PharmEcology: A pharmacological approach to understanding plant-herbivore interactions: an introduction to the symposium

A central goal in understanding the ecology and evolution of animals is to identify factors that constrain or expand breadth of diet. Selection of diet in many animals is often constrained by chemical deterrents (i.e., secondary metabolites) in available food items. The integration of chemistry and ecology has led to a significant understanding of the chemical complexity of prey (e.g., animals, plants, and algae) and the resultant foraging behavior of consumers. However, most of the literature on chemical defenses of marine and terrestrial prey lacks a mechanistic understanding of how consumers tolerate, or avoid, chemically-defended foods. In order to understand ecological patterns of foraging and co-evolutionary relationships between prey and consumers, we must advance our understanding of the physiological mechanisms responsible for chemical interactions. Such mechanistic studies require the integration of the discipline of pharmacology with ecology, which we call "PharmEcology." Pharmacology provides the tools and insight to investigate the fate (what the body does to a chemical) and action (what a chemical does to the body) of chemicals in living organisms, whereas ecology provides the insight into the interactions between organisms (e.g., herbivores) and their environment (e.g., plants). Although, the general concepts of pharmacology were introduced to ecologists studying plant-herbivore interactions over 30 years ago, the empirical use of pharmacology to understand mechanisms of chemical interactions has remained limited. Moreover, many of the recent biochemical, molecular and technical advances in pharmacology have yet to be utilized by ecologists. The PharmEcology symposium held at a meeting of the Society for Integrative and Comparative Biology in January of 2009 was developed to define novel research directions at the interface of pharmacology and ecology.     

Consider a Spherical Lizard: Animals, Models, and Approximations

Ecologists and physiologists have used biophysical models toanswer questions and investigate hypotheses about animal biologyfor over 20 years, but many investigators do not use such techniquesbecause such modelling is perceived as an arcane art. Indeed,there is no magic strategy to allow all ecologists to modelany biophysical problem accurately by means of simple recipes.In practice, biophysical ecology depends heavily on mathematicaland engineering principles. But, it need not be impenetrable.Here we discuss relatively simple models that can be incorporatedinto many ecological studies. We also discuss some of the importantapproximations and assumptions inherent in our treatments ofradiative, convective, evaporative, and conductive heat transfer.In so doing, we hope to encourage the use of such models, andto engender an appreciation of when and under what conditionspredictions from such models are most likely to be misleading.Thus, we hope to help ecologists to get into and, hopefully,out of trouble in biophysical ecology.     

流域生态学的发展困境——来自河流景观的启示

随着中国生态环境问题越来越多地呈现出流域特性,流域生态研究的重要性和紧迫性也日渐凸显。整合流域生态研究,形成一个有效的研究体系,流域生态学迄今未能予以实现。通过对"流域生态学"和"河流景观"这两个相近概念提出过程的比较研究,探讨流域生态学发展困境产生的原因,为流域生态研究体系的构建提供思路。分析结果显示流域生态学目前主要存在两个不足:1)因为提出流域生态学概念的关键现实需求不明确,导致难以确定其核心科学问题;2)因为没有相应的流域生态系统概念模型,进而也就难以带动相关研究落实跟进。要推进流域生态学的发展,第一步要做的就是明确流域生态研究体系构建的核心现实需求,并对流域生态系统进行一个概念模型上的相应设计。     

Kin selection-mutation balance: a model for the origin, maintenance, and consequences of social cheating

Social conflict, in the form of intraspecific selfish "cheating," has been observed in a number of natural systems. However, a formal, evolutionary genetic theory of social cheating that provides an explanatory, predictive framework for these observations is lacking. Here we derive the kin selection-mutation balance, which provides an evolutionary null hypothesis for the statics and dynamics of cheating. When social interactions have linear fitness effects and Hamilton's rule is satisfied, selection is never strong enough to eliminate recurrent cheater mutants from a population, but cheater lineages are transient and do not invade. Instead, cheating lineages are eliminated by kin selection but are constantly reintroduced by mutation, maintaining a stable equilibrium frequency of cheaters. The presence of cheaters at equilibrium creates a "cheater load" that selects for mechanisms of cheater control, such as policing. We find that increasing relatedness reduces the cheater load more efficiently than does policing the costs and benefits of cooperation. Our results provide new insight into the effects of genetic systems, mating systems, ecology, and patterns of sex-limited expression on social evolution. We offer an explanation for the widespread cheater/altruist polymorphism found in nature and suggest that the common fear of conflict-induced social collapse is unwarranted.     

