Ecology and ethics: relation of religious belief to ecological practice in the Biblical tradition

The Bible, without which Western civilization is inexplicable, has powerful ecological teachings that support an ecological worldview. While these teachings are not widely practised in our time. continuing degradation of ecological systems by humanity requires their re-examination by ecologists and the church. Such re-examination can help develop the mutual understanding necessary for making ethical ecological judgements and putting these teachings into practice in an appropriate manner. Among these teachings are the expectation that people will serve and keep the Creation (earthkeeping principle), that creatures and ecosystems not be relentlessly pressed (sabbath principle), that provisions must be made for the flourishing of the biosphere (fruitfulness principle), that the Earth be filled with biologically diverse and abundant life (fulfilment principle), that pressing the biosphere's absolute limits must be avoided (buffer principle), that people should seek contentment and not selfish gain (contentment principle), that people should seek biospheric integrity rather than self-interest (priority principle) and that people should not fail to act on what they know is right (praxis principle). Ecologists need to recognize and respect these and other biblical ecological teachings and be ready to assist churches in their care and keeping of Creation. And churches must join ecologists in the work of assuring the continued integrity of the biosphere.     

Causality and complexity: the myth of objectivity in science

Two distinctly different worldviews dominate today's thinking in science and in the world of ideas outside of science. Using the approach advocated by Robert M. Hutchins, it is possible to see a pattern of interaction between ideas in science and in other spheres such as philosophy, religion, and politics. Instead of compartmentalizing these intellectual activities, it is worthwhile to look for common threads of mutual influence. Robert Rosen has created an approach to scientific epistemology that might seem radical to some. However, it has characteristics that resemble ideas in other fields, in particular in the writings of George Lakoff, Leo Strauss, and George Soros. Historically, the atmosphere at the University of Chicago during Hutchins' presidency gave rise to Rashevsky's relational biology, which Rosen carried forward. Strauss was writing his political philosophy there at the same time. One idea is paramount in all this, and it is Lakoff who gives us the most insight into how the worldviews differ using this idea. The central difference has to do with causality, the fundamental concept that we use to build a worldview. Causal entailment has two distinct forms in Lakoff 's analysis: direct causality and complex causality. Rosen's writings on complexity create a picture of complex causality that is extremely useful in its detail, grounding in the ideas of Aristotle. Strauss asks for a return to the ancients to put philosophy back on track. Lakoff sees the weaknesses in Western philosophy in a similar way, and Rosen provides tools for dealing with the problem. This introduction to the relationships between the thinking of these authors is meant to stimulate further discourse on the role of complex causal entailment in all areas of thought, and how it brings them together in a holistic worldview. The worldview built on complex causality is clearly distinct from that built around simple, direct causality. One important difference is that the impoverished causal entailment that accompanies the machine metaphor in science is unable to give us a clear way to distinguish living organisms from machines. Complex causality finds a dichotomy between organisms, which are closed to efficient cause, and machines, which require entailment from outside. An argument can be made that confusing living organisms with machines, as is done in the worldview using direct cause, makes religion a necessity to supply the missing causal entailment.     

Ideas are not replicators but minds are

An idea is not a replicator because it does not consist of coded self-assembly instructions. It may retain structure as it passes from one individual to another, but does not replicate it. The cultural replicator is not an idea but an associatively-structured network of them that together form an internal model of the world, or worldview. A worldview is a primitive, uncoded replicator, like the autocatalytic sets of polymers widely believed to be the earliest form of life. Primitive replicators generate self-similar structure, but because the process happens in a piecemeal manner, through bottom-up interactions rather than a top-down code, they replicate with low fidelity, and acquired characteristics are inherited. Just as polymers catalyze reactions that generate other polymers, the retrieval of an item from memory can in turn trigger other items, thus cross-linking memories, ideas, and concepts into an integrated conceptual structure. Worldviews evolve idea by idea, largely through social exchange. An idea participates in the evolution of culture by revealing certain aspects of the worldview that generated it, thereby affecting the worldviews of those exposed to it. If an idea influences seemingly unrelated fields this does not mean that separate cultural lineages are contaminating one another, because it is worldviews, not ideas, that are the basic unit of cultural evolution.     

How can ecologists thrive during the global environmental crisis? Lessons from the ancient world

When striving to meet an immense challenge, how can we, as restoration ecologists, flourish? Given the ongoing environmental crisis, it is normal to experience ecological grief and discouragement. This article discusses how insights from the ancient philosophy of Stoicism can help environmental practitioners navigate these troubling times. To overcome ecological grief, ecologists can draw on three tenets from Stoic thought: distinguishing between what we can and cannot control; recognizing our contribution as part of a broader community of environmental managers; and focusing on the intent of our actions. We believe that these ideas can help ecologists shoulder the emotional burden of modern environmental practice and focus on working toward a diverse and resilient biosphere.     

