Intracellular Recording,Sensory Field Mapping,and Culturing Identified Neurons in the Leech,Hirudo medicinalis

The freshwater leech, Hirudo medicinalis, is a versatile model organism that has been used to address scientific questions in the fields of neurophysiology, neuroethology, and developmental biology. The goal of this report is to consolidate experimental techniques from the leech system into a single article that will be of use to physiologists with expertise in other nervous system preparations, or to biology students with little or no electrophysiology experience. We demonstrate how to dissect the leech for recording intracellularly from identified neural circuits in the ganglion. Next we show how individual cells of known function can be removed from the ganglion to be cultured in a Petri dish, and how to record from those neurons in culture. Then we demonstrate how to prepare a patch of innervated skin to be used for mapping sensory or motor fields. These leech preparations are still widely used to address basic electrical properties of neural networks, behavior, synaptogenesis, and development. They are also an appropriate training module for neuroscience or physiology teaching laboratories.     

Displayed Objects, Indigenous Identities, and Public Pedagogy

In this article, I describe how one group of student examines indigenous identity formation as dynamic and open to reinterpretation. Drawing on field observations and interviews with students in a 16-month ethnographic study, I examine how one group of students worked toward understanding how indigenous identity was determined by curatorial authority and historically defined museum practices. I argue that students can question the traditional pedagogical conceptions of indigenous culture that ought to be reconsidered within the public museum, and that working to historicize such conceptions makes more explicit student knowledge production of identity.     

Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution

We present a parameterized definition of gene clusters that allows us to control the emphasis placed on conserved order within a cluster. Though motivated by biological rather than mathematical considerations, this parameter turns out to be closely related to the bandwidth parameter of a graph. Our focus will be on how this parameter affects the characteristics of clusters: how numerous they are, how large they are, how rearranged they are, and to what extent they are preserved from ancestor to descendant in a phylogenetic tree. We infer the latter property by dynamic programming optimization of the presence of individual edges at the ancestral nodes of the phylogeny. We apply our analysis to a set of genomes drawn from the Yeast Gene Order Browser.     

Spinoza,Styron, and the Ethics of Healing

In this essay I discuss a passage from William Styron’s memoir of his long struggle with chronic severe depression, from the standpoint of a Spinozian understanding of agency and self-worth. In this passage Styron relates how in hearing a piece of music he was abruptly struck by a recollection of “all the joys [his] house had known” and how this brought a realization that it would be wrong for him to kill himself: wrong because it would be an abandonment of those who had shared in those joys and a “desecration” of himself. He tells how this realization led him to admit himself to hospital for treatment and thereby to a slow and difficult recovery. This, I propose, illustrates the Spinozian idea that the value of an individual life is properly understood in terms of that individual’s participation in the actualization of a shared value and that individual agency is empowered by the knowledge of such value.     

Using mathematical models to understand metabolism,genes, and disease

Mathematical models are a useful tool for investigating a large number of questions in metabolism, genetics, and gene–environment interactions. A model based on the underlying biology and biochemistry is a platform for in silico biological experimentation that can reveal the causal chain of events that connect variation in one quantity to variation in another. We discuss how we construct such models, how we have used them to investigate homeostatic mechanisms, gene–environment interactions, and genotype–phenotype mapping, and how they can be used in precision and personalized medicine.     

The Structure of Autocatalytic Sets: Evolvability, Enablement, and Emergence

This paper presents new results from a detailed study of the structure of autocatalytic sets. We show how autocatalytic sets can be decomposed into smaller autocatalytic subsets, and how these subsets can be identified and classified. We then argue how this has important consequences for the evolvability, enablement, and emergence of autocatalytic sets. We end with some speculation on how all this might lead to a generalized theory of autocatalytic sets, which could possibly be applied to entire ecologies or even economies.     

