When You Find Yourself in a Hole, Stop Digging: Comments on Earth Systems Engineering

In an earlier "Forum" article in this journal, Brad Allenby outlined his views of a new approach to managing the unintended consequences of human activity, "earth systems engineering." He argues that we must develop the tools, institutions, and moral and ethical systems to allow us to "assume an active management role for most global systems." I believe this to be a significant departure from a core concept of industrial ecology: learning from ecosystems how the natural world operates to be able to more effectively design and manage coupled human-natural systems. Such lessons are more likely to lead away from tightly managed, centralized approaches, and favor approaches with as little intervention as feasible. More important, I believe that we are far less likely to learn how to implement earth systems engineering than simpler approaches, hence less likely to minimize environmental damage.     

Synthetic spatial patterning in bacteria: advances based on novel diffusible signals

Engineering multicellular patterning may help in the understanding of some fundamental laws of pattern formation and thus may contribute to the field of developmental biology. Furthermore, advanced spatial control over gene expression may revolutionize fields such as medicine, through organoid or tissue engineering. To date, foundational advances in spatial synthetic biology have often been made in prokaryotes, using artificial gene circuits. In this review, engineered patterns are classified into four levels of increasing complexity, ranging from spatial systems with no diffusible signals to systems with complex multi-diffusor interactions. This classification highlights how the field was held back by a lack of diffusible components. Consequently, we provide a summary of both previously characterized and some new potential candidate small-molecule signals that can regulate gene expression in Escherichia coli. These diffusive signals will help synthetic biologists to successfully engineer increasingly intricate, robust and tuneable spatial structures.     

AIMS AND SCOPE

The Journal of Bionic Engineering publishes original research papers and reviews on all aspects of bionic science and engineering including fundamental understandings of animals and plants for bionic engineering, such as locomotion and behaviors of animals, structures, composites, morphology and physical properties of plants and natural materials, applications of such understandings in engineering, technology and designs.     

Envisioning ecological engineering education: An international survey of the educational and professional community

Nearly half a century ago, H.T. Odum envisioned a sustainable approach to systems design where human intervention would be supplementary to nature. He referred to this concept as ecological engineering and suggested that practitioners should receive an education beyond the rigors of engineering. To understand natural processes needed to design, develop, and restore natural systems successfully, Odum suggested ecological engineers should have an expanded knowledge of environmental systems and ecology. Furthermore, he recommended broadening educational exposure to social science and liberal arts. The field of ecological engineering has blossomed in the years since Odum expressed his vision, but universities have not adopted his suggested curriculum, and undergraduate engineering students have generally seen a reduction in social science and liberal arts courses. This paper compares Odum's vision with the surveyed visions of an international group of ecological engineers, who assessed the value and characteristics of an ecological engineering undergraduate education. The respondents’ perspectives vary with their location, education, and profession; however, most participants in this survey share Odum's vision, and are dissatisfied with existing curricula. Participants outside of the United States were more confident that something approaching Odum's vision for a program in ecological engineering could be delivered at the undergraduate level.     

Plant artificial chromosome technology and its potential application in genetic engineering

Genetic engineering with just a few genes has changed agriculture in the last 20 years. The most frequently used transgenes are the herbicide resistance genes for efficient weed control and the Bt toxin genes for insect resistance. The adoption of the first‐generation genetically engineered crops has been very successful in improving farming practices, reducing the application of pesticides that are harmful to both human health and the environment, and producing more profit for farmers. However, there is more potential for genetic engineering to be realized by technical advances. The recent development of plant artificial chromosome technology provides a super vector platform, which allows the management of a large number of genes for the next generation of genetic engineering. With the development of other tools such as gene assembly, genome editing, gene targeting and chromosome delivery systems, it should become possible to engineer crops with multiple genes to produce more agricultural products with less input of natural resources to meet future demands.     

