The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase

Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme — ribonucleotide reductase (RNR) — is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of ‘omics’, we discuss what makes the larger subunit of this enzyme (RNR-α) so interesting, highlighting its emerging cellular interactome based on its unique oligomeric dynamism that dictates its compartment-specific occupations. Linking the history of the field with the multivariable nature of this exceedingly sophisticated enzyme, we further discuss implications of new data pertaining to DNA-damage response, S-phase checkpoints, and ultimately tumor suppression. We hereby hope to provide ideas for those interested in these fields and exemplify conceptual frameworks and tools that are useful to study RNR's broader roles in biology.     

Medicine’s collision with false hope: The False Hope Harms (FHH) argument

The goal of this paper is to introduce the false hope harms (FHH) argument, as a new concept in healthcare. The FHH argument embodies a conglomerate of specific harms that have not convinced providers to stop endorsing false hope. In this paper, it is submitted that the healthcare profession has an obligation to avoid collaborating or participating in, propagating or augmenting false hope in medicine. Although hope serves important functions—it can be ‘therapeutic’ and important for patients’ ‘self-identity as active agents’— the presentation of false hope along the hope continuum entails a misconstrued balancing act. By not speaking up against unrealistic patient and family requests—including some requests for rights to try, resuscitative efforts in terminally ill patients, or other demands for non-beneficial treatments—healthcare providers precipitate harms, i.e., the FHH. These harms arise on both individual and communal levels and cannot be ignored. The goal of this paper is not to offer a definition of false hope, because the phenomenon of false hope is too complex for any simple definition. Instead, this paper seeks to make four points while outlining the FHH argument: consumer medicine and false hope are connected; providers and patients are very vulnerable in the system of consumer medicine; providers have a responsibility to stand up against false hope; and how the FHH argument could perhaps offer a footing to resist giving in to false hope.     

Meaning in Nature: Organic Manufacture?

The paper examines Marcello Barbieri’s (2007) Introduction to Biosemiotics. Highlighting debate within the biosemiotic community, it focuses on what the volume offers to those who explain human intellect in relation to what Turing called our ‘physical powers.’ In scrutinising the basis of world-modelling, parallels and contrasts are drawn with other work on embodied-embedded cognition. Models dominate biology. Is this a qualitative fact or does it point to biomechanisms? In evaluating the 18 contributions, it is suggested that the answers will shape the field. First, they will decide if biochemistry and explanatory reduction can be synergised by biosemantics. Second, they will show if our intellectual powers arise from biology. Does thinking use—not a language faculty—but what Marko? and colleagues call semiosis by the living? Resolution of such issues, it is suggested, can change how we view cognition. Above all, if the biomechanists win the day, cultural models can be regarded as extending natural meaning. On such a view, biomechanisms prompt us to act and perceive as we model our own natural models. This fits Craik’s vision: intellect gives us the alphanumerical ‘symbols’ that allow thoughts to have objective validity. For the biomechanist, this is explained—not by brains alone—but, rather, by acting under the constraints of historically extended sensoria.     

Adaptation,fitness and the selection-optimality links

We critically examine a number of aspects of Grafen’s ‘formal Darwinism’ project. We argue that Grafen’s ‘selection-optimality’ links do not quite succeed in vindicating the working assumption made by behavioural ecologists and others—that selection will lead organisms to exhibit adaptive behaviour—since these links hold true even in the presence of strong genetic and developmental constraints. However we suggest that the selection-optimality links can profitably be viewed as constituting an axiomatic theory of fitness. Finally, we compare Grafen’s project with Fisher’s ‘fundamental theorem of natural selection’, and we speculate about whether Grafen’s results can be extended to a game-theoretic setting.     

