The role of citizen science in monitoring biodiversity in Ireland

Citizen science is proving to be an effective tool in tracking the rapid pace at which our environment is changing over large geographic areas. It is becoming increasingly popular, in places such as North America and some European countries, to engage members of the general public and school pupils in the collection of scientific data to support long-term environmental monitoring. Participants in such schemes are generally volunteers and are referred to as citizen scientists. The Christmas bird count in the US is one of the worlds longest running citizen science projects whereby volunteers have been collecting data on birds on a specific day since 1900. Similar volunteer networks in Ireland have been in existence since the 1960s and were established to monitor the number and diversity of birds throughout the country. More recently, initiatives such as Greenwave (2006) and Nature Watch (2009) invite school children and members of the general public respectively, to record phenology data from a range of common species of plant, insect and bird. In addition, the Irish butterfly and bumblebee monitoring schemes engage volunteers to record data on sightings of these species. The primary purpose of all of these networks is to collect data by which to monitor changes in wildlife development and diversity, and in the case of Greenwave to involve children in hands-on, inquiry-based science. Together these various networks help raise awareness of key environmental issues, such as climate change and loss of biodiversity, while at the same time promote development of scientific skills among the general population. In addition, they provide valuable scientific data by which to track environmental change. Here we examine the role of citizen science in monitoring biodiversity in Ireland and conclude that some of the data collected in these networks can be used to fulfil Ireland’s statutory obligations for nature conservation. In addition, a bee thought previously to be extinct has been rediscovered and a range expansion of a different bee has been confirmed. However, it also became apparent that some of the networks play more of an educational than a scientific role. Furthermore, we draw on experience from a range of citizen science projects to make recommendations on how best to establish new citizen science projects in Ireland and strengthen existing ones.     

The effects of data collection and observation methods on uncertainty of social networks in wild primates

In social species, network centralities of group members shape social transmission and other social phenomena. Different factors have been found to influence the measurement of social networks, such as data collection and observation methods. In this study, we collected data on adults and juveniles and examined the effect of data collection method (ad libitum sampling vs. focal animal sampling) and observation method (interaction—grooming; play—vs. association—arm-length; 2 m; 5 m proximities—) on social networks in wild vervet monkeys. First, we showed using a bootstrapping method, that uncertainty of ad libitum grooming and play matrices were lesser than uncertainty of focal matrices. Nevertheless, grooming and play networks constructed from ad libitum and focal animal sampling were very similar and highly correlated. We improved the certainty of both grooming and play networks by pooling focal and ad libitum matrices. Second, we reported a high correlation between the proximity arm-length network and the focal grooming one making an arm-length proximity network a reasonable proxy for a grooming one in vervet monkeys. However, we did not find such a correlation between proximity networks and the play one. Studying the effects of methodological issues as data collection and observation methods can help improve understanding of what shapes social networks and which data collection method to choose to study sociality.     

Assessing internet survey data collection methods with ethnic nurse shift workers

An increasing number of ethnic minorities are expected to enter the United States workforce based on projected demographic changes. This includes American Indian/Alaskan Native (AI/AN) nurses. Sociocultural influences on sleep disturbances, sleepiness, and other aspects related to shift-work tolerance are of unrecognized importance. More minority nurses are needed to provide culturally congruent care; however, AI/AN nurses represent less than 1% of nurses located throughout the American workforce. This article aims to verify the feasibility of Internet data collection (Web-based survey) methods and instrument stability as the first part of a two-phase study comparing individual differences and shift-work-related sleep disturbances between AI/AN and White non-Hispanic (WNH) nurses. In the first phase, an Internet survey was used to reach a cross-section of AI/AN and WNH nurses. The on-line survey was composed of accepted shift-work-related instruments. Items estimating sleep disturbances, sociocultural choices, time awareness, polychronicity, morningness/eveningness, ethnic identity, and demographic questions were asked. The survey was linked to a series of Web pages describing the study purpose, inclusion and exclusion criteria, consent form, Web survey, and the second phase of the study in which subjects were invited to participate in actigraphy measurements. The survey was pilot-tested for error codes, item confusion, length, and completion time. Forced-answer questions were added asking ethnicity, age group, license type, state where licensed, and legal name on nursing license before accessing the survey. Data were saved periodically, cued by the word “continue.” The database was located on a secure server and password protected. Nurses were recruited using published articles and printed advertisements, hospital e-mail systems, national nursing organization Web sites (minoritynurse.com; NANAINA.org), nursing Web site discussion groups, snow-balling, and word of mouth. The site was accessed 656 times with the Internet survey being completed by 138 WNH and 56 AI/AN nurses meeting the inclusion criteria. Except for the polychronicity measure (PAI3), instruments measuring time awareness, chronotype, and situational sleepiness achieved acceptable reliability coefficients with Internet data collection. Using pull-down menus would improve questions asking specific times. Internet data collection with different ethnic groups is possible; however, accessing the target population may be difficult. Despite extensive recruitment efforts, few AI/AN nurses participated. Computer literacy and failing to relate to the study's purpose may have limited the interest of the AI/AN nurses. It is possible to recruit nurse shift workers and collect individual difference and sleep disturbance data through the Internet; however, the researcher must remain vigilant throughout the process.     