Biohumanities: rethinking the relationship between biosciences, philosophy and history of science, and society

We argue that philosophical and historical research can constitute a "Biohumanities" that deepens our understanding of biology itself engages in constructive "science criticism," helps formulate new "visions of biology," and facilitates "critical science communication." We illustrate these ideas with two recent "experimental philosophy" studies of the concept of the gene and of the concept of innateness conducted by ourselves and collaborators. We conclude that the complex and often troubled relations between science and society are critical to both parties, and argue that the philosophy and history of science can help to make this relationship work.     

Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes

The techniques that are usually used to detect transposable elements (TEs) in nucleic acid sequences rely on sequence similarity with previously characterized elements. However, these methods are likely to miss many elements in various organisms. We tested two strategies for the detection of unknown elements. The first, which we call "TBLASTX strategy," searches for TE sequences by comparing the six-frame translations of the nucleic acid sequences of known TEs with the genomic sequence of interest. The second, "repeat-based strategy," searches genomic sequences for long repeats and clusters them in groups of similar sequences. TE copies from a given family are expected to cluster together. We tested the Drosophila melanogaster genomic sequence and the recently sequenced Anopheles gambiae genome in which most TEs remain unknown. We showed that the "TBLASTX strategy" is very efficient as it detected at least 332 new TE families in D. melanogaster and 400 in A. gambiae. This was unexpected in Drosophila as TEs of this organism have been extensively studied. The "repeat-based strategy" appeared to be very inefficient because of two problems: (i) TE copies are heavily deleted and few copies share homologous regions, and (ii) segmental duplications are frequent and it is not easy to distinguish them from TE copies.     

Engineering issues of microbial ecology in space agriculture]

Closure of the materials recycle loop for water-foods-oxygen is the primary purpose of space agriculture on Mars and Moon. A microbial ecological system takes a part of agriculture to process our metabolic excreta and inedible biomass and convert them to nutrients and soil substrate for cultivating plants. If we extend the purpose of space agriculture to the creation and control of a healthy and pleasant living environment, we should realize that our human body should not be sterilized but exposed to the appropriate microbial environment. We are proposing a use of hyper-thermophilic aerobic composting microbial ecology in space agriculture. Japan has a broad historical and cultural background on this subject. There had been agriculture that drove a closed loop of materials between consuming cities and farming villages in vicinity. Recent environmental problems regarding garbage collection and processing in towns have motivated home electronics companies to innovate "garbage composting" machines with bacterial technology. Based on those matured technology, together with new insights on microbiology and microbial ecology, we have been developing a conceptual design of space agriculture on Moon and Mars. There are several issues to be answered in order to prove effectiveness of the use of microbial systems in space. 1) Can the recycled nutrients, processed by the hyper-thermal aerobic composting microbial ecology, be formed in the physical and chemical state or configuration, with which plants can uptake those nutrients? A possibility of removing any major components of fertilizer from its recycle loop is another item to be evaluated. 2) What are the merits of forming soil microbial ecology around the root system of plants? This might be the most crucial question. Recent researches exhibit various mutually beneficial relationships among soil microbiota and plants, and symbiotic ecology in composting bacteria. It is essential to understand those features, and define how to conduct preventive maintenance for keeping cultivating soil healthy and productive. 3) Does microbial ecology contribute to building sustainable and expandable human habitation by utilizing the on site extraterrestrial resources? We are assessing technical feasibility of converting regolith to farming soil and structural materials for space agriculture. In the case of Mars habitation, carbon dioxide and a trace amount of nitrogen in atmosphere, and potassium and phosphor in minerals are the sources we consider. Excess oxygen can be accumulated by woods cultivation and their use for lumber. 4) Is the operation of space agriculture robust and safe, if it adopts hyper-thermophilic aerobic microbial ecology? Any ecological system is complex and non-linear, and shows latency and memory effects in its response. It is highly important to understand those features to design and operate space agriculture without falling into the fatal failure. Assessment should be made on the microbial safety and preparation of the preventive measures to eliminate negative elements that would either retard agricultural production or harm the healthy environment. It is worth to mention that such space agriculture would be an effective engineering testbed to solve the global problem on energy and environment. Mars and Moon exploration itself is a good advocate of healthy curiosity expressed by the sustainable civilization of our humankind. We propose to work together towards Mars and Moon with microbial ecology to assure pleasant habitation there.     