Hormonal systems,human social bonding,and affiliation

Which hormones are implicated in human social bonding and affiliation? And how does field research speak to this issue? We begin by laying out a broad view of how endocrine hormones in general modulate life history allocations of energy and other resources, and the ways in which their neuromodulatory functions must be understood within a broader conceptualization of how they have been shaped to affect allocations. We then turn to four specific hormones or hormone families that have received much attention: oxytocin, opioids, prolactin, and progesterone. Each plays a role in regulating psychological capacities and propensities that underlie individuals' interactions with important social targets. Yet in no case is it clear exactly what regulatory roles these hormones play. We suggest several directions for future research.     

Classification, disease, and diagnosis

Classification shapes medicine and guides its practice. Understanding classification must be part of the quest to better understand the social context and implications of diagnosis. Classifications are part of the human work that provides a foundation for the recognition and study of illness: deciding how the vast expanse of nature can be partitioned into meaningful chunks, stabilizing and structuring what is otherwise disordered. This article explores the aims of classification, their embodiment in medical diagnosis, and the historical traditions of medical classification. It provides a brief overview of the aims and principles of classification and their relevance to contemporary medicine. It also demonstrates how classifications operate as social framing devices that enable and disable communication, assert and refute authority, and are important items for sociological study.     

WATER MOTION, MARINE MACROALGAL PHYSIOLOGY, AND PRODUCTION

Water motion is a key determinant of marine macroalgal production, influencing directly or indirectly physiological rates and community structure. Our understanding of how marine macroalgae interact with their hydrodynamic environment has increased substantially over the past 20 years, due to the application of tools such as flow visualization to aquatic vegetation, and in situ measurements of seawater velocity and turbulence. This review considers how the hydrodynamic environment in which macroalgae grow influences their ability to acquire essential resources and how macroalgae might respond physiologically to fluctuations in their hydrodynamic regime with a focus on: (1) the biochemical processes occurring within the diffusion boundary layer (DBL) that might reduce rates of macroalgal production; (2) time scales over which measurements of velocity and DBL processes should be made, discussing the likelihood of in situ mass transfer limitation; (3) if and how macroalgal morphology influences resource acquisition in slow flows; and (4) ecobiomechanics and how hydrodynamic drag might influence resource acquisition and allocation. Finally, the concept that macroalgal production is enhanced in wave-exposed versus sheltered habitats is discussed.     

Forensic fictions: Science,television production,and modern storytelling

This essay uses interviews with television creators, writers, and producers to examine how media practitioners utilise, negotiate and transform forensic science in the production of televisual stories including the creation of unique visuals, character exploration, narrative progression, plot complication, thematic development, and adding a sense of authenticity. Television as a medium has its own structures and conventions, including adherence to a show’s franchise, which put constraints on how stories are told. I demonstrate how television writers find forensic science to be an ideal tool in navigating television’s narrative constraints by using forensics to create conflicts, new obstacles, potential solutions, and final solutions in their stories. I show how television writers utilise forensic science to provide the scientific certainty their characters require to catch the criminal, but also how uncertainty is introduced in a story through the interpretation of the forensics by the show’s characters. I also argue that televisual storytellers maintain a flexible notion of scientific realism based on the notion of possibility that puts them at odds with scientists who take a more demanding conception of scientific accuracy based on the concept of probability.     

Ion hydration: Implications for cellular function, polyelectrolytes, and protein crystallization

Only oppositely charged ions with matching absolute free energies of hydration spontaneously form inner sphere ion pairs in free solution [K.D.Collins, Ions from the Hofmeister series and osmolytes: effects on proteins in solution and in the crystallization process, Methods 34 (2004) 300-311.]. We approximate this with a Law of Matching Water Affinities which is used to examine the issues of (1) how ions are selected to be compatible with the high solubility requirements of cytosolic components; (2) how cytosolic components tend to interact weakly, so that association or dissociation can be driven by environmental signals; (3) how polyelectrolytes (nucleic acids) differ from isolated charges (in proteins); (4) how ions, osmolytes and polymers are used to crystallize proteins; and (5) how the "chelate effect" is used by macromolecules to bind ions at specific sites even when there is a mismatch in water affinity between the ion and the macromolecular ligands.     

