Balancing data sharing requirements for analyses with data sensitivity

Data sensitivity can pose a formidable barrier to data sharing. Knowledge of species current distributions from data sharing is critical for the creation of watch lists and an early warning/rapid response system and for model generation for the spread of invasive species. We have created an on-line system to synthesize disparate datasets of non-native species locations that includes a mechanism to account for data sensitivity. Data contributors are able to mark their data as sensitive. This data is then ‘fuzzed’ in mapping applications and downloaded files to quarter-quadrangle grid cells, but the actual locations are available for analyses. We propose that this system overcomes the hurdles to data sharing posed by sensitive data.     

Marine invertebrates,model organisms,and the modern synthesis: epistemic values,evo-devo,and exclusion

A central reason that undergirds the significance of evo-devo is the claim that development was left out of the Modern synthesis. This claim turns out to be quite complicated, both in terms of whether development was genuinely excluded and how to understand the different kinds of embryological research that might have contributed. The present paper reevaluates this central claim by focusing on the practice of model organism choice. Through a survey of examples utilized in the literature of the Modern synthesis, I identify a previously overlooked feature: exclusion of research on marine invertebrates. Understanding the import of this pattern requires interpreting it in terms of two epistemic values operating in biological research: theoretical generality and explanatory completeness. In tandem, these values clarify and enhance the significance of this exclusion. The absence of marine invertebrates implied both a lack of generality in the resulting theory and a lack of completeness with respect to particular evolutionary problems, such as evolvability and the origin of novelty. These problems were salient to embryological researchers aware of the variation and diversity of larval forms in marine invertebrates. In closing, I apply this analysis to model organism choice in evo-devo and discuss its relevance for an extended evolutionary synthesis.

Data depth, data completeness, and their influence on quantitative genetic estimation in two contrasting bird populations

Evolutionary biologists increasingly use pedigree‐based quantitative genetic methods to address questions about the evolutionary dynamics of traits in wild populations. In many cases, phenotypic data may have been collected only for recent parts of the study. How does this influence the performance of the models used to analyse these data? Here we explore how data depth (number of years) and completeness (number of observations) influence estimates of genetic variance and covariance within the context of an existing pedigree. Using long‐term data from the great tit Parus major and the mute swan Cygnus olor, species with different life‐histories, we examined the effect of manipulating the amount of data included on quantitative genetic parameter estimates. Manipulating data depth and completeness had little influence on estimated genetic variances, heritabilities, or genetic correlations, but (as expected) did influence confidence in these estimates. Estimated breeding values in the great tit were not influenced by data depth but were in the mute swan, probably because of differences in pedigree structure. Our analyses suggest the ‘rule of thumb’ that data from 3 years and a minimum of 100 individuals per year are needed to estimate genetic parameters with acceptable confidence, and that using pedigree data is worthwhile, even if phenotypes are only available toward the tips of the pedigree.     

Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing

Cardiac experimental electrophysiology is in need of a well-defined Minimum Information Standard for recording, annotating, and reporting experimental data. As a step towards establishing this, we present a draft standard, called Minimum Information about a Cardiac Electrophysiology Experiment (MICEE). The ultimate goal is to develop a useful tool for cardiac electrophysiologists which facilitates and improves dissemination of the minimum information necessary for reproduction of cardiac electrophysiology research, allowing for easier comparison and utilisation of findings by others. It is hoped that this will enhance the integration of individual results into experimental, computational, and conceptual models. In its present form, this draft is intended for assessment and development by the research community. We invite the reader to join this effort, and, if deemed productive, implement the Minimum Information about a Cardiac Electrophysiology Experiment standard in their own work.     

Same river,different values and why it matters

Summary Examination of the values that people assign to specific natural places is likely to be useful for environmental decision‐making but is an underdeveloped area of socio‐psychological research. A mail survey was used to examine the differences and similarities in values assigned by people to the Loddon River in south‐eastern Australia. Environmental, social and economic values were explored across five different community types: urban residents, rural residents, natural resource management (NRM) professionals, environmental group members (EGM) and landholders. While urban residents, rural residents and landholders had similar responses, NRM professionals and EGM placed much stronger emphasis on environmental values derived from the river, and much less emphasis on economic values. Members of two community types (EGM and NRM professionals) responded in a relatively homogenous way, within a narrow range of response options. By contrast, three community types (urban residents, rural residents and landholders) responded in more diverse ways. There were similarities in the social values (historical and aesthetic) expressed by the different community types, suggesting common points for stakeholder engagement in the management of the river. Results point to the need for environmental managers to ensure that consultation is not limited to the most actively engaged sectors of the community, as their responses may not be representative of other groups.     