Quantitative Industrial Ecology & Ecological Economics

This article presents a theoretical foundation for integrating three otherwise disparate areas of human thought and understanding: technology, ecology, and economics. The article presents the mathematical foundations for quantifying the biophysical (mass, energy, and informational) aspects of economic production systems and their interaction with natural systems. These mathematical relationships are required for the on-going ecological and economic design of technological production networks by enterprise management, thereby extending the scope and scale of quantitative engineering design from the domain of individual technologies to networks of technologies at enterprise, corporate, and industrial levels of technological organization.
The analytical framework extends the practical utility of ecology, as an applied natural science, from passive environmental monitoring and prediction to active institutional participation in an informational feedback control strategy pursuant to economically abating the ecological risks of industrial growth, development, and modernization at local, regional, and global levels of ecological organization. And it provides the applied natural-science underpinnings and the informational feedback control institutions required to support economics as an applied social science. In this context ecological risk-control pricing is presented as a supplement to conventional economic policies at local, regional, and national levels of economic organization.     

Defining ecology: Ecological theories,mathematical models,and applied biology in the 1960s and 1970s

Ever since the early decades of this century, there have emerged a number of competing schools of ecology that have attempted to weave the concepts underlying natural resource management and natural-historical traditions into a formal theoretical framework. It was widely believed that the discovery of the fundamental mechanisms underlying ecological phenomena would allow ecologists to articulate mathematically rigorous statements whose validity was not predicated on contingent factors. The formulation of such statements would elevate ecology to the standing of a rigorous scientific discipline on a par with physics. However, there was no agreement as to the fundamental units of ecology. Systems ecologists sought to identify the fundamental organization that tied the physical and biological components of ecosystems into an irreducible unit: the ecosystem was their fundamental unit. Population ecologists sought, instead, to identify the biological mechanisms regulating the abundance and distribution of plant and animal species: to these ecologists, the individual organism was the fundamental unit of ecology, and the physical environment was nothing more than a stage upon which the play of individuals in perennial competition took place. As Joel Hagen has pointed out, the two schools were thus dividied by fundamentally different and irreconcilable assumptions about the nature of ecosystems.Notwithstanding these divisive efforts to elevate the image of ecology, the discipline remained in the shadows of American academia until the mid-1960s, when systems ecologists succeeded in projecting ecology onto the national scene. They did so by seeking closer involvement with practical problems: they argued before Congress that their approach to the theoretical problems of ecology was uniquely suited to the solution of the impending environmental crisis. With the establishment of the International Biological Program, they succeeded in attracting unprecedented levels of funding for systems ecology research. Theoretical population ecologists, on the other hand, found themselves consigned to the outer regions of this new institutional landscape. The systems ecologists' successful capture of the limelight and the purse brought the divisions between them and population ecologists into sharper relief — hence the hardening of the division of ecology observed by Hagen.⁴⁵     

Light-dependant biostabilisation of sediments by stromatolite assemblages

For the first time we have investigated the natural ecosystem engineering capacity of stromatolitic microbial assemblages. Stromatolites are laminated sedimentary structures formed by microbial activity and are considered to have dominated the shallows of the Precambrian oceans. Their fossilised remains are the most ancient unambiguous record of early life on earth. Stromatolites can therefore be considered as the first recognisable ecosystems on the planet. However, while many discussions have taken place over their structure and form, we have very little information on their functional ecology and how such assemblages persisted despite strong eternal forcing from wind and waves. The capture and binding of sediment is clearly a critical feature for the formation and persistence of stromatolite assemblages. Here, we investigated the ecosystem engineering capacity of stromatolitic microbial assemblages with respect to their ability to stabilise sediment using material from one of the few remaining living stromatolite systems (Highborne Cay, Bahamas). It was shown that the most effective assemblages could produce a rapid (12-24 h) and significant increase in sediment stability that continued in a linear fashion over the period of the experimentation (228 h). Importantly, it was also found that light was required for the assemblages to produce this stabilisation effect and that removal of assemblage into darkness could lead to a partial reversal of the stabilisation. This was attributed to the breakdown of extracellular polymeric substances under anaerobic conditions. These data were supported by microelectrode profiling of oxygen and calcium. The structure of the assemblages as they formed was visualised by low-temperature scanning electron microscopy and confocal laser microscopy. These results have implications for the understanding of early stromatolite development and highlight the potential importance of the evolution of photosynthesis in the mat forming process. The evolution of photosynthesis may have provided an important advance for the niche construction activity of microbial systems and the formation and persistence of the stromatolites which came to dominate shallow coastal environments for 80% of the biotic history of the earth.     