Orthology relations, symbolic ultrametrics, and cographs

Orthology detection is an important problem in comparative and evolutionary genomics and, consequently, a variety of orthology detection methods have been devised in recent years. Although many of these methods are dependent on generating gene and/or species trees, it has been shown that orthology can be estimated at acceptable levels of accuracy without having to infer gene trees and/or reconciling gene trees with species trees. Thus, it is of interest to understand how much information about the gene tree, the species tree, and their reconciliation is already contained in the orthology relation on the underlying set of genes. Here we shall show that a result by Böcker and Dress concerning symbolic ultrametrics, and subsequent algorithmic results by Semple and Steel for processing these structures can throw a considerable amount of light on this problem. More specifically, building upon these authors’ results, we present some new characterizations for symbolic ultrametrics and new algorithms for recovering the associated trees, with an emphasis on how these algorithms could be potentially extended to deal with arbitrary orthology relations. In so doing we shall also show that, somewhat surprisingly, symbolic ultrametrics are very closely related to cographs, graphs that do not contain an induced path on any subset of four vertices. We conclude with a discussion on how our results might be applied in practice to orthology detection.     

The Semiglades: The Collision of Restoration,Social Values,and the Ecosystem Concept

Defining success targets in restoration and how social values affect them are two commonly discussed issues in restoration today. We believe that how success is commonly defined—with vague terms such as “healthy ecosystem” or cited as a return to a previous, historic state—needs to be reevaluated. With the increasing number of novel ecosystems, there is an increasing conflict between the ecosystem concept, social values, and restoration. This arises from the fact that ecosystems are defined by the values of the scientists describing them, necessarily constraining the ecosystem to a generally static concept. It is not directly the concept, but how it is perceived through our filter of social values that represses the creativity and innovation needed in restoration today. Within restoration, we feel that the ecosystem concept does a disservice by ignoring the increasing number of novel systems, and that hinders real progress in a time when hesitation can be costly. To best illustrate this, we offer the example of restoration of the Florida Everglades and how it has become a novel system in pattern and process. We suggest renaming the Everglades “The Semiglades” in hopes of opening a dialog to expose social/ecosystem biases and include novel landscapes in management and planning.     

Writing failure: knowledge production,temporalities, ethics,and traces

This volume follows failures out into the world, exploring how they unfold ethnographically. Taking a longer view shows how objects, narratives, and diagnoses of failures may be crafted, acted on, suffered, resisted – unmade or recomposed. Thus while tropes and diagnoses of failure can temporarily (re)organize, narrate, and stabilize the world, the kinds of failures explored here also indicate a mode of uncontainable excess that refuses the boundedness of knowledge objects, temporalities, and spaces. This volume offers three main interventions. The first concerns knowledge production: how objects of failure are crafted through selective ways of knowing that occlude both other modes of apprehension at different scales and failure's many affective valences. The second thinks through the knotted temporalities – whether pasts, futures, suspended presents, or repetition and sedimentation – that make and are made by failure. Finally, writing about unfurling failures requires careful attention to non-linear reverberations and traces as well as to open-ended and mobile narratives that produce different social and material effects.     

More than just noise: Chance,mating success,and sexual selection

Chance plays a critical but underappreciated role in determining mating success. In many cases, we tend to think of chance as background noise that can be ignored in studies of mating dynamics. When the influence of chance is consistent across contexts, chance can be thought of as background noise; in other cases, however, the impact of chance on mating success can influence our understanding of how mates are acquired and how sexual selection operates. In particular, when the importance of chance covaries with biological or ecological factors in a systematic manner—that is, when chance becomes consistently more or less important under certain conditions—then chance is important to consider if we want to fully understand the operation of mate acquisition and sexual selection. Here, we present a model that explores how chance covaries with factors such as sex ratio, adult population size, and mating regime in determining variation in mating success. We find that in some cases, chance covaries with adult population size and the operational sex ratio to create variation in mating success. We discuss how chance can influence our more general understanding of the operation of mating dynamics and sexual selection.     