The Protein Data Bank and lessons in data management

The Protein Data Bank (PDB) is a widely used biological databaseof macromolecular structures with a long history. This historyis treated as lessons learned and is used to highlight whatare believed to be the best practices important to developersof biological databases today. While the focus is on data quality,data representation and the information technology to supportthese data, the non-data and technology issues cannot be ignored.The role of the human factor in the form of users, collaborators,scientific society and ad hoc committees is also included.      

Soil softness, nest initiation and nest sharing in the wasp, Cerceris antipodes (Hymenoptera: Sphecidae)

Abstract. 1. The relationship between soil softness and nest initiation was studied at two aggregations of a ground nesting sphecid wasp, Cerceris antipodes Smith, in New South Wales, Australia.
2. Nests of C.antipodes were initiated throughout the active season. Nests were started more frequently during moist conditions and when more wasps were active.
3. Nest initiation was clumped on days after periods of rain. Nest initiation was only observed when the soil was soft.
4. Two experimental plots that were watered had significantly softer soil and more nests initiated on them than two control plots. Searching female wasps spent considerably more time on the watered plots than the controls.
5. Nest initiation through hard surface soils presents a problem to C.antipodes. Soil softness must be considered in any analysis of nest sharing in this species.     

Data requirements and data sources for biodiversity priority area selection

The data needed to prioritize areas for biodiversity protection are records of biodiversity features — species, species assemblages, environmental classes — for each candidate area. Prioritizing areas means comparing candidate areas, so the data used to make such comparisons should be comparable in quality and quantity. Potential sources of suitable data include museums, herbariums and natural resource management agencies. Issues of data precision, accuracy and sampling bias in data sets from such sources are discussed and methods for treating data to minimize bias are reviewed.     

Intra-consortium data sharing in multi-national, multi-institutional genomic studies: gaps and guidance

Growing investments in health research by governments and charitable organizations have fueled an increase in collaborative research projects between investigators from affluent and developing countries. Current international guidelines are silent on common intra-consortium data-sharing issues that arise in the context of such collaborations. A lack of guidance on intra-consortium data sharing threatens to undermine the success of crucial research ventures. In this work we outline some of the practical problems commonly faced by investigators working in multi-institutional, international genomic collaborations and offer recommendations on these issues. A data sharing policy should be prospectively negotiated and concluded between collaborators as early as possible. Sponsors of research, including those from developing countries, should issue detailed guidance on the above and related issues as doing so will facilitate research and catalyze scientific progress.     

武汉和天津园林植物叶片热值比较研究

对天津和武汉两地一些园林植物叶片的春季干重热值、灰分含量和去灰分热值进行了比较 ,结果发现 ,无论在武汉还是天津 ,所测园林植物的干重热值均表现为乔木 >灌木 >草本的递减趋势 ,灰分含量则呈现相反的趋势即草本 >灌木 >乔木 ,去灰分热值在武汉与干重热值的趋势一致 ,但在天津却是乔木 >草本 >灌木。同一类型的植物干重热值都是低纬度的武汉高于高纬度的天津 ,灰分含量相反 :天津高于武汉 ;乔木和灌木的去灰分热值也是武汉高于天津 ,草本植物例外。两地共有的 7种植物平均值相比 ,干重热值和去灰分热值都是武汉 >天津 ,同一植物种相比 ,7种植物中 ,有 5种植物的干重热值和去灰分热值的地区差异与平均值一致 ,即武汉 >天津 ,只有刺槐和白三叶例外。     

Local values for harvested forest plants in Madre de Dios,Peru: Towards a more contextualised interpretation of quantitative ethnobotanical data

