Industrial Ecology and Ecological Engineering

Ecological engineering (EE) and industrial ecology (IE) strive to balance humanity's activities with nature. The disciplines have emerged separately but share theoretical foundations and philosophies on how to address today's complex environmental issues. Although EE and IE share motive, goals, theories, and philosophies, there are many differences. These similarities and differences may make for a strong symbiotic relationship between the two fields. The goals of this article are (1) to compare and contrast the two fields to identify opportunities for collaboration and integration and (2) to suggest three cross-disciplinary focal areas that bridge EE and IE.
The first symbiotic area, ecosystem engineering for byproduct recovery, is defined as the design, creation, and management of living ecosystems (e.g., forests, wetlands) that utilize the by-products of industrial systems. Examples of this exist, including constructed wetlands for lead recovery and phyto-mining of nickel tailings. The second symbiotic focus is entitled "ecosystem analogues for industrial ecology", which fits with a founding principle of IE to strive to have industry emulate the energy efficiencies and material cycles of natural ecosystems. This focal area quantifies the ecological analogy and exploits the tremendous library of design alternatives that nature has developed over thousands of years to deal with varied resource situations. The third focal area is termed "eco-system information engineering." The means by which living ecosystems have created robust knowledge systems and information cycles should be understood in terms useful for managing current society's information explosion. As industrial society evolves toward the information society, holistic models are needed that account for the available energy and material resources required to operate effective information ecosystems, such as service industries.     

Lessons,narratives, and research directions for a sustainable circular economy

The current enthusiasm for the circular economy (CE) offers a unique opportunity to advance the impact of research on sustainability transitions. Diverse interpretations of CE by scholars, however, produce partly opposing assessments of its potential benefits, which can hinder progress. Here, we synthesize policy-relevant lessons and research directions for a sustainable CE and identify three narratives—optimist, reformist, and skeptical—that underpin the ambiguity in CE assessments. Based on 54 key CE scholars’ insights, we identify three research needs: the articulation and discussion of ontologically distinct CE narratives; bridging of technical, managerial, socio-economic, environmental, and political CE perspectives; and critical assessment of opportunities and limits of CE science–policy interactions. Our findings offer practical guidance for scholars to engage reflexively with the rapid expansion of CE knowledge, identify and pursue high-impact research directions, and communicate more effectively with practitioners and policymakers.     

How to monitor environmental pressures of a circular economy: An assessment of indicators

Understanding how a circular economy (CE) can reduce environmental pressures from economic activities is crucial for policy and practice. Science provides a range of indicators to monitor and assess CE activities. However, common CE activities, such as recycling and eco‐design, are contested in terms of their contribution to environmental sustainability. This article assesses whether and to what extent current approaches to assess CE activities sufficiently capture environmental pressures to monitor progress toward environmental sustainability. Based on a material flow perspective, we show that most indicators do not capture environmental pressures related to the CE activities they address. Many focus on a single CE activity or process, which does not necessarily contribute to increased environmental sustainability overall. Based on these results, we suggest complementing CE management indicators with indicators capturing basic environmental pressures related to the respective CE activity. Given the conceptual linkage between CE activities, resource extraction, and waste flows, we suggest that a resource‐based footprint approach accounting for major environmental inputs and outputs is necessary—while not sufficient—to assess the environmental sustainability of CE activities. As footprint approaches can be used across scales, they could aid the challenging process of developing indicators for monitoring progress toward an environmentally sustainable CE at the European, national, and company levels.     

PASBio: predicate-argument structures for event extraction in molecular biology

Background  

The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sentence structure. A consensus in the IE community is emerging on the necessity for exploiting deeper knowledge structures such as through the relations between a verb and its arguments shown by predicate-argument structure (PAS). PAS is of interest as structures typically correspond to events of interest and their participating entities. For this to be realized within IE a key knowledge component is the definition of PAS frames. PAS frames for non-technical domains such as newswire are already being constructed in several projects such as PropBank, VerbNet, and FrameNet. Knowledge from PAS should enable more accurate applications in several areas where sentence understanding is required like machine translation and text summarization. In this article, we explore the need to adapt PAS for the MB domain and specify PAS frames to support IE, as well as outlining the major issues that require consideration in their construction.     