Bayesian data analysis in population ecology: motivations,methods, and benefits

During the 20th century ecologists largely relied on the frequentist system of inference for the analysis of their data. However, in the past few decades ecologists have become increasingly interested in the use of Bayesian methods of data analysis. In this article I provide guidance to ecologists who would like to decide whether Bayesian methods can be used to improve their conclusions and predictions. I begin by providing a concise summary of Bayesian methods of analysis, including a comparison of differences between Bayesian and frequentist approaches to inference when using hierarchical models. Next I provide a list of problems where Bayesian methods of analysis may arguably be preferred over frequentist methods. These problems are usually encountered in analyses based on hierarchical models of data. I describe the essentials required for applying modern methods of Bayesian computation, and I use real-world examples to illustrate these methods. I conclude by summarizing what I perceive to be the main strengths and weaknesses of using Bayesian methods to solve ecological inference problems.     

Game theory and plant ecology

The fixed and plastic traits possessed by a plant, which may be collectively thought of as its strategy, are commonly modelled as density‐independent adaptations to its environment. However, plant strategies may also represent density‐ or frequency‐dependent adaptations to the strategies used by neighbours. Game theory provides the tools to characterise such density‐ and frequency‐dependent interactions. Here, we review the contributions of game theory to plant ecology. After briefly reviewing game theory from the perspective of plant ecology, we divide our review into three sections. First, game theoretical models of allocation to shoots and roots often predict investment in those organs beyond what would be optimal in the absence of competition. Second, game theoretical models of enemy defence suggest that an individual's investment in defence is not only a means of reducing its own tissue damage but also a means of deflecting enemies onto competitors. Finally, game theoretical models of trade with mutualistic partners suggest that the optimal trade may reflect competition for access to mutualistic partners among plants. In short, our review provides an accessible entrance to game theory that will help plant ecologists enrich their research with its worldview and existing predictions.     

Physiological stress in ecology: lessons from biomedical research

Increasingly, levels of the 'stress hormones' cortisol and corticosterone are being used by ecologists as indicators of physiological stress in wild vertebrates. The amplitude of hormonal response is assumed to correlate with the overall health of an animal and, by extension, the health of the population. However, much of what is known about the physiology of stress has been elucidated by the biomedical research community. I summarize five physiological mechanisms that regulate hormone release during stress that should be useful to ecologists and conservationists. Incorporating these physiological mechanisms into the design and interpretation of ecological studies will make these increasingly popular studies of stress in ecological settings more rigorous.     

Ecological rigidity and the hardness of selection in the wild

Hutchinson's ecological theater and evolutionary play is a classical view of evolutionary ecology—ecology provides a template in which evolution occurs. An opposing view is that ecological and evolutionary changes are like two actors on a stage, intertwined by density and frequency dependence. These opposing views correspond to hard and soft selection, respectively. Although often presented as diametrically opposed, both types of selection can occur simultaneously, yet we largely lack knowledge of the relative importance of hard versus soft selection in the wild. I use a dataset of 3000 individual gall makers from 15 wild local populations over 5 years to investigate the hardness of selection. I show that enemy attack consistently favors some gall sizes over others (hard selection) but that these biases can be fine-tuned by density and frequency dependence (soft selection). As a result, selection is hard and soft in roughly equal measures, but the importance of each type varies as species interactions shift. I conclude that eco-evolutionary dynamics should occur when a mix of hard and soft selection acts on a population. This work contributes to the rapprochement of disparate views of evolutionary ecology—ecology is neither a rigid theater nor a flexible actor, but instead embodies components of both.     

Bioethics and culture: an African perspective

The project of Bioethics seems to me to require paying attention to the cultural realities and assumptive frame of reference of different peoples. I assume that this must be one of the views of the organizers of this conference too and that this is why the idea of country reports is taken seriously. If I am right about this, then it makes sense for me to start my discussion with a very brief discussion of some aspects of the cultural realities of Africa with particular reference to the Yoruba of Nigeria. Then I will discuss how this world view raises issues for bioethics. Two aspects of people's worldview relevant to bioethical issues are their conception of the human person and their conception of cause. What they consider themselves to be, and what they consider to be the principles of causation will normally influence their attitudes to health and illness and their choices regarding health care. I will briefly discuss these issues with regard to the Yoruba worldview.     

The anarchist's guide to ecological theory. Or, we don't need no stinkin' laws

Several ecologists have recently suggested that ecology has several laws. This conclusion contrasts with the views of some philosophers of science, who have suggested that biology cannot have laws. I argue that the debate has been confused because two very different types of law can be recognised: correlative and causal laws. Once we recognise that there is a difference, the argument against causal laws becomes stronger, and instead I suggest that ecologists should recognise that they can and do produce generalisations that are used to build models – nomological machines – that describe the ecological systems they are studying.     