自然生态价值、生态资产管理及价值实现的生态经济学基础研究——科学概念、基础理论及实现途径

自然界的生态系统为人类繁衍发展提供各式各样的生活、生产和生计的环境条件与自然资源。基于自然规律的生态系统管理是人类社会不断认知自然生态价值、保护利用自然环境和资源、创造积累生态资产、维持社会经济系统永续发展的基本途径。以此为核心认知的区域生态经济学或经济生态学,正在成为探讨人类世地球系统演变及社会经济可持续发展问题的科学研究前沿。本文以大尺度区域宏观生态系统科学为学术视角,以生态系统的多功能性与多元价值观为基础,综合论述了自然生态价值、生态资产、生态产品等基本概念;从生态学、社会学和经济学融合角度,分析讨论了生态资产形成与变化、生态产品生产与消费、生态投资与生态资产损益等过程原理;提出了区域生态资产的系统经营与生态价值实现途径,期望为我国及区域生态系统价值及生态资产的评估,生态产业及生态价值实现体系的发展提供理论和方法学参考。     

Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways

Cells are filled with biosensors, molecular systems that measure the state of the cell and respond by regulating host processes. In much the same way that an engineer would monitor a chemical reactor, the cell uses these sensors to monitor changing intracellular environments and produce consistent behavior despite the variable environment. While natural systems derive a clear benefit from pathway regulation, past research efforts in engineering cellular metabolism have focused on introducing new pathways and removing existing pathway regulation. Synthetic biology is a rapidly growing field that focuses on the development of new tools that support the design, construction, and optimization of biological systems. Recent advances have been made in the design of genetically-encoded biosensors and the application of this class of molecular tools for optimizing and regulating heterologous pathways. Biosensors to cellular metabolites can be taken directly from natural systems, engineered from natural sensors, or constructed entirely in vitro. When linked to reporters, such as antibiotic resistance markers, these metabolite sensors can be used to report on pathway productivity, allowing high-throughput screening for pathway optimization. Future directions will focus on the application of biosensors to introduce feedback control into metabolic pathways, providing dynamic control strategies to increase the efficient use of cellular resources and pathway reliability.     

Synthetic tissue biology: tissue engineering meets synthetic biology

We propose the term "synthetic tissue biology" to describe the use of engineered tissues to form biological systems with metazoan-like complexity. The increasing maturity of tissue engineering is beginning to render this goal attainable. As in other synthetic biology approaches, the perspective is bottom-up; here, the premise is that complex functional phenotypes (on par with those in whole metazoan organisms) can be effected by engineering biology at the tissue level. To be successful, current efforts to understand and engineer multicellular systems must continue, and new efforts to integrate different tissues into a coherent structure will need to emerge. The fruits of this research may include improved understanding of how tissue systems can be integrated, as well as useful biomedical technologies not traditionally considered in tissue engineering, such as autonomous devices, sensors, and manufacturing.     