Nullius in Verba1: Advancing Data Transparency in Industrial Ecology

With the growth of the field of industrial ecology (IE), research and results have increased significantly leading to a desire for better utilization of the accumulated data in more sophisticated analyses. This implies the need for greater transparency, accessibility, and reusability of IE data, paralleling the considerable momentum throughout the sciences. The Data Transparency Task Force (DTTF) was convened by the governing council of the International Society for Industrial Ecology in late 2016 to propose best‐practice guidelines and incentives for sharing data. In this article, the members of the DTTF present an overview of developments toward transparent and accessible data within the IE community and more broadly. We argue that increased transparency, accessibility, and reusability of IE data will enhance IE research by enabling more detailed and reproducible research, and also facilitate meta‐analyses. These benefits will make the results of IE work more timely. They will enable independent verification of results, thus increasing their credibility and quality. They will also make the uptake of IE research results easier within IE and in other fields as well as by decision makers and sustainability practitioners, thus increasing the overall relevance and impact of the field. Here, we present two initial actions intended to advance these goals: (1) a minimum publication requirement for IE research to be adopted by the Journal of Industrial Ecology; and (2) a system of optional data openness badges rewarding journal articles that contain transparent and accessible data. These actions will help the IE community to move toward data transparency and accessibility. We close with a discussion of potential future initiatives that could build on the minimum requirements and the data openness badge system.     

Circular economy: A new research field?

Action to pursue the circular economy (CE) transition is burgeoning in the government and the private sector. Does this action signal that CE is a distinct field of research with a unique disciplinary identity? This article argues that CE has reached field status, through its own epistemic communities characterized by increasingly shared methodological perspectives and normative ideals, and through institutionalized knowledge development through research journals and authority structures. The recent growth of CE research points toward more contextualized and nuanced operationalizations of the concept, evidence that the field is approaching a threshold state of maturity. Drawing on observations from academic literature and discussions with researchers and experts, we trace the process by which CE has arrived at the status of a field. The article concludes with reflections on research directions.     

Lifting Industrial Ecology Modeling to a New Level of Quality and Transparency: A Call for More Transparent Publications and a Collaborative Open Source Software Framework

Industrial ecology (IE) is a maturing scientific discipline. The field is becoming more data and computation intensive, which requires IE researchers to develop scientific software to tackle novel research questions. We review the current state of software programming and use in our field and find challenges regarding transparency, reproducibility, reusability, and ease of collaboration. Our response to that problem is fourfold: First, we propose how existing general principles for the development of good scientific software could be implemented in IE and related fields. Second, we argue that collaborating on open source software could make IE research more productive and increase its quality, and we present guidelines for the development and distribution of such software. Third, we call for stricter requirements regarding general access to the source code used to produce research results and scientific claims published in the IE literature. Fourth, we describe a set of open source modules for standard IE modeling tasks that represent our first attempt at turning our recommendations into practice. We introduce a Python toolbox for IE that includes the life cycle assessment (LCA) framework Brightway2, the ecospold2matrix module that parses unallocated data in ecospold format, the pySUT and pymrio modules for building and analyzing multiregion input‐output models and supply and use tables, and the dynamic_stock_model class for dynamic stock modeling. Widespread use of open access software can, at the same time, increase quality, transparency, and reproducibility of IE research.     

森林-农业景观格局变化的社会-生态系统模拟模型方法进展

社会-生态系统（SES）模拟模型是景观格局分析和决策的有效工具,能表征景观格局变化的社会-生态效应及景观决策的复杂反馈机制。文献综述了森林-农业景观格局的SES模型方法进展发现：（1）多数模型对景观过程与社会经济决策的反馈关系分析不足;（2）应集成多种情景模拟和景观效应分析方法,完善现有SES模型的理论方法基础;（3）通过集成格局优化模型和自主体模型会有效改进SES模型功能,具体途径包括：集成情景-生态效应的景观格局模拟方法、完善景观决策的理论基础、加强集成模型的不确定性分析、降低模型复杂性和综合定性-定量数据等。研究结果有助于理解多尺度森林-农业景观格局在社会-生态系统中的重要作用,能更好地支持跨学科集成模型开发与应用。     