A social science view on the FRAME symposium: identities and networks

This paper, written by two social scientists, presents a social science perspective on the issues raised at the FRAME symposium on Human Alternatives to Animal Studies. Drawing upon the authors' experience of conducting research with stem cell scientists, issues around access to human tissue for in vitro uses are considered. The paper concludes by raising questions pertinent to both interested social scientists and the Three Rs agenda.     

Evolution of interdisciplinarity in biodiversity science

The study of biodiversity has grown exponentially in the last thirty years in response to demands for greater understanding of the function and importance of Earth's biodiversity and finding solutions to conserve it. Here, we test the hypothesis that biodiversity science has become more interdisciplinary over time. To do so, we analyze 97,945 peer‐reviewed articles over a twenty‐two‐year time period (1990–2012) with a continuous time dynamic model, which classifies articles into concepts (i.e., topics and ideas) based on word co‐occurrences. Using the model output, we then quantify different aspects of interdisciplinarity: concept diversity, that is, the diversity of topics and ideas across subdisciplines in biodiversity science, subdiscipline diversity, that is, the diversity of subdisciplines across concepts, and network structure, which captures interactions between concepts and subdisciplines. We found that, on average, concept and subdiscipline diversity in biodiversity science were either stable or declining, patterns which were driven by the persistence of rare concepts and subdisciplines and a decline in the diversity of common concepts and subdisciplines, respectively. Moreover, our results provide evidence that conceptual homogenization, that is, decreases in temporal β concept diversity, underlies the observed trends in interdisciplinarity. Together, our results reveal that biodiversity science is undergoing a dynamic phase as a scientific discipline that is consolidating around a core set of concepts. Our results suggest that progress toward addressing the biodiversity crisis via greater interdisciplinarity during the study period may have been slowed by extrinsic factors, such as the failure to invest in research spanning across concepts and disciplines. However, recent initiatives such as the Intergovernmental Science‐Policy Platform on Biodiversity and Ecosystem Services (IPBES) may attract broader support for biodiversity‐related issues and hence interdisciplinary approaches to address scientific, political, and societal challenges in the coming years.     

Testing the use of specimen collection data and GIS in biodiversity exploration and conservation decision making in Guyana

This paper presents the results of a study conducted at the request of the Government of Guyana by the Centre for the Study of Biological Diversity at the University of Guyana, and the Smithsonian Institution. The purpose of the study was to evaluate the utility of using systematic collections in identifying areas with a high priority for conservation. A biodiversity database and a gazetteer were assembled and interpreted primarily through the use of maps generated in ARC/INFO and ArcView. The data were examined to determine coverage and completeness, and while in general the results support a continued use of the methodology for making informed decisions in conservation related issues, several recommendations are offered in order to enhance the data. The primary use of the results of this study is in the identification of areas of interest for conservation and in the location of eleven areas covering most ecoregions in Guyana that are in need of additional study. The eleven areas have been chosen to avoid areas that are already allocated to logging and mining concessions or Amerindian lands. While it is true that this study would benefit from additional data and further analysis of those data, it is also true that decisions concerning areas for conservation in Guyana are being made in the near future, and if any data are to be used in this process, it will be those data presented in this paper.     

Discovering and developing primary biodiversity data from social networking sites: A novel approach

Detailed, authoritative Digital Accessible Knowledge (DAK) about biodiversity is crucial to any biodiversity informatics or conservation project. In most developing nations, significant DAK gaps exist both geographically and taxonomically. This paper explores a novel source of photo-vouchered biodiversity occurrence data, in the form of records associated with photos posted on social networking sites (SNSs). SNSs like Flickr, Facebook, and Picasaweb allow naturalists to share images and associated metadata with other users. I explore the idea of discovering and organizing massive numbers of biodiversity occurrence records now available on SNSs. I present a proof-of-concept with Flickr as the SNS and the Snowy Owl (Bubo scandiacus) and the Monarch Butterfly (Danaus plexippus) as target species, but methods presented here can easily be used for any other SNS, region, or species group, particularly for developing, mega-diverse countries where the need for biodiversity DAK is particularly acute. These approaches are broadly applicable to animal and plant groups that are photographed and that can be identified from photographs with some degree of confidence (e.g., birds, butterflies, cetaceans, orchids, dragonflies, amphibians, plants), and thus offer a rich new source of biodiversity data.     