A framework for understanding physical ecosystem engineering by organisms

While well‐recognized as an important kind of ecological interaction, physical ecosystem engineering by organisms is diverse with varied consequences, presenting challenges for developing and using general understanding. There is also still some uncertainty as to what it is, and some skepticism that the diversity of engineering and its effects is amenable to conceptual integration and general understanding. What then, are the key cause/effect relationships and what underlies them? Here we develop, enrich and extend our extant understanding of physical ecosystem engineering into an integrated framework that exposes the essential cause/effect relationships, their underpinnings, and the interconnections that need to be understood to explain or predict engineering effects. The framework has four cause/effect relationships linking four components: 1. An engineer causes structural change; 2. Structural change causes abiotic change; 3. Structural and abiotic change cause biotic change; 4. Structural, abiotic and biotic change can feedback to the engineer. The first two relationships describe an ecosystem engineering process and abiotic dynamics, while the second two describe biotic consequence for other species and the engineer. The four relationships can be parameterized and linked using time‐indexed equations that describe engineered system dynamics. After describing the relationships we discuss the utility of the framework; how it might be enriched; and briefly how it can be used to identify intersections of ecosystem engineering with fields outside ecology.     

CRISPR/Cas systems versus plant viruses: engineering plant immunity and beyond

Molecular engineering of plant immunity to confer resistance against plant viruses holds great promise for mitigating crop losses and improving plant productivity and yields, thereby enhancing food security. Several approaches have been employed to boost immunity in plants by interfering with the transmission or lifecycles of viruses. In this review, we discuss the successful application of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) (CRISPR/Cas) systems to engineer plant immunity, increase plant resistance to viruses, and develop viral diagnostic tools. Furthermore, we examine the use of plant viruses as delivery systems to engineer virus resistance in plants and provide insight into the limitations of current CRISPR/Cas approaches and the potential of newly discovered CRISPR/Cas systems to engineer better immunity and develop better diagnostics tools for plant viruses. Finally, we outline potential solutions to key challenges in the field to enable the practical use of these systems for crop protection and viral diagnostics.

CRISPR-Cas systems unlock the potential of understanding the molecular basis of plant virus interactions, engineering immunity against plant viruses, and developing sensitive and specific diagnostics.     

Building a genome engineering toolbox in nonmodel prokaryotic microbes

The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO₂, and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop “design rules” for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.     

Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages

Marine cyanobacteria of the genera Synechococcus and Prochlorococcus are the most abundant photosynthetic organisms on earth, spanning vast regions of the oceans and contributing significantly to global primary production. Their viruses (cyanophages) greatly influence cyanobacterial ecology and evolution. Although many cyanophage genomes have been sequenced, insight into the functional role of cyanophage genes is limited by the lack of a cyanophage genetic engineering system. Here, we describe a simple, generalizable method for genetic engineering of cyanophages from multiple families, that we named REEP for REcombination, Enrichment and PCR screening. This method enables direct investigation of key cyanophage genes, and its simplicity makes it adaptable to other ecologically relevant host-virus systems. T7-like cyanophages often carry integrase genes and attachment sites, yet exhibit lytic infection dynamics. Here, using REEP, we investigated their ability to integrate and maintain a lysogenic life cycle. We found that these cyanophages integrate into the host genome and that the integrase and attachment site are required for integration. However, stable lysogens did not form. The frequency of integration was found to be low in both lab cultures and the oceans. These findings suggest that T7-like cyanophage integration is transient and is not part of a classical lysogenic cycle.Subject terms: Microbial ecology, Bacteriophages     

合成生物学及其在生物技术中的应用进展

合成生物学是一门21世纪生物学的新兴学科,它着眼生物科学与工程科学的结合,把生物系统当作工程系统"从下往上"进行处理,由"单元"(unit)到"部件"(device)再到"系统"(system)来设计,修改和组装细胞构件及生物系统.合成生物学是分子和细胞生物学、进化系统学、生物化学、信息学、数学、计算机和工程等多学科交叉的产物.目前研究应用包括两个主要方面:一是通过对现有的、天然存在的生物系统进行重新设计和改造,修改已存在的生物系统,使该系统增添新的功能.二是通过设计和构建新的生物零件、组件和系统,创造自然界中尚不存在的人工生命系统.合成生物学作为一门建立在基因组方法之上的学科,主要强调对创造人工生命形态的计算生物学与实验生物学的协同整合.必须强调的是,用来构建生命系统新结构、产生新功能所使用的组件单元既可以是基因、核酸等生物组件,也可以是化学的、机械的和物理的元件.本文跟踪合成生物学研究及应用,对其在DNA水平编程、分子修饰、代谢途径、调控网络和工业生物技术等方面的进展进行综述.     

