The unholy trinity: taxonomy, species delimitation and DNA barcoding

Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the 'DNA barcoding' initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings--Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'.     

Who learns from whom? Supporting users and developers of a major biodiversity e-infrastructure

Support systems play an important role for the communication between users and developers of software. We studied two support systems, an issues tracker and an email service available for Scratchpads, a Web 2.0 social networking tool that enables communities to build, share, manage and publish biodiversity information on the Web. Our aim was to identify co-learning opportunities between users and developers of the Scratchpad system by asking which support system was used by whom and for what type of questions. Our results show that issues tracker and emails cater to different user mentalities as well as different kind of questions and suggest ways to improve the support system as part of the development under the EU funded ViBRANT programme.     

Biodiversity information platforms: From standards to interoperability

One of the most serious bottlenecks in the scientific workflows of biodiversity sciences is the need to integrate data from different sources, software applications, and services for analysis, visualisation and publication. For more than a quarter of a century the TDWG Biodiversity Information Standards organisation has a central role in defining and promoting data standards and protocols supporting interoperability between disparate and locally distributed systems.Although often not sufficiently recognized, TDWG standards are the foundation of many popular Biodiversity Informatics applications and infrastructures ranging from small desktop software solutions to large scale international data networks. However, individual scientists and groups of collaborating scientist have difficulties in fully exploiting the potential of standards that are often notoriously complex, lack non-technical documentations, and use different representations and underlying technologies. In the last few years, a series of initiatives such as Scratchpads, the EDIT Platform for Cybertaxonomy, and biowikifarm have started to implement and set up virtual work platforms for biodiversity sciences which shield their users from the complexity of the underlying standards. Apart from being practical work-horses for numerous working processes related to biodiversity sciences, they can be seen as information brokers mediating information between multiple data standards and protocols.The ViBRANT project will further strengthen the flexibility and power of virtual biodiversity working platforms by building software interfaces between them, thus facilitating essential information flows needed for comprehensive data exchange, data indexing, web-publication, and versioning. This work will make an important contribution to the shaping of an international, interoperable, and user-oriented biodiversity information infrastructure.     

Ethics and Epistemology in Big Data Research

Biomedical innovation and translation are increasingly emphasizing research using “big data.” The hope is that big data methods will both speed up research and make its results more applicable to “real-world” patients and health services. While big data research has been embraced by scientists, politicians, industry, and the public, numerous ethical, organizational, and technical/methodological concerns have also been raised. With respect to technical and methodological concerns, there is a view that these will be resolved through sophisticated information technologies, predictive algorithms, and data analysis techniques. While such advances will likely go some way towards resolving technical and methodological issues, we believe that the epistemological issues raised by big data research have important ethical implications and raise questions about the very possibility of big data research achieving its goals.     

La collaboration entre les taxonomistes et les groupes de travail de la C.I.L.B.

Summary The author examines in his report some aspects of the relations existing between the ecologists of the C.I.L.B. working teams and the taxonomists which collaborate with the identification centre, and between these taxonomists and the identification centre itself. The collaboration between taxonomists and ecologists must certainly be encouraged by the C.I.L.B., especially with regard to those biological control projects such as the Olive fly and the San Jose Scale, where behavioural caracters of the parasitic species may be determinant for their identification. Emphasis is given to the importance of the behavioural caracters in taxonomy and examples of this are reported. The collaboration between taxonomists and the identification centre of the C.I.L.B. would be favoured through the following: 1. The establishment of a card file at the C.I.L.B. head-quarters on the entomophagous insect species and their known hosts for a future publication of a synoptic catalog for the palaearctic region; 2. The institution of fellowships for taxonomists to study Museum collections; 3. The establishment of a homotype collection at the C.I.L.B. headquarters, which will constitute, with the file card system, a solid base for the future development of taxonomic work; 4. The reservation of a day for discussions about nomenclature questions at every C.I.L.B. meeting of taxonomists. The author recommends to address reprints concerning the taxonomy and systematic of entomophagous species to the C.I.L.B. headquaters (Entomologisches Institut der E.T.H., Universit?tstrasse 2, Zürich 6, Switzerland) for the establishment of an extensive reference collection to be used for publication of the bibliography on this subject.      

Digital biology: an emerging and promising discipline

This article examines the role of computation and quantitative methods in modern biomedical research to identify emerging scientific, technical, policy and organizational trends. It identifies common concerns and practices in the emerging community of computationally-oriented bio-scientists by reviewing a national symposium, Digital Biology: the Emerging Paradigm, held at the National Institutes of Health in Bethesda, Maryland, November 6th and 7th 2003. This meeting showed how biomedical computing promises scientific breakthroughs that will yield significant health benefits. Three key areas that define the emerging discipline of digital biology are: scientific data integration, multi-scale modeling and networked science. Each area faces unique technical challenges and information policy issues that must be addressed as the field matures. Here we summarize the emergent challenges and offer suggestions to academia, industry and government on how best to expand the role of computation in their scientific activities.     

