempt to evoke an understanding of trauma not as an individual possession or etiological event, but rather as a referential dissonance in the neoliberal context. This referential dissonance emerges from the gap between the historical languages that inform subjectivities. I explore how such a gap can create contexts in which the everyday itself both threatens the disarticulation of the subject and produces injurious affective relationships. In this way, I interrogate relationships between trauma, recovery, and the everyday.     

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?     

Brief communication: Effect of size biases in the coefficient of variation on assessing intraspecific variability in the prosimian skeleton

Lack of independence of data points or the pooling fallacy has been suggested as a potential problem in the study of handedness in nonhuman primates, particularly as it relates to whether hand use responses should be recorded as individual events or bouts of activity. Here, I argue that there is no evidence that the concept of statistical independence of data points or the pooling fallacy is a problem in the evaluation of population‐level handedness in previous studies in nonhuman primates. I further argue these statistical concepts have been misapplied to the characterization of individual hand preferences. Finally, I argue that recording hand use responses as bouts rather than events has no significant effect on reports of hand use in nonhuman primates and, in fact, may unintentionally bias hand use toward the null hypothesis. Several suggestions for improvement in the measurement and statistical determination of individual handedness are offered in the article. Am J Phys Anthropol 151:151–157, 2013. © 2013 Wiley Periodicals, Inc.     

Reflections on basic science

After almost 50 years in science, I believe that there is an acceptable, often advantageous chasm between open-ended basic research-free exploration without a practical destination and in which the original ideas may fade into new concepts-and translational research or clinical research. My basic research on crystalline (proteins conferring the optical properties of the eye lens) led me down paths I never would have considered if I were conducting translational research. My investigations ranged from jellyfish to mice and resulted in the gene-sharing concept, which showed that the same protein can have distinct molecular functions depending upon its expression pattern and, conversely, that different proteins can serve similar functional roles. This essay portrays basic science as a creative narrative, comparable to literary and artistic endeavors. Preserving the autonomy of open-ended basic research and recognizing its artistic, narrative qualities will accelerate the development of innovative concepts, create a rich resource of information feeding translational research, and have a positive impact by attracting creative individuals to science.     

The next step in biology: a periodic table?

Systems biology is an approach to explain the behaviour of a system in relation to its individual components. Synthetic biology uses key hierarchical and modular concepts of systems biology to engineer novel biological systems. In my opinion the next step in biology is to use molecule-to-phenotype data using these approaches and integrate them in the form a periodic table. A periodic table in biology would provide chassis to classify, systematize and compare diversity of component properties vis-a-vis system behaviour. Using periodic table it could be possible to compute higher- level interactions from component properties. This paper examines the concept of building a bio-periodic table using protein fold as the fundamental unit.     

The next step in biology: A periodic table?

Systems biology is an approach to explain the behaviour of a system in relation to its individual components. Synthetic biology uses key hierarchical and modular concepts of systems biology to engineer novel biological systems. In my opinion the next step in biology is to use molecule-to-phenotype data using these approaches and integrate them in the form a periodic table. A periodic table in biology would provide chassis to classify, systematize and compare diversity of component properties vis-a-vis system behaviour. Using periodic table it could be possible to compute higher-level interactions from component properties. This paper examines the concept of building a bio-periodic table using protein fold as the fundamental unit.     

Conceptual problems and scale limitations of defining ecological communities: a critique of the CI concept (Community of Individuals)

Recently, Looijen & van Andel (1999) proposed a new definition of an ecological community by using two criteria: (1) restricting membership by taxonomic relatedness, and (2) defining boundaries by the intersection of the area of population range boundaries. I analyze the implications of their definition and explore the limitations of the approach. Overall, I show this definition to be highly scale-limited, to not encompass many ecological concepts developed for the community level, and to have hidden assumptions that are not met in natural systems. An alternative model of the ecological community is proposed as a contrast, a model based on the community of an individual, in which individuals and interactions are used to develop the larger entity of an ecological community. This alternative model illustrates that the principal problems Looijen & van Andel (1999) discussed about previous community concepts with respect to application to vegetation classification are not ‘problems’ but are characteristics of ecological communities. Any definition of an ecological community must be able to incorporate these characteristics as well as current ecological concepts used at the community level.     