“海绵城市”建设的关键科学问题与思考

"海绵城市"是学术界、政府和企业界特别关注的热点之一,具有有效防止城市雨洪灾害、改善水生态和水环境、提高生物多样性等多方面的服务功能,有助于城市社会经济发展。在目前全国范围内发生城市内涝的严重情况下,科学地进行"海绵城市"建设显得尤为重要。对"海绵城市"的研究背景、概念与内涵、建设途径、主要技术、国内发展现状等进行了总结和归纳,并提出"海绵城市"建设的关键科学问题,并进行深入思考,建立"SPONGE"框架来概括整个"海绵城市"的建设内容,为今后的"海绵城市"研究和建设提供参考。     

Redesigning the Industrial Ecology of the Automobile

This article explores the potential of industrial ecology to inform the redesign of an existing industry: that which is concerned with the production, sale, and support of automobiles. In so doing, it brings together the concepts embedded in industrial ecology with issues of economic scale, product design or technology, process technology, and the way in which new combinations of these features can result in an alternative structure for the automotive industry that has the potential to enhance sustainability performance. In so doing, the article advances the general argument that the economic, technical, and spatial organization of production and consumption are co-determined in a manner that collectively shapes the industrial ecology of an industry. In contradistinction to the prevailing industry, the article then advances the concept of micro factory retailing as an alternative framework for the industry that would result in significantly different performance in terms of industrial ecology.     

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

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

When should potentially false research findings be considered acceptable?

Ioannidis estimated that most published research findings are false, but he did not indicate when, if at all, potentially false research results may be considered as acceptable to society. We combined our two previously published models to calculate the probability above which research findings may become acceptable. A new model indicates that the probability above which research results should be accepted depends on the expected payback from the research (the benefits) and the inadvertent consequences (the harms). This probability may dramatically change depending on our willingness to tolerate error in accepting false research findings. Our acceptance of research findings changes as a function of what we call "acceptable regret," i.e., our tolerance of making a wrong decision in accepting the research hypothesis. We illustrate our findings by providing a new framework for early stopping rules in clinical research (i.e., when should we accept early findings from a clinical trial indicating the benefits as true?). Obtaining absolute "truth" in research is impossible, and so society has to decide when less-than-perfect results may become acceptable.     

Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases

Chelt, a cholera-like toxin from Vibrio cholerae, and Certhrax, an anthrax-like toxin from Bacillus cereus, are among six new bacterial protein toxins we identified and characterized using in silico and cell-based techniques. We also uncovered medically relevant toxins from Mycobacterium avium and Enterococcus faecalis. We found agriculturally relevant toxins in Photorhabdus luminescens and Vibrio splendidus. These toxins belong to the ADP-ribosyltransferase family that has conserved structure despite low sequence identity. Therefore, our search for new toxins combined fold recognition with rules for filtering sequences--including a primary sequence pattern--to reduce reliance on sequence identity and identify toxins using structure. We used computers to build models and analyzed each new toxin to understand features including: structure, secretion, cell entry, activation, NAD+ substrate binding, intracellular target binding and the reaction mechanism. We confirmed activity using a yeast growth test. In this era where an expanding protein structure library complements abundant protein sequence data--and we need high-throughput validation--our approach provides insight into the newest toxin ADP-ribosyltransferases.     

Access to essential medicines: a Hobbesian social contract approach

Medicines that are vital for the saving and preserving of life in conditions of public health emergency or endemic serious disease are known as essential medicines. In many developing world settings such medicines may be unavailable, or unaffordably expensive for the majority of those in need of them. Furthermore, for many serious diseases (such as HIV/AIDS and tuberculosis) these essential medicines are protected by patents that permit the patent-holder to operate a monopoly on their manufacture and supply, and to price these medicines well above marginal cost. Recent international legal doctrine has placed great stress on the need to globalise intellectual property rights protections, and on the rights of intellectual property rights holders to have their property rights enforced. Although international intellectual property rights law does permit compulsory licensing of protected inventions in the interests of public health, the use of this right by sovereign states has proved highly controversial. In this paper I give an argument in support of states' sovereign right to expropriate private intellectual property in conditions of public health emergency. This argument turns on a social contract argument for the legitimacy of states. The argument shows, further, that under some circumstances states are not merely permitted compulsory to license inventions, but are actually obliged to do so, on pain of failure of their legitimacy as sovereign states. The argument draws freely on a loose interpretation of Thomas Hobbes's arguments in his Leviathan, and on an analogy between his state of War and the situation of public health disasters.     