Ecological networks: delving into the architecture of biodiversity

In recent years, the analysis of interaction networks has grown popular as a framework to explore ecological processes and the relationships between community structure and its functioning. The field has rapidly grown from its infancy to a vibrant youth, as reflected in the variety and quality of the discussions held at the first international symposium on Ecological Networks in Coimbra—Portugal (23–25 October 2013). The meeting gathered 170 scientists from 22 countries, who presented data from a broad geographical range, and covering all stages of network analyses, from sampling strategies to effective ways of communicating results, presenting new analytical tools, incorporation of temporal and spatial dynamics, new applications and visualization tools.¹ During the meeting it became evident that while many of the caveats diagnosed in early network studies are successfully being tackled, new challenges arise, attesting to the health of the discipline.     

Is color data from citizen science photographs reliable for biodiversity research?

1. Color research continuously demands better methods and larger sample sizes. Citizen science (CS) projects are producing an ever‐growing geo‐ and time‐referenced set of photographs of organisms. These datasets have the potential to make a huge contribution to color research, but the reliability of these data need to be tested before widespread implementation.
2. We compared the difference between color extracted from CS photographs with that of color extracted from controlled lighting conditions (i.e., the current gold standard in spectrometry) for both birds and plants. First, we tested the ability of CS photographs to quantify interspecific variability by assessing > 9,000 CS photographs of 537 Australian bird species with controlled museum spectrometry data. Second, we tested the ability of CS photographs to quantify intraspecific variability by measuring petal color data for two plant species using seven methods/sources with varying levels of control.
3. For interspecific questions, we found that by averaging out variability through a large sample size, CS photographs capture a large proportion of across species variation in plumage color within the visual part of the spectrum (R² = 0.68–0.71 for RGB space and 0.72–0.77 for CIE‐LAB space). Between 12 and 14 photographs per species are necessary to achieve this averaging effect for interspecific studies. Unsurprisingly, the CS photographs taken with commercial cameras failed to capture information in the UV part of the spectrum. For intraspecific questions, decreasing levels of control increase the color variation but averaging larger sample sizes can partially mitigate this, aside from particular issues related to saturation and irregularities in light capture.
4. CS photographs offer a very large sample size across space and time which offers statistical power for many color research questions. This study shows that CS photographs contain data that lines up closely with controlled measurements within the visual spectrum if the sample size is large enough, highlighting the potential of CS photographs for both interspecific and intraspecific ecological or biological questions. With regard to analyzing color in CS photographs, we suggest, as a starting point, to measure multiple random points within the ROI of each photograph for both patterned and unpatterned patches and approach the recommended sample size of 12–14 photographs per species for interspecific studies. Overall, this study provides groundwork in analyzing the reliability of a novel method, which can propel the field of studying color forward.

     

The identifiability of gene regulatory networks: the role of observation data

Journal of Biological Physics - Identifying gene regulatory networks (GRN) from observation data is significant to understand biological systems. Conventional studies focus on improving the...     

Environmental degradation and the ambiguous social role of science and technology