The Independent Evolution Method Is Not a Viable Phylogenetic Comparative Method

Phylogenetic comparative methods (PCMs) use data on species traits and phylogenetic relationships to shed light on evolutionary questions. Recently, Smaers and Vinicius suggested a new PCM, Independent Evolution (IE), which purportedly employs a novel model of evolution based on Felsenstein’s Adaptive Peak Model. The authors found that IE improves upon previous PCMs by producing more accurate estimates of ancestral states, as well as separate estimates of evolutionary rates for each branch of a phylogenetic tree. Here, we document substantial theoretical and computational issues with IE. When data are simulated under a simple Brownian motion model of evolution, IE produces severely biased estimates of ancestral states and changes along individual branches. We show that these branch-specific changes are essentially ancestor-descendant or “directional” contrasts, and draw parallels between IE and previous PCMs such as “minimum evolution”. Additionally, while comparisons of branch-specific changes between variables have been interpreted as reflecting the relative strength of selection on those traits, we demonstrate through simulations that regressing IE estimated branch-specific changes against one another gives a biased estimate of the scaling relationship between these variables, and provides no advantages or insights beyond established PCMs such as phylogenetically independent contrasts. In light of our findings, we discuss the results of previous papers that employed IE. We conclude that Independent Evolution is not a viable PCM, and should not be used in comparative analyses.     

An interdisciplinary study on indicators: A comparative review of quality-of-life,macroeconomic, environmental,welfare and sustainability indicators

It is generally recognised that indicator-based research forms a substantial part both of the everyday practice and of the current theoretical pursuits in an extensive set of different scientific fields that relate to the socio-economic and the environmental sphere. However, the lack of an endogenous indicator's theory hinders the enhancement of indicator's research into an autonomous scientific field and subdues the indicators study to the broader ecological, social, or economic context. Thus, scientists are often bounded to the study of indicators within their specialisation area, as evidenced by the very limited number of interdisciplinary studies on the use of indicators that have been published. Based on this deficiency of the current literature, the paper elaborates on the use of indicators in the socio-economic and the environmental area, focusing on fields in which indicators are essential to their practice. Namely, the paper reviews quality-of-life, macroeconomic, environmental, welfare and sustainability indicators in order to detect similarities and differences, pertain to their practice and to the theoretical frameworks in which indicators are utilised. The study concludes that quality-of-life, welfare and sustainability indicators are supported by weak theoretical foundations, as a result to the choice of the respective fields to exploit the possible benefits of an empirical interdisciplinary perspective, a fact that leads the use of indicators to methodological inconsistencies. In contrast, macroeconomic and environmental indicators are supported by a coherent theoretical body, which is reflected in their well-organised structure and leads to their sound practice. Last but not least, the study suggests that the way the aforementioned two fields utilise indicators can provide useful guidance to the formation of future objectives in the quality-of-life, welfare and sustainability indicators’ research. Specifically, their corresponding fields should moderate their interest on composite indicators and, instead, their future research should be focused, so much on the identification of their field's key indicators that play a crucial role to the interpretation of the complex phenomena studied, as on the identification of the relationships that link these key indicators together.     

生态足迹分析应用于区域可持续发展生态评估的缺陷

可持续发展的生态评估是当前国际生态经济学与可持续发展研究的前沿问题之一,生态足迹从生物生产的角度可以定量评估一个国家或地区发展的生态持续性程度,是近年来发展迅速的一种生物物理量衡量方法。尽管生态足迹分析具有指标指示意义明确、评估结果全球可比与模型方法简便、资料易获取、可操作性强等优点,但在理论方法上仍存在不足之处。综合国内外区域生态足迹分析的最新进展,生态足迹分析应用于区域可持续发展生态评估的理论缺陷主要表现为以下6点：①弱可持续性评价,难以完整反映系统的可持续性状态;②静态模型,缺乏预测功能;③长时间序列生态足迹研究的合理性有待商榷;④全球平均生产力的相对性,导致评估结果的非绝对性;⑤过于强调土地的数量,而忽略土地的质量;⑥假定各类生物生产性土地类型的空间互斥性,忽视兼业性。     

Postsecondary Education in Industrial Ecology Across the World

In recent years, industrial ecology (IE) has become increasingly integrated into formal education as a distinct body of work. The aim of this article is to describe the state of IE in postsecondary education across the world by providing an inventory of programs and courses offered from a search conducted during the summer of 2012. Although some interpretation of the results is conducted, the aim of this article is to provide a snapshot of the state of IE in higher education in 2012 and serve as a starting point for future work. Data were collected on IE courses and programs across the world by Internet search in order to determine the prevalence of IE in postsecondary curricula. Subsequently, 190 universities and colleges from 46 countries were identified as offering courses and/or programs in IE. From this research, a total of 409 courses and 78 programs were inventoried and course content was analyzed (where available). The results indicate that IE is mainly studied at the graduate level within engineering and environmental disciplines, although undergraduate‐level curricula are emerging. In terms of disciplinary departments offering said curricula, IE is presented as a topic of instruction in varied fields of study, such as business and administration, and the arts. From the course syllabi analyzed, the main subjects being taught within IE education are introductory principles and general tools. Advanced or specialized aspects of the field are also covered, however, less frequently.     