Study design and parameter estimability for spatial and temporal ecological models

The statistical tools available to ecologists are becoming increasingly sophisticated, allowing more complex, mechanistic models to be fit to ecological data. Such models have the potential to provide new insights into the processes underlying ecological patterns, but the inferences made are limited by the information in the data. Statistical nonestimability of model parameters due to insufficient information in the data is a problem too‐often ignored by ecologists employing complex models. Here, we show how a new statistical computing method called data cloning can be used to inform study design by assessing the estimability of parameters under different spatial and temporal scales of sampling. A case study of parasite transmission from farmed to wild salmon highlights that assessing the estimability of ecologically relevant parameters should be a key step when designing studies in which fitting complex mechanistic models is the end goal.     

Human welfare and its connection to nature: What have we learned from crop pollination studies?

Human welfare depends on the function of natural systems. This idea is paradigmatic to ecologists and has been the theme of a growing branch of applied ecology. I examine the narrative of human dependence on nature by considering the literature on crop pollination by animals and its importance for food production. Making the connections between human welfare and natural systems is seen as a way to better motivate society to make better decisions, but the debate around crop pollination has been surprisingly contentious. There have been confusing messages, disagreements on the facts, an unfortunate focus on dire projections for the future and a lesser focus on solutions. Most of these problems arise not from poor science but instead from poor communication of complex ideas and differences in perspective, such as the deep disciplinary gap between agricultural scientists and ecologists. By understanding these problems, we can improve the way we do our science and communicate our ideas. I argue that ecologists should continue to communicate the principle that human welfare depends on the function of natural systems and discuss how we can do so in a way that is more genuinely connected to society's needs, such as growing food. If we succeed, we will be changing an intellectually interesting conversation into a dialogue that influences how society interacts with nature.     

Ecological frames of mind: the role of cognition in behavioral ecology.

Cognitive psychology is the study of how information, from the senses and from memory, is used in the production of behavior. Investigation of the specifics of behavioral adaptation has already led some behavioral ecologists into the domain of animal cognition. I make several arguments for the benefits and the necessity of a sophisticated assessment by ecologists of the cognitive aspects of behavioral adaptation. First, because cognition typically serves to produce adaptive behavior, cognitive structure and function should reflect ecological demands; studies of cognition in ecological contexts are opportunities to understand adaptation. Furthermore, constraints on cognitive properties may help determine how behavior meets the environment. Studies of spatial memory in food-caching corvids exemplify how cognitive aspects of behavior may both reflect and determine specifics of adaptation. Second, many models in behavioral ecology assume certain cognitive abilities, such as timing or counting. Cognitive theory and methodology should be used to determine whether animals possess these abilities. I have provided examples. Third, consideration of cognitive function can lead to original ideas about the details of behavioral adaptation. Without a thorough integration of cognitive psychology with behavioral ecology, our understanding of the relation between behavior and selective pressures will be compromised.     

Variation Thresholds for Extinction and Their Implications for Conservation Strategies

We examine the degree to which fitting simple dynamic models to time series of population counts can predict extinction probabilities. This is both an active branch of ecological theory and an important practical topic for resource managers. We introduce an approach that is complementary to recently developed techniques for estimating extinction risks (e.g., diffusion approximations) and, like them, requires only count data rather than the detailed ecological information available for traditional population viability analyses. Assuming process error, we use four different models of population growth to generate snapshots of population dynamics via time series of the lengths commonly available to ecologists. We then ask to what extent we can identify which of several broad classes of population dynamics is evident in the time series snapshot. Along the way, we introduce the idea of "variation thresholds," which are the maximum amount of process error that a population may withstand and still have a specified probability of surviving for a given length of time. We then show how these thresholds may be useful to both ecologists and resource managers, particularly when dealing with large numbers of poorly understood species, a common problem faced by those designing biodiversity reserves.     