Conclusion Recent anxieties about the deterioration of the global environment have had the effect of intensifying the ambiguity that surrounds the social roles of scientists and engineers. This has happened not merely, as suggested at the outset, because the environmental crisis has made their roles more conspicuous. Nor is it merely because recent disasters have alerted us to new, or hitherto unrecognized, social consequences of using the latest science-based technologies. What also requires recognition is that ideas about the social role of modern science and engineering are embedded in, hence mediated by, larger views of the world. Within such American worldviews, moreover, the status of science and engineering is closely bound up with their perceived effect upon the environment.In the dominant culture, accordingly, the respect given to scientists and engineers is in large measure dependent on their ability to play the central role assigned to them in the historical narrative about progress. As the ostensible heroes of that popular story, they are expected to lead the way in realizing the promise of prosperity and general well-being. The environmental crisis surely has diminished the credibility of that story, thereby causing the social role of science and engineering to seem more dubious — more ambiguous. To be sure, the crisis also may have the effect, for very different reasons, of increasing the power and responsibility of organized science. But the late twentieth-century task of damage control cannot possibly elicit anything like the respect accorded to organized science by the earlier belief in progress.It also is important to recall, finally, that the narrative of progress itself has undergone a disillusioning transformation. The early Enlightenment version of the story depicted scientists and engineers working in the service of a social and political ideal that all people could share. But the later technocratic concept of progress, with its sterile instrumentalist notion of advancing the power of science-based technology as an end in itself, is far less likely to inspire trust. Its patent inadequacies have had the effect of enhancing the appeal, if only by contrast, of the seemingly anti-science ideologies of pastoralism and primitivism. All of which might be taken to suggest that if the scientific and engineering professions want to recover some of the respect and status they once had, they would be well advised to join with sympathetic humanists and social scientists in recuperating some of the idealism that the project of modern science formerly derived from its place within the ideology of progress. That might entail the sacrifice of their technocratic posture of neutrality, dissociating themselves from people and institutions responsible for environmental degradation, and their help in formulating a new concept — which is to say, new criteria — of progress to which they might commit themselves. A primary test of any proposed social policy under this new dispensation surely would be whether it would improve, or at a minimum protect, the life-enhancing capacities of the global ecosystem. *** DIRECT SUPPORT *** A8402064 00011 *** DIRECT SUPPORT *** A8402064 00012 *** DIRECT SUPPORT *** A8402064 00013     

Biodiversity loss and the taxonomic bottleneck: emerging biodiversity science

Human domination of the Earth has resulted in dramatic changes to global and local patterns of biodiversity. Biodiversity is critical to human sustainability because it drives the ecosystem services that provide the core of our life-support system. As we, the human species, are the primary factor leading to the decline in biodiversity, we need detailed information about the biodiversity and species composition of specific locations in order to understand how different species contribute to ecosystem services and how humans can sustainably conserve and manage biodiversity. Taxonomy and ecology, two fundamental sciences that generate the knowledge about biodiversity, are associated with a number of limitations that prevent them from providing the information needed to fully understand the relevance of biodiversity in its entirety for human sustainability: (1) biodiversity conservation strategies that tend to be overly focused on research and policy on a global scale with little impact on local biodiversity; (2) the small knowledge base of extant global biodiversity; (3) a lack of much-needed site-specific data on the species composition of communities in human-dominated landscapes, which hinders ecosystem management and biodiversity conservation; (4) biodiversity studies with a lack of taxonomic precision; (5) a lack of taxonomic expertise and trained taxonomists; (6) a taxonomic bottleneck in biodiversity inventory and assessment; and (7) neglect of taxonomic resources and a lack of taxonomic service infrastructure for biodiversity science. These limitations are directly related to contemporary trends in research, conservation strategies, environmental stewardship, environmental education, sustainable development, and local site-specific conservation. Today’s biological knowledge is built on the known global biodiversity, which represents barely 20% of what is currently extant (commonly accepted estimate of 10 million species) on planet Earth. Much remains unexplored and unknown, particularly in hotspots regions of Africa, South Eastern Asia, and South and Central America, including many developing or underdeveloped countries, where localized biodiversity is scarcely studied or described. "Backyard biodiversity", defined as local biodiversity near human habitation, refers to the natural resources and capital for ecosystem services at the grassroots level, which urgently needs to be explored, documented, and conserved as it is the backbone of sustainable economic development in these countries. Beginning with early identification and documentation of local flora and fauna, taxonomy has documented global biodiversity and natural history based on the collection of "backyard biodiversity" specimens worldwide. However, this branch of science suffered a continuous decline in the latter half of the twentieth century, and has now reached a point of potential demise. At present there are very few professional taxonomists and trained local parataxonomists worldwide, while the need for, and demands on, taxonomic services by conservation and resource management communities are rapidly increasing. Systematic collections, the material basis of biodiversity information, have been neglected and abandoned, particularly at institutions of higher learning. Considering the rapid increase in the human population and urbanization, human sustainability requires new conceptual and practical approaches to refocusing and energizing the study of the biodiversity that is the core of natural resources for sustainable development and biotic capital for sustaining our life-support system. In this paper we aim to document and extrapolate the essence of biodiversity, discuss the state and nature of taxonomic demise, the trends of recent biodiversity studies, and suggest reasonable approaches to a biodiversity science to facilitate the expansion of global biodiversity knowledge and to create useful data on backyard biodiversity worldwide towards human sustainability.     