Scenario analysis of the future of medicines.

Planning future policy for medicines poses difficult problems. The main players in the drug business have their own views as to how the world around them functions and how the future of medicines should be shaped. In this paper we show how a scenario analysis can provide a powerful teaching device to readjust peoples'' preconceptions. Scenarios are plausible, not probable or preferable, portraits of alternative futures. A series of four of alternative scenarios were constructed: "sobriety in sufficiency," "risk avoidance," "technology on demand," and "free market unfettered." Each scenario was drawn as a narrative, documented quantitatively wherever possible, that described the world as it might be if particular trends were to dominate development. The medical community and health policy markers may use scenarios to take a long term view in order to be prepared adequately for the future.     

Industrial Ecology as a Cultural Phenomenon: On Objectivity as a Normative Position

Taking a recent column by Braden Allenby in this journal as a starting point, we argue the need for researchers in the field of industrial ecology to reflect upon its normative aspects. We argue that the field will advance through an explicit discourse on such issues as epistemological positions, the inherent normative nature of using metaphors, and the way in which the field of study relates to the field of practice.
In "Culture and Industrial Ecology," Allenby raises, and begins to address, some critical questions that define the field of industrial ecology. We suggest that his arguments dismiss too lightly issues that are central to this developing field. The purpose of this reply is to open up for further discussion what industrial ecology is, and what it is not.
We begin by summarizing Allenby's line of reasoning. We explore his arguments around the notion of objectivity and the questions he raises about the relationship among objective science, normative positions, opinions, and fads. While Allenby makes a strong plea for industrial ecology to maintain objectivity and avoid normative positions, we contend that any positions on what should or should not be included in a field of study carry normative intent. Although science might seek to be objective in its method, scientists are rarely free of such normative positions. These positions need to be explicit and open to debate. Also, Allenby's position implies that industrial ecology as a field of study should be separated from industrial ecology as a field of practice. We argue that the interrelation of these fields provides important advantages.
Our main concern is that Allenby's position forestalls discussion on important issues at the heart of the field of study. We examine some key issues around the concept of objectivity and propose an agenda for research on the cultural and ideological aspects of industrial ecology.     

平衡与非平衡生态学在锡林河流域典型草原放牧系统中的应用

为认识放牧系统的复杂性和稳定性 ,产生了放牧系统的平衡生态学和非平衡生态学原理。放牧系统的平衡生态学原理假定 :一旦干扰在系统中发生 ,系统将偏离平衡态 ;而当干扰解除后 ,系统将自动返回原来的状态或在新的领域实现平衡。在对内蒙古锡林河流域典型草原放牧系统动态的研究中 ,来自平衡生态学的 Clem ents- Duksterhuis演替理论提供了一个基本的研究框架。尽管已经证实对退化不太严重的典型草原放牧系统 ,平衡生态学原理是适用的 ,但是对于这一地区严重退化的放牧系统的动态 ,它显然并不能给予合理的解释。事实上许多放牧系统动态遵循非平衡生态学原理。在非平衡放牧系统中 ,稳定的状态是不会实现的 ,因为在这样的系统中 ,非生物变量对于植被的动态似乎起着决定性的影响 ,从而也决定着草食动物的种群动态。状态与过渡模型基于非平衡生态学原理 ,它能够解释过度放牧下典型草原生态系统的崩溃或灌丛化 ,因此它适于该地区严重退化的典型草原放牧系统的动态。鉴于内蒙古锡林河流域典型草原放牧系统普遍严重退化的现实 ,未来该地退化放牧系统的研究应更多地应用非平衡生态学原理 ,并且严重退化的草原生态系统的恢复试验 ,特别是灌丛化草原的重建也应置于它的指导之下     