On the Compliance of Women Engineers with a Gendered Scientific System

There has been considerable effort in the last decade to increase the participation of women in engineering through various policies. However, there has been little empirical research on gender disparities in engineering which help underpin the effective preparation, co-ordination, and implementation of the science and technology (S&T) policies. This article aims to present a comprehensive gendered analysis of engineering publications across different specialties and provide a cross-gender analysis of research output and scientific impact of engineering researchers in academic, governmental, and industrial sectors. For this purpose, 679,338 engineering articles published from 2008 to 2013 are extracted from the Web of Science database and 974,837 authorships are analyzed. The structures of co-authorship collaboration networks in different engineering disciplines are examined, highlighting the role of female scientists in the diffusion of knowledge. The findings reveal that men dominate 80% of all the scientific production in engineering. Women engineers publish their papers in journals with higher Impact Factors than their male peers, but their work receives lower recognition (fewer citations) from the scientific community. Engineers—regardless of their gender—contribute to the reproduction of the male-dominated scientific structures through forming and repeating their collaborations predominantly with men. The results of this study call for integration of data driven gender-related policies in existing S&T discourse.     

天然生物地球电池效应、形成机制及生态学意义

天然生物地球电池(biogeobattery)是一种发生在地球表层氧化-还原界面的自然现象,是微生物在厌氧区域氧化有机碳、硫化物等电子供体,产生的电子经胞外介体"长距离"传输至好氧区,从而与空间上隔离的氧气等电子受体发生还原反应的过程。由于生物电流的偶联,使得过去认为因空间隔离而难以发生的氧化-还原反应,可以快速、即时的进行。Biogeobattery的科学本质是:通过微生物驱动电子流动,偶联空间上隔离的生物地球化学过程。Biogeobattery可能容易发生在有机物丰富、具备氧化-还原界面的生境,如海底沉积物环境、有机物污染区域等;它对于有机物厌氧矿化、温室气体排放、C/N/S等元素地球化学循环、污染物自然恢复等关键生物地球化学过程有重要影响,具有重大生态学意义,正成为地球科学、微生物学及生态学共同关注的国际前沿和热点。从"人工"biogeobattery(沉积物微生物燃料电池)入手,阐述了biogeobattery效应及其形成机制,从电池的电势、阴极-阳极响应关系、传导介质等方面详细介绍其研究方法,论述了biogeobattery的生态学意义,展望了研究重点。     

Ecological engineering: A rationale for standardized curriculum and professional certification in the United States

The demand for engineering solutions to ecosystem–level problems has increased as the impact of human activities has expanded to global proportions. While the science of restoration ecology has been developed to address many critical ecosystem management issues, the high degree of complexity and uncertainty associated with these issues demands a more quantitative approach. Ecological engineering uses science-based quantification of ecological processes to develop and apply engineering-based design criteria for sustainable systems. We suggest that in the United States ecological engineering curricula should be offered at the graduate level and should require rigorous Accreditation Board of Engineering and Technology-accredited (or equivalent) undergraduate preparation in engineering fundamentals. In addition to strengthening students’ mastery of engineering theory and application, the graduate curriculum should provide core courses in ecosystem theory including quantitative ecology, systems ecology, restoration ecology, ecological engineering, ecological modeling, and ecological engineering economics. Advanced courses in limnology, environmental plant physiology, ecological economics, and specific ecosystem design should be provided to address students’ specific professional objectives. Finally, professional engineering certification must be developed to insure the credibility of this new engineering specialization.