The method of synthesis in ecology

Synthesis of results from different investigations is an important activity for ecologists but when compared with analysis the method of synthesis has received little attention. Ecologists usually proceed intuitively and this can lead to a problem in defining differences between the syntheses made by different scientists. It also leads to criticism from scientists favoring analytical approaches that the construction of general theory is an activity that does not follow the scientific method. We outline a methodology for scientific inference about integrative concepts and the syntheses made in constructing them and illustrate how this can be applied in the development of general theory from investigations into particular ecological systems. The objective is to construct a causal scientific explanation. This has four characteristics. (1) It defines causal and/or organizational processes that describe how systems function. (2) These processes are consistent – under the same conditions they will produce the same effect. (3) A causal scientific explanation provides general information about events of a similar kind. (4) When experiments are possible then a designed manipulation will produce a predictable response. The essential characteristic of making synthesis to construct a causal scientific explanation is that it is progressive and we judge progress made by assessing the coherence of the explanation using six criteria: acceptability of individual propositions including that they have been tested with data, consistency of concept definitions, consistency in the type of concepts used in making the explanation, that ad hoc propositions are not used, that there is economy in the number of propositions used, that the explanation applies to broad questions. We illustrate development of a causal scientific explanation for the concept of long-lived pioneer tree species, show how the coherence of this explanation can be assessed, and how it could be improved.     

Ditch the niche – is the niche a useful concept in ecology or species distribution modelling?

In this first of three papers we examine the use of niche concepts in ecology and especially in species distribution modelling (SDM). This paper deliberately focuses on the lack of clarity found in the term ‘niche’. Because its meanings are so diverse, the term niche tends to create confusion and requires constant qualification. The literature houses many idiosyncratic ideas of what the niche is, but few examples where niche is more explanatory than the terminologies of population and community ecology or the statistical methods used to implement SDM analyses. In many cases the original (and inspirational) concepts are not directly applicable to our modern applications (e.g. set theory). There are some conceptual limitations found in individual definitions of niche (e.g. the fundamental niche concept), so it is perhaps understandable why more neutral terminology is becoming popular in SDM. An examination of the literature reveals a wide range of uncritical use of niche terminology. Our findings in this paper do not necessarily support the position of niche as a universally useful concept.     

The nature of species: A rejoinder to Zachos et al.

I argue strongly that the Phylogenetic Species Concept offers the only way of defining species that makes them testable, as any scientific hypothesis should be. The criticisms made by Zachos et al. (in press) are not cogent, and do not offer a means of testing species proposals. Nonetheless, their comments on species concepts in conservation do provide support to the value of the Phylogenetic Species Concept.     

Introduction: Culture Without Cultures—The Culture Effect

Anthropology has often been handmaiden to administrative and political activity that requires bounded social groups mapped onto territories and possessing defining characteristics such as language, values and behaviours. This introductory essay sets the scene for the papers in this Issue which show that actual sets of social relations in their particular places cannot easily be made to conform with this hermetic construct. Acknowledging this, post‐colonial theory has been driven to theorise borderlands, hybridisation and metissage, liminal and interstitial social spaces. Yet these necessarily reinforce and privilege primary concepts of the pure and the central, the bounded and situated. This paper places the hermetic view of culture in its formative period, which also saw the emergence of nationalism and scientific atomism. The paper proposes that positing pure and bounded cultures, even as an idealised abstraction, is an error of theory which is influenced by an attachment to metaphors of the material world, usually ‘Euclidean’. Finally, the paper explores ways that analyses of cultural interrelation, such as those in this Special Issue, can proceed without imagining a resulting ‘culture’, and what this may do for the political landscape of localised cultural rights.     

How to teach procedures,problem solving,and concepts in microbial genetics

Flow diagrams, algorithms, decision logic tables, and concept maps are presented as methods for teaching practical procedures, problem solving, and basic concepts in microbial genetics. For practical procedures the aim is to present the sequence of operations clearly, to diagnose and correct possible errors, and to encourage the student to design investigations efficiently. Procedures for problem solving are discussed which give a logical sequence of questions with yes/no answers leading to a finite number of possible solutions. The use of concept maps in the planning of courses and in illustrating the relationships between different aspects of microbial genetics is discussed. It is suggested that the flexible use of these methods should lead to an improved understanding of microbial genetics.     