Fuzzy Cognitive Maps of Social-Ecological Complexity: Applying Mental Modeler to the Bonneville Salt Flats

Although often limited in terms of extent or accuracy, mental models—i.e., explanations of the surrounding world and how things work within it—provide confidence and frameworks to navigate life's uncertainties. Unfortunately, differing and yet similar mental models held collectively by groups can lead to problematic behavior, misunderstandings, and conflict on large scales. Such challenges are likely familiar to natural resource managers who, in the course of their work, must consider issues that are neither simple nor exclusively ecological or social in nature. Building mental models of various groups’ understanding of a complex natural resource may help managers address the impacts of resource-related behaviors but can be a difficult task when collecting modeling data from large and diverse user groups. Using a sequential, exploratory approach, our study addresses the utility of surrogate mental modeling to explore (a) mental models held by key players from six stakeholder groups associated with Utah's Bonneville Salt Flats (US), and (b) whether these key players were confident that their personal subjective models represented their own group's thinking about Bonneville. We sought to illuminate and compare stakeholder groups’ mental models of subjectively important social and ecological concepts related to Bonneville through the use of fuzzy cognitive maps (FCMs; i.e., semi-quantitative representations of mental models) constructed in Mental Modeler. Analysis revealed differences among groups’ FCMs and levels of perceived complexity, as well as areas of agreement regarding the strength, direction, and character of certain social-ecological relationships. Intersections and divergences in stakeholder mental models may provide logical starting points for communal knowledge-building that can perhaps lessen tension among groups attributable to conceptual misunderstandings of resource-specific complexity.     

A reversal of the shift towards earlier spring phenology in several Mediterranean reptiles and amphibians during the 1998–2013 warming slowdown

Herps, especially amphibians, are particularly susceptible to climate change, as temperature tightly controls many parameters of their biological cycle—above all, their phenology. The timing of herps’ activity or migration period—in particular the dates of their first appearance in spring and first breeding—and the shift to earlier dates in response to warming since the last quarter of the 20^th century has often been described up to now as a nearly monotonic trend towards earlier phenological events. In this study, we used citizen science data opportunistically collected on reptiles and amphibians in the northern Mediterranean basin over a period of 32 years to explore temporal variations in herp phenology. For 17 common species, we measured shifts in the date of the species’ first spring appearance—which may be the result of current changes in climate—and regressed the first appearance date against temperatures and precipitations. Our results confirmed the expected overall trend towards earlier first spring appearances from 1983 to 1997, and show that the first appearance date of both reptiles and amphibians fits well with the temperature in late winter. However, the trend towards earlier dates was stopped or even reversed in most species between 1998 and 2013. We interpret this reversal as a response to cooling related to the North Atlantic Oscillation (NAO) in the late winter and early spring. During the positive NAO episodes, for certain species only (mainly amphibians), the effect of a warm weather, which tends to advance the phenology, seems to be counterbalanced by the adverse effects of the relative dryness.     

Whatever happened to economic anthropology?1

In the 1970s, economic anthropology, along with kinship and ecological anthropology, was regarded as a core discipline in the teaching of anthropology. The centrality of all these subjects was reflected in the debates of the time. For economic anthropology, understanding the articulation of modes of production was the problem; the holy trinity—tribe, peasant, capitalist—provided the key terms of the debate. These terms, and this problem, are history. The discipline of anthropology has been de‐cored over the past 30 years: economic anthropology, kinship and ecological anthropology are not even on the agenda in many universities today (ANU included). This presents us with a paradox because these academic trends are in inverse proportion to the importance of contemporary developments in the economy, the family and ecology as global problems facing humanity. This paradox must be addressed not by arguing for a rehabilitation of the core subjects of the 1970s—those days are long gone—but by taking a critical look at the implicit theories of value that inform anthropological thinking about the economy, the family and ecology today. I shall argue that, along with neoliberalism, ‘agency’ has been the key term of the new paradigm that emerged in the 1970s, that this paradigm is about to become history and that new ways of thinking about the economy will have to emerge as we all become victims of the ‘financialisation’ of Europe, the industrialisation of Asia and the desiccation of Australia.     