生物多样性与稳定性机制研究进展

随着全球生物多样性的迅速丧失,生物多样性与生态系统稳定性的关系已成为人类面临的重要科学问题。许多研究表明生物多样性与稳定性存在正相互关系,但其内在机制尚不能被很好地理解并且存在争议。对生物多样性与稳定性的研究历史做简短的回顾,然后根据时间稳定性的计算方法将时间稳定性分为平均值、方差之和以及协方差之和3个统计组成部分,在此基础上对现在常见的生物多样性-稳定性机制进行分类和详细介绍。并对现在生物多样性和稳定研究的争论进行总结。建议未来生物多样性稳定性关系的研究应该建立更加综合的理论,增加实验时间,应用整合分析(meta-analysis)对已发表实验结果进行综合分析,此外,应多关注非生物量/多度的属性,控制物种属性而不是仅仅控制物种的数量。     

An invitation to ecological economics

The emerging interdisciplinary field of ecological economics should be a recognized research priority. Only through a combination of sound ecology and good economics can we hope to manage our exploitation of the biosphere in a manner that is both sustainable and efficient. This article is an invitation to ecologists to use economic tools and to participate in ecological economic debate. To this end, we review basic ecological economic concepts and discuss how the field has arisen, what benefits it offers, and what challenges it must overcome.     

Applications of stable isotope analyses to avian ecology

In the past 20 years the use of stable isotope analysis has become increasingly common in ecological studies. In fact, in some instances these techniques have yielded remarkable insights into the foraging preferences and migrations of birds. Despite these advances and the potential of the approach, it is possibly still not as widely used as might be expected. In this paper we aim to illustrate the potential of the approach in the hope of encouraging more avian ecologists to think again about how these techniques might provide insights in the systems on which they work. We discuss some of the principles behind the approach, and review some of the more recent ornithological studies that have used stable isotope techniques to trace trophic pathways or infer migratory origins. We follow this by discussing some of the latest ideas on how stable isotopes may be used to generate community metrics and close by detailing the important assumptions and caveats that should be considered before undertaking any studies using this technique.     

Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research

Recent advances in molecular technologies have opened up unprecedented opportunities for molecular ecologists to better understand the molecular basis of traits of ecological and evolutionary importance in almost any organism. Nevertheless, reliable and systematic inference of functionally relevant information from these masses of data remains challenging. The aim of this review is to highlight how the Gene Ontology (GO) database can be of use in resolving this challenge. The GO provides a largely species-neutral source of information on the molecular function, biological role and cellular location of tens of thousands of gene products. As it is designed to be species-neutral, the GO is well suited for cross-species use, meaning that, functional annotation derived from model organisms can be transferred to inferred orthologues in newly sequenced species. In other words, the GO can provide gene annotation information for species with nonannotated genomes. In this review, we describe the GO database, how functional information is linked with genes/gene products in model organisms, and how molecular ecologists can utilize this information to annotate their own data. Then, we outline various applications of GO for enhancing the understanding of molecular basis of traits in ecologically relevant species. We also highlight potential pitfalls, provide step-by-step recommendations for conducting a sound study in nonmodel organisms, suggest avenues for future research and outline a strategy for maximizing the benefits of a more ecological and evolutionary genomics-oriented ontology by ensuring its compatibility with the GO.     

Stochastic ecological network occupancy (SENO) models: a new tool for modeling ecological networks across spatial scales

Stochastic ecological network occupancy (SENO) models predict the probability that species will occur in a sample of an ecological network. In this review, we introduce SENO models as a means to fill a gap in the theoretical toolkit of ecologists. As input, SENO models use a topological interaction network and rates of colonization and extinction (including consumer effects) for each species. A SENO model then simulates the ecological network over time, resulting in a series of sub-networks that can be used to identify commonly encountered community modules. The proportion of time a species is present in a patch gives its expected probability of occurrence, whose sum across species gives expected species richness. To illustrate their utility, we provide simple examples of how SENO models can be used to investigate how topological complexity, species interactions, species traits, and spatial scale affect communities in space and time. They can categorize species as biodiversity facilitators, contributors, or inhibitors, making this approach promising for ecosystem-based management of invasive, threatened, or exploited species.     

The relationship between biogeography and ecology: envelopes,models, predictions

This paper reviews ideas on the relationship between the ecology of clades and their distribution. Ecological biogeography represents a tradition that dates back to ancient times. It assumes that the distribution of organisms is explained by factors of present environment, especially climate. In contrast, modern systematics, following its origins in the Renaissance, concluded with Darwin that ‘neither the similarity nor the dissimilarity of the inhabitants of various regions can be accounted for by their climatal and other physical conditions’. In many cases, species distribution models – ecological niche models – based on the current environment of a species (its environmental envelope) fail to predict the actual distribution of the species. In particular, they often over‐predict distributions. In addition, a group's niche often varies in space and time. These results provide valuable evidence that Darwin was correct, and many ecologists now recognise that there is a problem with the niche theory of distribution. Current ecological processes explain distribution at smaller scales than do biogeographical and evolutionary processes, but the latter can lead to patterns that are much more local than many ecologists have assumed. Biogeographical phenomena often occur at a much smaller scale than that of the Wallacean regions. In areas that have been subjected to marine inundation or intense tectonism, many centres of endemism are only tens of kilometres across. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 456–468.