Informing and influencing the interface between biodiversity science and biodiversity policy in South Africa

South Africa, as a megadiverse country (±21 700 vascular plants, 4800 vertebrates and 68 900 invertebrates described), is presently engaged with an extended, modified Global Strategy for Plant Conservation (GSPC). The country is fortunate in having a strong tradition of systematics research and, inter alia, houses several million preserved plant specimens (±1 million databased and georeferenced), allowing taxonomists and conservationists to track both the occurrence and distribution of indigenous and naturalized plant species. These rich local resources have been extensively drawn upon to deliver, with varying degrees of success, the 16 outcome-oriented GSPC 2010 Targets. The National Environmental Management: Biodiversity Act (NEMBA, 2004), the National Biodiversity Strategy and Action Plan (NBSAP) and the National Biodiversity Framework (NBF) have provided a robust legislative, enabling and policy framework for making operational and advancing GSPC-related efforts. However, within an emerging economy, the conservation of biodiversity has competed for government resources with housing, sanitation, primary education, basic health care and crime prevention, delivery of which translates to the currency of politicians: votes. A key challenge identified by local (and global) biodiversity scientists for the current GSPC phase is broad-scale advocacy, communicating the changing state of nature, and the inter-relatedness of biodiversity and human well-being. The nature of meeting this challenge is explored.     

Interactome networks: the state of the science

A report on the joint Cold Spring Harbor/Wellcome Trust Meeting 'Interactome Networks', Hinxton, UK, 31 August-4 September 2005.

High-throughput analyses are identifying the DNA, RNA, proteins and metabolites within a biological system with increasing accuracy and speed. As a result, we now have a relatively detailed understanding of the components that make up the dynamic and temporal characteristics of the cell. In most cases, however, we know very little about how the individual components work together to carry out specific biological functions. To get over this hurdle, it will be necessary to map how individual biomolecules interact with one another within a larger network of molecular interactions (the so-called 'interactome') in the cell as a whole.

Mapping this network is the shared goal of an increasing number of researchers from the UK, Europe, US, and Japan, who gathered at the first annual Cold Spring Harbor/Wellcome Trust meeting on interactome networks in Hinxton. This meeting provided an opportunity to review the recent experimental and computational advances that have been applied to uncover biomolecular interactions. Here we report a few of the key advances in the areas of new interaction-mapping techniques, new experimental reagents and resources, and new computational tools for understanding interaction networks that were presented at the meeting.

     

Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science

The Scratchpad Virtual Research Environment (http://scratchpads.eu/) is a flexible system for people to create their own research networks supporting natural history science. Here we describe Version 2 of the system characterised by the move to Drupal 7 as the Scratchpad core development framework and timed to coincide with the fifth year of the project's operation in late January 2012. The development of Scratchpad 2 reflects a combination of technical enhancements that make the project more sustainable, combined with new features intended to make the system more functional and easier to use. A roadmap outlining strategic plans for development of the Scratchpad project over the next two years concludes this article.     

从知识创新展望21世纪生物多样性科学

首先简要介绍汤佩松(1983)创新植物学,随后根据其创新思想分析了生物多样性三个层次研究的现状和问题。提出了一个根据DNA 序列变异尺度为标准的新的遗传多样性等级制度。为了避免物种和其他分类群的随意性, 建议以DNA 序列变异作为可操作的分类单元(OTU)和国际上进化上显著单元(ESU)相呼应。下一世纪的分子系统学和分子生态学可能重点研究DNA 变异, 特别是重复序列的变化对生物生命活动的调控, 在分子水平上揭示结构和功能的进化和适应。第三部分讨论Diversitas五个核心课题, 说明分子水平研究和生物技术对生物多样性保护和持续利用的重要性和迫切性。最后评论了" 天人合一" 为代表的反科学主义思潮, 坚持科学进步。     

Capture and collection of lampreys: the state of the science

The need for native lamprey conservation, improved lamprey fishery management, and better assessment of non-indigenous lamprey control measures has resulted in increased effort to survey lamprey populations and assess their status. Depending on the study objectives and target species/life stage, collection methods vary dramatically. We therefore provide a comprehensive review of sampling considerations and techniques used to capture, collect, handle, and enumerate both juvenile and adult lamprey life stages. Surveys for lamprey are often constrained by the lack of basic biological information, such as reliable characters for field identification of larvae (ammocoetes), migratory timing of anadromous forms, and spawning/nest building behavior of adults. However, there are a number of studies that have documented habitat preferences of the relatively sedentary ammocoetes. Consequently, existing sampling protocols have focused on the development of stratified sampling that targets optimal ammocoete habitat. In addition to this approach, we discuss methods and gear that can be used to survey migratory life stages, lamprey nests, and difficult-to-sample, deepwater ammocoete habitats.