Observing neck movements evokes an excitatory response in the sympathetic nervous system associated with fear of movement in patients with chronic neck pain

Abstract

The objective of this study was to evaluate the response of the sympathetic-excitatory nervous system in patients with chronic neck pain compared with a control group of asymptomatic subjects who underwent an intervention of watching activities involving movements in the neck region. Thirty participants were divided into two groups: patients with chronic neck pain (n?=?15) and the control group (n?=?15). The patients’ neck disability, fear of movement and catastrophism were assessed with a self-report. The recorded variables related to the autonomic nervous system were skin conductance and skin temperature. The ANOVA test revealed significant differences in the increase in skin conductance in the chronic neck pain group after observing the activities (both in the photographs and video) at the end of the observation and 5?minutes after the intervention (p?<?.01; d?>?0.80). There were no significant differences in skin temperature. Ultimately, the correlation analysis revealed a moderate positive correlation between kinesiophobia and skin conductance at 30?seconds (r?=?0.53) and at 60?seconds (r?=?0.52) of observing the activities in the video for the chronic neck pain group. Based on the results of the present study, we suggest that observing activities involving neck movements causes an activation of the sympathetic-excitatory nervous system in patients with chronic neck pain. These changes could be related to a fear of movement when faced with visual exposure to neck movements that could be interpreted as ‘harmful’ or ‘dangerous’.     

Aldo Leopold’s Land Health from a Resilience Point of View: Self-renewal Capacity of Social–Ecological Systems

Health approaches to ecology have a strong basis in Aldo Leopold’s thinking, and contemporary ecohealth in turn has a strong philosophical basis in Leopold. To commemorate the 125th anniversary of Leopold’s birth (1887–1948), we revisit his ideas, specifically the notions of stewardship (land ethic), productive use of ecosystems (land), and ecosystem renewal. We focus on Leopold’s perspective on the self-renewal capacity of the land, as understood in terms of integrity and land health, from the contemporary perspective of resilience theory and ecological theory more generally. Using a broad range of literature, we explore insights and implications of Leopold’s work for today’s human–environment relationships (integrated social–ecological systems), concerns for biodiversity, the development of agency with respect to stewardship, and key challenges of his time and of ours. Leopold’s seminal concept of land health can be seen as a triangulation of productive use, self-renewal, and stewardship, and it can be reinterpreted through the resilience lens as the health of social–ecological systems. In contemporary language, this involves the maintenance of biodiversity and ecosystem services, and the ability to exercise agency both for conservation and for environmental justice.     

What constitutes evidence of community structure? A reply to van der Maarel,Noest & Palmer

Abstract. Van der Maarel et al. (1995) — hereafter VNP — criticize our analyses of Öland limestone grassland. They have four general objections, addressed below. 1. VNP attribute our significant results to randomness (‘volatility’); however, significant deviation from randomness cannot be explained by randomness. VNP's conclusion of volatility derives from results that are inconsistent with ours. Their ecological interpretation assumes spatial and temporal near-constancy in the vegetation; we demonstrate that these assumptions are not correct. 2. We discussed physical limitations to plant module packing. VNP give estimated module sizes. We appreciate this information, though data on actual module sizes and overlap patterns would be required before the real module packing effects could be determined. If module packing were really the main cause of deficits of variance in richness, the effect would not fluctuate between sites and years, as VNP admit it does. 3. The shape of the richness frequency distribution is a potentially interesting additional form of analysis, albeit one that we had chosen not to include in our analysis. However, it is surprising that VNP dismiss analysis of richness variance, but then interpret a more subtle aspect of the richness distribution — the skewness. VNP's redefinition of the terms‘Niche facilitation’for a deficit of low richness values, and ‘Niche limitation’ for a deficit of high values, leads them to misrepresent our arguments. They are mistaken in suggesting that niche limitation will necessarily lead to a skewed curve: they do not allow for the fact that the species frequencies, on which the null model is based already, incorporate effects of species interactions.‘Niche facilitation’, as defined by VNP, would lead to a variance excess, not a deficit as they assume. 4. VNP's criticism of a priori guild classifications had already been met by our use of the intrinsic guild approach. Guild analyses offer the best way forward. VNP use principally the methodology of 1987. There have been a number of methodological advances since that time. We used these advances in our original paper specifically to circumvent the kinds of problems that they identify. We agree with VNP that it would be very useful to explore the mechanisms behind assembly rules with experiments, but the logical first step is to identify potential assembly rules, as we have been attempting to do. We conclude that, whilst VNP make some interesting observations, none of their criticisms invalidate our results or conclusions. Our original approach stands as the best known approach, we believe, for searching for community structure in such data, and we reaffirm the validity of our ecological conclusions.     