Tooth crown heights, tooth wear, sexual dimorphism and jaw growth in hominoids

The aim of this review is to bring together data that link tooth morphology with tooth function and tooth growth: We aim to show how the microanatomy of hominoid teeth is providing evidence about rates of tooth growth that are likely to be a consequence of both masticatory strategy and social behaviour. First, we present data about incisor and molar tooth wear in wild short chimpanzees that demonstrate how crown heights are likely to be related to relative tooth use in a broad sense. Following this we review recent studies that describe the microanatomy of hominoid tooth enamel and show how these studies are providing evidence about tooth crown formation times in hominoids, as well as improving estimates for the age at death of certain juvenile fossil hominids. Next, we outline what is known about the mechanisms of tooth growth in the sexually dimorphic canine teeth of chimpanzees and compare these patterns of growth with tooth growth patterns in the canines of three fossil hominids from Laetoli, Tanzania. Finally, we discuss how selection pressures that operate to increase or reduce the size of anterior teeth interact with jaw size. We argue that the space available to grow developing teeth in the mandibles of juvenile hominoids is determined by the growth patterns of the mandibles, which in turn reflect masticatory strategy. The consequences of selection pressure to grow large or small anterior teeth are likely to be reflected in the times at which these teeth are able to emerge into occlusion.     

Context, ethics and pharmacogenetics

Most of the literature on pharmacogenetics assumes that the main problems in implementing the technology will be institutional ones (due to funding or regulation) and that although it involves genetic testing, the ethical issues involved in pharmacogenetics are different from, even less than, 'traditional' genetic testing. Very little attention has been paid to how clinicians will accept this technology, their attitudes towards it and how it will affect clinical practice. This paper presents results from interviews with clinicians who are beginning to use pharmacogenetics and explores how they view the ethics of pharmacogenetic testing, its use to exclude some patients from treatment, and how this kind of testing fits into broader debates around genetics. In particular this paper examines the attitudes of breast cancer and Alzheimer's disease specialists. The results of these interviews will be compared with the picture of pharmacogenetics painted in the published literature, as a way of rooting this somewhat speculative writing in clinical practice.     

Domestic Transitions, Desiccation, Agricultural Intensification, and Livelihood Diversification among Rural Households on the Central Plateau, Burkina Faso

ABSTRACT   Understanding how and why domestic groups alter their function and form has long been a theme within anthropology. Numerous accounts have detailed the processes that drive household transformations and their underlying mechanisms. Mostly, these studies describe how domestic groups fission and fuse between extended and nuclear forms. In recent years, scholars have emphasized that these transformations should be understood within larger contexts of social and environmental change. Mossi communities on the Central Plateau of Burkina Faso provide an excellent opportunity to explore such processes because the large extended households documented 30 years ago were predicted to decline and eventually disappear. In this study, I examine dynamics of household transformations and test the validity of this prediction. I use perspectives from sustainability science and computer-simulation modeling to understand how regional desiccation, agricultural intensification, and livelihood diversification articulate with domestic transitions.     

A triage framework for managing novel,hybrid, and designed marine ecosystems

The novel ecosystem (NE) concept has been discussed in terrestrial restoration ecology over the last 15 years but has not yet found much traction in the marine context. Against a background of unprecedented environmental change, managers of natural marine resources have portfolios full of altered systems for which restoration to a previous historical baseline may be impractical for ecological, social, or financial reasons. In these cases, the NE concept is useful for weighing options and emphasizes the risk of doing nothing by forcing questions regarding the value of novelty and how it can best be managed in the marine realm. Here, we explore how the concept fits marine ecosystems. We propose a scheme regarding how the NE concept could be used as a triage framework for use in marine environments within the context of a decision framework that explicitly considers changed ecosystems and whether restoration is the best or only option. We propose a conceptual diagram to show where marine NEs fit in the continuum of unaltered to shifted marine ecosystems. Overall, we suggest that the NE concept is of interest to marine ecologists and resource managers because it introduces a new vocabulary for considering marine systems that have been changed through human actions but have not shifted to an alternate stable state. Although it remains to be seen whether the concept of marine NEs leads to better conservation and restoration decisions, we posit that the concept may help inform management decisions in an era of unprecedented global marine change.