This study builds on earlier quantitative ethnobotanical studies to develop an approach which represents local values for useful forest species, in order to explore factors affecting those values. The method, based on respondents ranking of taxa, compares favourably with more time-consuming quantitative ethnobotanical techniques, and allows results to be differentiated according to social factors (gender and ethnic origin), and ecological and socio-economic context. We worked with 126 respondents in five indigenous and five immigrant communities within a forest-dominated landscape in the Peruvian Amazonia. There was wide variability among responses, indicating a complex of factors affecting value. The most valued family is Arecaceae, followed by Fabaceae and Moraceae. Overall, fruit and non-commercialised construction materials predominate but women tend to value fruit and other non-timber species more highly than timber, while the converse is shown by men. Indigenous respondents tend to value more the species used for fruit, domestic construction and other NTFPs, while immigrants tend to favour commercialised timber species. Across all communities, values are influenced by both markets and the availability of the taxa; as the favourite species become scarce, others replace them in perceived importance. As markets become more accessible, over-exploitation of the most valuable species and livelihood diversification contribute to a decrease in perceived value of the forest.     

Our view of islands: Joining the values of science and society

Both the public and the scientific perception of an island's value are important in deciding its future, with regard to the levels of access, protection and funding for research. There is a popular belief that the preservation of islands equates to the slightly idiosyncratic conservation of unique remote habitats, where the value of any island is its isolation. However, by understanding how scientists use islands, a different picture emerges; islands may be seen also as integrated, or representative fragments of the world that contribute to biodiversity and scientific theory far beyond their narrow geographical boundaries. Here, we broadly review the full scope of values science places on islands. We resolve four central perspectives by which scientists view islands, based on how islands are incorporated into their research: (i) species‐level studies; (ii) island‐level studies; (iii) islands as model systems; and (iv) islands as part of a global network. Recognising this diverse value system helps enlarge our understanding of islands and reforges their importance to the public and policy makers.     

Biodiversity and environmental values: in search of a universal earth ethic

While biodiversity protection has become a widely accepted goal of environmental protectionists, no such agreement exists regarding why it is important. Two, competing theories of natural value – here called ‘Economism’ and ‘Intrinsic Value Theory’ – are often cited to support the goal. Environmentalists, who have recently proposed the articulation of a universal ‘Earth Charter’ to express the shared values humans derive from nature, have cited both of these theories as support for biodivesity protection. Unfortunately these theories, which are expressed as polar opposites, do not work well together and the question arises: is there a shared value that humans place on nature? It is argued that these two value theories share four questionable assumptions: (1) a sharp distinction between ‘intrinsic’ and ‘instrumental’ value; (2) an entity orientation; (3) moral monism; and (4) placeless evaluation. If these four assumptions are denied, an alternative value system emerges which recognizes a continuum of ways humans value nature, values processes rather than only entities, is pluralistic, and values biodiversity in place. An alternative theory of value, which emphasizes protecting processes rather than protecting objects, and which values nature for the creativity of its processes, is proposed as a more attractive theory for expressing the universal values of nature that should motivate an Earth Charter and the goal of biodiversity protection.     

Recognition of Aboriginal rights, interests and values in river research and management: Perspectives from northern Australia

Summary Aboriginal people perceive land and water as equal components of country, and hold distinct perspectives on water relating to identity and attachment to place, environmental knowledge, resource security, and the exercise of custodial responsibilities to manage interrelated parts of customary estates. This paper documents Aboriginal perspectives from certain areas in northern Australia, defined as the region of tropical savannas stretching from Townsville to Broome, and offers a number of suggestions for improving current knowledge of Aboriginal values and Aboriginal participation rates in water and catchment management. The paper highlights the cultural significance of rivers and water in selected northern regions, and provides a preliminary outline of research and management priorities as determined by key north Australian Aboriginal land management organizations. Priorities include developing the capacity for collaborative aquatic resource management, conservation of traditional ecological knowledge, riparian resource inventories and threat assessment, as well as improved Aboriginal participation in catchment management and water policy. Although there is a strong north Australian focus to this paper, the issues raised are relevant to water and natural resource management policy throughout Australia.     

Sharing digital micrographs and other data files between computers

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.