The sociocultural sustainability of livestock farming: an inquiry into social perceptions of dairy farming

Over the past 50 years, the scale and intensity of livestock farming have increased significantly. At the same time, Western societies have become more urbanised and fewer people have close relatives involved in farming. As a result, most citizens have little knowledge or direct experience of what farming entails. In addition, more people are expressing concerns over issues such as farm animal welfare. This has led to increasing public demand for more sustainable ways of livestock farming. To date, little research has been carried out on the social pillar of sustainable livestock farming. The aim of this study is to provide insights into the sociocultural sustainability of livestock farming systems. This study reviews the key findings of earlier published interdisciplinary research about the social perceptions of dairy farming in the Netherlands and Norway (Boogaard et al., 2006, 2008, 2010a and 2010b) and synthesises the implications for sociocultural sustainability of livestock farming. This study argues that the (sociocultural) sustainable development of livestock farming is not an objective concept, but that it is socially and culturally constructed by people in specific contexts. It explains the social pillar of the economics/ecological/social model sustainability in terms of the fields of tensions that exist between modernity, traditions and naturality - 'the MTN knot' - each of which has positive and negative faces. All three angles of vision can be seen in people's attitudes to dairy farming, but the weight given to each differs between individuals and cultures. Hence, sociocultural sustainability is context dependent and needs to be evaluated according to its local meaning. Moreover, sociocultural sustainability is about people's perceptions of livestock farming. Lay people might perceive livestock farming differently and ascribe different meanings to it than experts do, but their 'reality' is just as real. Finally, this study calls for an ongoing collaboration between social and animal scientists in order to develop livestock farming systems that are more socioculturally sustainable.     

跨通道迁移及其认知神经机制

跨通道迁移是指将在一种感觉通道获得的知识应用于另一感觉通道的能力。跨通道迁移的相关研究探索了大脑表征不同感觉通道信息的方式,为减少重复学习、提高认知加工效率提供了新的见解。为较好地概括跨通道迁移的特点和机制,本文首先介绍了在物体识别、类别学习和时间知觉等不同领域对跨通道迁移效应的实验研究,之后介绍了支持跨通道迁移的表征类型和相关理论,梳理了跨通道迁移产生的理论及采用事件相关电位（ERP）和功能磁共振成像（fMRI）等技术探讨跨通道迁移神经机制的研究进展,并指出了影响跨通道迁移的因素。最后,对目前跨通道迁移研究成果及其潜在应用进行了总结,并对这一领域未来的研究问题进行了展望。     

Visualizing connectivity of ecological and evolutionary concepts—An exploration of research on plant species rarity

Understanding the ecological and evolutionary factors that influence species rarity has important theoretical and applied implications, yet the reasons why some species are rare while others are common remain unresolved. As a novel exploration of scientific knowledge, we used network analysis conceptually to visualize the foci of a comprehensive base of >800 studies on plant species rarity within the context of ecology and evolution. In doing so, we highlight existing research strengths that could substantiate novel syntheses and gaps that could inspire new research. Our results reveal strong integrated foci on population dynamics with other ecological concepts. In contrast, despite the potential for ecological and evolutionary processes to interact, few studies explored the interplay of environmental factors and microevolutionary patterns. The cellular and molecular biology, physiology, and plasticity of rare plant species within both ecological and evolutionary contexts similarly provide avenues for impactful future investigations.     

University of British Columbia Food System Project: Towards Sustainable and Secure Campus Food Systems

In this profile article, we report what we consider to be a rich learning experience which intertwines pedagogy and research: a process of community-based action research which has initiated a transition towards the sustainability of the University of British Columbia’s (UBC) food system. We call this initiative the UBC Food System Project (UBCFSP). The UBCFSP is a jointly initiated project between the Faculty of Land and Food Systems and the UBC Sustainability Office, and includes nine UBC organizational partners and one collaborator. The project emerged out of the recognition that our global, national, regional, and local food systems are increasingly characterized as socially, ecologically, and economically insecure and unsustainable. As a result, these food systems are experiencing an array of vulnerabilities, particularly those that are demonstrated by profound disruptions in our ecosystem and in a worldwide epidemic of malnutrition. The overall objective of the project is to conduct a campus-wide UBC food system sustainability assessment, where barriers that hinder and opportunities to make transitions towards food system sustainability are being collaboratively identified and implemented. This article is part of a series intending to share the experiences gathered so far through the project. The purpose of this profile is to provide a brief overview of the UBC Food System Project, including the context and significance, both the pedagogical approach and research methods, and some accomplishments to date.     