Primed for Change: Developing Ecological Restoration for the 21st Century

Restoration is a young and swiftly developing field. It has been almost a decade since the inception of one of the field's foundational documents—the Society for Ecological Restoration International Primer on Ecological Restoration (Primer). Through a series of organized discussions, we assessed the Primer for its currency and relevance in the modern field of ecological restoration. We focused our assessment on the section entitled “The Nine Attributes of a Restored Ecosystem” and grouped each of the attributes into one of four categories: species composition, ecosystem function, ecosystem stability, and landscape context. We found that in the decade since the document's inception, the concepts, methods, goals, and thinking of ecological restoration have shifted significantly. We discuss each of the four categories in this light with the aim of offering comments and suggestions on options for updating the Primer. We also include a fifth category that we believe is increasingly acknowledged in ecological restoration: the human element. The Primer is an important document guiding the practice of restoration. We hope that this critical assessment contributes to its ongoing development and relevance and more generally to the development of restoration ecology, particularly in our current era of rapid environmental change.     

Grasshopper calling songs convey information about condition and health of males

Females of the grasshopper Chorthippus biguttulus invest much more in the offspring than do males. As a consequence, females are the more selective sex and exert a sexual selection on males by responding to the songs of certain conspecific males while rejecting others. What kind of information about the sender may a female obtain from a male’s song, in addition to its species identity? We searched for correlations between a series of song features and morphometric parameters of individual males. In addition, also the immunocompetence of males was assessed by implanting small pieces of nylon thread. We found significant, positive correlations between certain song characteristics and indicators of male size and immunocompetence. Thus, grasshopper females may—in principle—be able to judge a male’s condition and health from the acoustic signals he produces.     

Competition can lead to unexpected patterns in tropical ant communities

Ecological communities are structured by competitive, predatory, mutualistic and parasitic interactions combined with chance events. Separating deterministic from stochastic processes is possible, but finding statistical evidence for specific biological interactions is challenging. We attempt to solve this problem for ant communities nesting in epiphytic bird’s nest ferns (Asplenium nidus) in Borneo’s lowland rainforest. By recording the frequencies with which each and every single ant species occurred together, we were able to test statistically for patterns associated with interspecific competition. We found evidence for competition, but the resulting co-occurrence pattern was the opposite of what we expected. Rather than detecting species segregation—the classical hallmark of competition—we found species aggregation. Moreover, our approach of testing individual pairwise interactions mostly revealed spatially positive rather than negative associations. Significant negative interactions were only detected among large ants, and among species of the subfamily Ponerinae. Remarkably, the results from this study, and from a corroborating analysis of ant communities known to be structured by competition, suggest that competition within the ants leads to species aggregation rather than segregation. We believe this unexpected result is linked with the displacement of species following asymmetric competition. We conclude that analysing co-occurrence frequencies across complete species assemblages, separately for each species, and for each unique pairwise combination of species, represents a subtle yet powerful way of detecting structure and compartmentalisation in ecological communities.     

The human microbiome in evolution

The trillions of microbes living in the gut—the gut microbiota—play an important role in human biology and disease. While much has been done to explore its diversity, a full understanding of our microbiomes demands an evolutionary perspective. In this review, we compare microbiomes from human populations, placing them in the context of microbes from humanity’s near and distant animal relatives. We discuss potential mechanisms to generate host-specific microbiome configurations and the consequences of disrupting those configurations. Finally, we propose that this broader phylogenetic perspective is useful for understanding the mechanisms underlying human–microbiome interactions.     