On the integrated frameworks of species concepts: Mayden’s hierarchy of species concepts and de Queiroz’s unified concept of species

Richard L. Mayden and Kevin de Queiroz have devised and developed ‘a hierarchy of species concepts’ and ‘a unified species concept’, respectively. Although their integrated frameworks of species concepts are rather different as to how to integrate the diverse modern concepts of species, the end result is that they are likely to agree on species recognition in nature, because they virtually share the same major components (i.e. evolutionary or lineage concept of species; same way of delimiting species), and have the same important consequences. Both the hierarchical and unified frameworks, however, are interpreted to have shortcoming regarding the way of integrating the modern species concepts. I reformulate these ideas into a framework of species concepts as follows: It treats the idea of species as population‐level evolutionary lineages (sensu Wiley 1978 ) as the concept for species category, and it adopts the contingent biological properties of species (e.g. internal reproductive isolation, diagnosability, monophyly) as operational criteria in delimiting species. I also suggest that existing and revised versions of the integrated framework of species concepts all are not new species concepts, but versions of the evolutionary species concept, because they treat the evolutionary (or lineage) species concept as the concept for species category.     

What is wrong with absolute individual fitness?

One of the most basic facts about evolution is that fitness is a relative concept. It does not matter how well an organism survives and reproduces, only that it does so better than other organisms bearing alternative traits. Nevertheless, many evolutionary arguments are framed in terms of absolute individual fitness. The absolute fitness criterion (AFC) can be justified in terms of relative fitness only given certain assumptions that are frequently violated in nature. In particular, interactions must occur in groups that are randomly formed and phenotypic variation among groups must be tightly coupled to genetic variation. Complicating the genotype-phenotype relationship can cause phenotypic variation among groups to become nonrandom, even when the groups are randomly formed, favoring traits that do not maximize absolute individual fitness. Complex genotype-phenotype relationships and complex population structures require explicit models of evolutionary change based on relative fitness differences within and among groups.     

Environmental stress and adaptational responses: consequences for human health outcomes

With the dramatic pace of modernization of the world's population, human adaptation as a theoretical construct and paradigm will likely become a focal scientific issue involving scientists from many disciplinary areas during the 21st Century. Macro and micro environments are in rapid flux and human populations are exposed to rapid change. The concept of adaptation, at least in the field of biological anthropology and human biology, will likely remain tied to evolutionary processes and concepts of selection and fitness. In this paper, we discuss the theoretical constructs of adaptation and adaptability and select three current examples from our ongoing research that involve studies of adaptation and evolutionary processes in modernizing populations in different locations worldwide.     

An organism-centered approach to some community and ecosystem concepts

We present a discussion of the ecological concept of the niche based on the perspective of the individual organism, rather than that of a population or species. This discussion is then expanded to include other related ecological concepts such as guild, environment, habitat and functional group.Using the individual as the focus permits the development of a system of concepts which, we believe, approximate the way that ecological interactions occur in nature.     

The Texture of the Real: Experimentation and Experience in Schizophrenia

The dominance of the neurosciences in psychiatric research raises questions about the relationship between research practices and the lived experience of mental illness. Here, I use data from a group of researchers focusing on neurocognition in schizophrenia to explore the problem of representation in psychiatric research and the forms that neuroscientific evidence assumes for those who produce it. These researchers grappled with the complexity of schizophrenia not by narrowing disease concepts to biological facts but by referencing measurement techniques to generate new versions of schizophrenia. By linking experimental findings to inchoate concepts of personhood and social experience, I found that they reframed and reinforced cultural values, including that those with schizophrenia are destined to a debased and deficient existence. I argue that cognition has emerged as an essential feature of schizophrenia not only because of its representational utility but also because of the ontological work the concept performs. In closing, I present some implications for the neurobiological and social sciences.