Hypotheses in urban ecology: building a common knowledge base

Urban ecology is a rapidly growing research field that has to keep pace with the pressing need to tackle the sustainability crisis. As an inherently multi-disciplinary field with close ties to practitioners and administrators, research synthesis and knowledge transfer between those different stakeholders is crucial. Knowledge maps can enhance knowledge transfer and provide orientation to researchers as well as practitioners. A promising option for developing such knowledge maps is to create hypothesis networks, which structure existing hypotheses and aggregate them according to topics and research aims. Combining expert knowledge with information from the literature, we here identify 62 research hypotheses used in urban ecology and link them in such a network. Our network clusters hypotheses into four distinct themes: (i) Urban species traits & evolution, (ii) Urban biotic communities, (iii) Urban habitats and (iv) Urban ecosystems. We discuss the potentials and limitations of this approach. All information is openly provided as part of an extendable Wikidata project, and we invite researchers, practitioners and others interested in urban ecology to contribute additional hypotheses, as well as comment and add to the existing ones. The hypothesis network and Wikidata project form a first step towards a knowledge base for urban ecology, which can be expanded and curated to benefit both practitioners and researchers.     

Importance of basic research in applied phycology

Utilization of algae has extended considerably from the middle of this century, with the consequence of more and more applied research in various directions and fields, the most important of which deals with phycocolloid production and algal cultivation to provide raw material and foodstuff. It is noteworthy that this research can not avoid the use of knowledge obtained by basic research; applied phycology is especially indebted to basic research in adopting biotechnologies which are typically coming from basic research. In counterpart, such a situation is beneficial to basic research. According to the dependence of applied phycology to basic research and the fact that restricted research programs only are nowadays financially supported, the fate of all research seems to be questionable.     

Teachers' journal club: bridging between the dynamics of biological discoveries and biology teachers

Since biology is one of the most dynamic research fields within the natural sciences, the gap between the accumulated knowledge in biology and the knowledge that is taught in schools, increases rapidly with time. Our long-term objective is to develop means to bridge between the dynamics of biological discoveries and the biology teachers and students. Here we report on our recent initiative towards this objective in which we established a journal club forum as a means towards the professional development of biology teachers. We used the journal club format, which is common within the scientific community, in order to engage biology teachers in a constructivist type of learning in which they acquire new skills and at the same time are continuously updated as to biological discoveries, and can then develop updated activities for their biology students. We suggest using the journal club format for the long-term professional development of biology teachers.     

Cigarette smoke extracts delay wound healing in the stomach: involvement of polyamine synthesis

The association between cigarette smoking and peptic ulcer diseases has been well established. Ornithine decarboxylase (ODC) is crucial for the gastroprotective and mucosal growth promoting effects in gastric ulcer healing. The aim of this study is to elucidate the possible mechanism of how inhibition of ODC activity is involved in the delay of ulcer healing, if any, by cigarette smoke extracts (CSE). CSE were fractionated into chloroform extract (CE) and ethanol extract (EE). In in vivo study, rats with acetic acid-induced ulcers were given CE or EE intragastrically (2.5 or 5 mg/kg) once daily for 3 days. Ulcer sizes were significantly larger after CE or EE administration, followed by an increase in myeloperoxidase activity and a reduction in cell proliferation. However, both CSE stimulated the number of microvessels following the increase of basic fibroblast growth factor. In in vitro studies, the effect of CE or EE (10, 40, or 100 microg/ml) on cell migration and cell proliferation were measured using an in vitro wound model and [(3)H]-thymidine incorporation assay, respectively. Both CSE delayed cell migration and decreased cell proliferation, which were accompanied with a reduction in ODC activity. Exogenous spermidine (5 or 10 microM) could reverse the inhibitory action on cell proliferation and ODC activity induced by CSE. In conclusion, both CSE significantly delayed ulcer healing as a result of reduction in cell proliferation and cell migration. All these effects are, in part, related to the reduction of polyamine synthesis.