Perspective taking and decision-making in educational game play: A mixed-methods study

Video games have the potential to be contexts for moral learning. We investigated whether Quandary, a video game designed to promote ethical thinking and moral considerations for decision-making, would help promote positive skills such as perspective taking and empathy in adolescents. We examined the effect of playing Quandary on 131 middle school students on self-reported measures of moral thinking via mixed-method randomized control trials. In addition, we conducted qualitative analyses of one-on-one participant interviews and short-answer responses to capture experiences and reflections from playing Quandary, as well as the depth in which students across conditions responded to the interview questions. We found that short-term quantitative indicators did not show change across conditions; however, qualitative analyses revealed thematic responses that are consistent with the core components of the Quandary game, and that students in the Quandary condition showed a greater depth of response to interview questions. This work is a first step in exploring the potential for virtual game play on children’s social, emotional, and cognitive development.     

The Evolutionary Origin of Biological Function and Complexity

The identification of dynamic kinetic stability (DKS) as a stability kind that governs the evolutionary process for both chemical and biological replicators, opens up new avenues for uncovering the chemical basis of biological phenomena. In this paper, we utilize the DKS concept to explore the chemical roots of two of biology’s central concepts—function and complexity. It is found that the selection rule in the world of persistent replicating systems—from DKS less stable to DKS more stable—is the operational law whose very existence leads to the creation of function from of a world initially devoid of function. The origin of biological complexity is found to be directly related to the origin of function through an underlying connection between the two phenomena. Thus the emergence of both function and complexity during abiogenesis, and their growing expression during biological evolution, are found to be governed by the same single driving force, the drive toward greater DKS. It is reaffirmed that the essence of biological phenomena can be best revealed by uncovering biology’s chemical roots, by elucidating the physicochemical principles that governed the process by which life on earth emerged from inanimate matter.     

On Supporting Children's Initiative

The simple distinction between negative and positive emotions does not add very much to the understanding of the nature of human emotions. One type of pleasure is not similar to another. One type of pain is not comparable with another experience of suffering. It has to be taken into account that emotions, as evaluative processes of different types, are mostly automatic. In the case of humans, however, emotions are also partly based on deliberative thinking and reflection. Purely affective reactions arise as a consequence of subcortical mechanisms. This means that some emotions are automatic and based on uncontrolled, and even unconscious premises. On the other hand, evaluation can be due to reflective judgments, based on concepts that allow an understanding of what is positive or negative in reality. This understanding is not only from one's own point of view but also from a general point of view. Moreover, it is an understanding not only related to the present but also to the past or future (anticipated) reality. In this type of specifically human emotions, affects are provoked as a consequence of deliberative appraisals. The author postulates the categorization of the negative and the positive emotions, referring to different automatic and reflective sources. These sources are: (1) affective (homeostatic and hedonic)—leading to automatic emotions, and conceptual (concepts of the ideal self and abstract axiological concepts of good and evil)—leading to reflective emotions.     

Emotional regulation of pain: the role of noradrenaline in the amygdala

The perception of pain involves the activation of the spinal pathway as well as the supra-spinal pathway,which targets brain regions involved in affective and cognitive processes.Pain and emotions have the capacity to influence each other reciprocally;negative emotions,such as depression and anxiety,increase the risk for chronic pain,which may lead to anxiety and depression.The amygdala is a key-player in the expression of emotions,receives direct nociceptive information from the parabrachial nucleus,and is densely innervated by noradrenergic brain centers.In recent years,the amygdala has attracted increasing interest for its role in pain perception and modulation.In this review,we will give a short overview of structures involved in the pain pathway,zoom in to afferent and efferent connections to and from the amygdala,with emphasis on the direct parabrachio-amygdaloid pathway and discuss the evidence for amygdala’s role in pain processing and modulation.In addition to the involvement of the amygdala in negative emotions during the perception of pain,this brain structure is also a target site for many neuromodulators to regulate the perception of pain.We will end this article with a short review on the effects of noradrenaline and its role in hypoalgesia and analgesia.