Bacillus thuringiensis: a biotechnology model

This paper is on the different biotechnological approaches that have been used to improve Bacillus thuringiensis (Bt) for the control of agricultural insect pests and have contributed to the successful use of this biological control agent; it describes how a better knowledge of the high diversity of Bt strains and toxins genes together with the development of efficient host-vector systems has made it possible to overcome a number of the problems associated with Bt based insect control measures. First we present an overview of the biology of Bt and of the mode of action of its insecticidal toxins. We then describe some of the progress that has been made in furthering our knowledge of the genetics of Bt and of its insecticidal toxin genes and in the understanding of their regulation. The paper then deals with the use of recombinant DNA technology to develop new Bt strains for more effective pest control or to introduce the genes encoding partial-endotoxins directly into plants to produce insect-resistant trangenic plants. Several examples describing how biotechnology has been used to increase the production of insecticidal proteins in Bt or their persistence in the field by protecting them against UV degradation are presented and discussed. Finally, based on our knowledge of the mechanism of transposition of the Bt transposon Tn4430, we describe the construction of a new generation of recombinant strains of Bt, from which antibiotic resistance genes and other non-Bt DNA sequences were selectively eliminated, using a new generation of site-specific recombination vectors. In the future, continuing improvement of first generation products and research into new sources of resistance is essential to ensure the long-term control of insect pests. Chimeric toxins could also be produced so as to increase toxin activity or direct resistance towards a particular type of insect. The search for new insecticidal toxins, in Bt or other microorganisms, may also provide new weapons for the fight against insect damage.     

Nutritional Correlates of Koala Persistence in a Low-Density Population

It is widely postulated that nutritional factors drive bottom-up, resource-based patterns in herbivore ecology and distribution. There is, however, much controversy over the roles of different plant constituents and how these influence individual herbivores and herbivore populations. The density of koala (Phascolarctos cinereus) populations varies widely and many attribute population trends to variation in the nutritional quality of the eucalypt leaves of their diet, but there is little evidence to support this hypothesis. We used a nested design that involved sampling of trees at two spatial scales to investigate how leaf chemistry influences free-living koalas from a low-density population in south east New South Wales, Australia. Using koala faecal pellets as a proxy for koala visitation to trees, we found an interaction between toxins and nutrients in leaves at a small spatial scale, whereby koalas preferred trees with leaves of higher concentrations of available nitrogen but lower concentrations of sideroxylonals (secondary metabolites found exclusively in eucalypts) compared to neighbouring trees of the same species. We argue that taxonomic and phenotypic diversity is likely to be important when foraging in habitats of low nutritional quality in providing diet choice to tradeoff nutrients and toxins and minimise movement costs. Our findings suggest that immediate nutritional concerns are an important priority of folivores in low-quality habitats and imply that nutritional limitations play an important role in constraining folivore populations. We show that, with a careful experimental design, it is possible to make inferences about populations of herbivores that exist at extremely low densities and thus achieve a better understanding about how plant composition influences herbivore ecology and persistence.     

House to Palace, Village to State: Scaling up Architecture and Ideology

It would seem desirable for any state to gum an ideological foothold in local knowledge and symbols to facilitate the assimilation of its order by average citizens and to argue for its legitimacy. However, given the "lived reality" of local knowledge and Us practical and symbolic "efficacy," as guaranteed in part through the skills of ritual specialise not in the service of the skiie. the introduction and maintenance of state ideology is neither an issue of facile appropriation o/local symbols nor a straightforward imposition on local knowledge. The complexity of the architectural and ideological scaling up from traditional house to "palace" and polity are discussed lor nineteenth-century Imerina, Madagascar, using ethnohistorical. archaeological, and ethnographic information. We attempt to present this argument through the use of evocative concrete imagery, one stylistic aspect of local knowledge, rather than through an exclusive use of analytical, abstract declarations. [Madagascar, symbolic organization of space, state origins, ideology, local knowledge]     

Medicinal mushrooms and cancer therapy: translating a traditional practice into Western medicine

Modern medical practice relies heavily on the use of highly purified pharmaceutical compounds whose purity can be easily assessed and whose pharmaceutical activity and toxicity show clear structure-function relationships. In contrast, many herbal medicines contain mixtures of natural compounds that have not undergone detailed chemical analyses and whose mechanism of action is not known. Traditional folk medicine and ethno-pharmacology coupled to bioprospecting have been an important source of many anticancer agents as well as other medicines. With the current decline in the number of new molecular entities from the pharmaceutical industry, novel anticancer agents are being sought from traditional medicine. As the example of medicinal mushrooms demonstrates, however, translating traditional Eastern practices into acceptable evidence-based Western therapies is difficult. Different manufacturing standards, criteria of purity, and under-powered clinical trials make assessment of efficacy and toxicity by Western standards of clinical evidence difficult. Purified bioactive compounds derived from medicinal mushrooms are a potentially important new source of anticancer agents; their assimilation into Western drug discovery programs and clinical trials also provides a framework for the study and use of other traditional medicines.