Data issues in the life sciences

We review technical and sociological issues facing the Life Sciences as they transform into more data-centric disciplines - the "Big New Biology". Three major challenges are: 1) lack of comprehensive standards; 2) lack of incentives for individual scientists to share data; 3) lack of appropriate infrastructure and support. Technological advances with standards, bandwidth, distributed computing, exemplar successes, and a strong presence in the emerging world of Linked Open Data are sufficient to conclude that technical issues will be overcome in the foreseeable future. While motivated to have a shared open infrastructure and data pool, and pressured by funding agencies in move in this direction, the sociological issues determine progress. Major sociological issues include our lack of understanding of the heterogeneous data cultures within Life Sciences, and the impediments to progress include a lack of incentives to build appropriate infrastructures into projects and institutions or to encourage scientists to make data openly available.     

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

Fungal research is experiencing a new wave of methodological improvements that most probably will boost mycology as profoundly as molecular phylogeny has done during the last 15 years. Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research. In order to realise the full potential of these exciting techniques by accelerating biodiversity assessments, identification procedures of fungi need to be adapted to the emerging demands of modern large-scale ecological studies. But how should fungal species be identified in the near future? While the answer might seem trivial to most microbiologists, taxonomists working with fungi may have other views. In the present review, we will analyse the state of the art of the so-called barcoding initiatives in the light of fungi, and we will seek to evaluate emerging trends in the field. We will furthermore demonstrate that the usability of DNA barcoding as a major tool for identification of fungi largely depends on the development of high-quality sequence databases that are thoroughly curated by taxonomists and systematists.     

In reply to hertwich & pease, Int. J. LCA 3 (4) 180 — 181, “ISO 14042 restricts use and development of impact assessment”

Life Cycle Impact Assessment describes indicators and does not predict actual impacts. The value of an LCA is its comprehensive review of all stages of a product’s life cycle and its synoptic view of all relevant environmental issues. The current version of the 14042 draft describes the uniqueness of Life Cycle Impact Assessment approach which is distinct from other assessment techniques. The wording was designed to help users of the standard understand how and why LCIA is distinct from other assessment methods. In closing, we would like to highlight our opinion that the present document on the level of a DIS is sound, stable and practical within the ISO 14040 series of standards. We do not agree withHertwich & Pease that the present document prevents the use of LCIA. It makes a choice regarding the exclusion of weighting across categories in order to prevent misuse in deriving inappropriate claims. And for characterisation it has achieved a well founded synthesis. In addition, we strongly believe that this standard will stimulate the international scientific discussion of LCA and will substantially contribute to enhanced and more valuable applications of LCA in the future.     

Current progress in DNA barcoding and future implications for entomology

DNA barcoding is a technique for identifying organisms based on a short, standardized fragment of genomic DNA. The standardized sequence region is called a DNA barcode because it is like a barcode tag for each taxon. Since the proposition of this concept and the launch of a large project named the Barcode of Life, this simple technique has attracted attention from taxonomists, ecologists, conservation biologists, agriculturists, plant‐quarantine officers and others, and the number of studies using the DNA barcode has rapidly increased. The extreme diversity of insects and their economical, epidemiological and agricultural importance have made this group a major target of DNA barcoding. However, there is some controversy about the utility of DNA barcoding. In this review, we present an overview of DNA barcoding and its application to entomology. We also introduce current advances and future implications of this promising technique.     

The need for a more effective biological nomenclature for the 21st century

HAWKSWORTH, D. L., 1992. The need for a more effective biological nomenclature for the 21st century. The procedures of biological nomenclature are now under immense pressure to change. Users are frustrated by the instability of names and lack of consensus, and increasingly undertake work previously the province of taxonomists; data are presented to show they tend to ignore unwelcome changes. Taxonomists themselves are deflected from both systematic and phylogenetic investigations, and documenting the world's biodiversity, by nomenclatural matters. A survey of 60 U.K. botanical taxonomists revealed that about half spent 10–75% of their research time on nomenclatural matters; extrapolated to the U.K. as a whole, botanical nomenclature could occupy up to 52 full-time posts at a cost of £ 1.3 million. Further, an analysis of 15 monographs of fungal genera showed that overall 85% of the names investigated were not accepted. The major problems to confront relate to concepts of priority, effective and valid publication, illegitimacy, types, ambiregnal organisms and the decision-making bodies. While most of these issues have been overcome by bacteriologists, only now are those concerned with botanical and zoological nomenclature starting to tackle them in earnest. A more effective biological nomenclature could be produced by extending the concept of lists of nomenclaturally protected names. This would resolve questions of effective and valid publication, priority, and application. Such lists would primarily assist taxonomists by dealing with much of the nomenclatural ‘noise’ of the past. Registration procedures are needed to complement such lists for names introduced in the future. The need for standard names and classifications fixed for limited periods is increasingly being met by specialist user groups and also concerns some taxonomists, but is best handled outside formal systems by appropriate specialist bodies. Increased harmonization of the Codes is possible when facing common problems and essential to resolve the difficulties posed by ambiregnal organisms. The image of taxonomy is adversely affected by unsatisfactory nomenclatural systems. Taxonomists should be responsible and refrain from changing names only for nomenclatural reasons while these matters are in discussion. Users and taxonomists need to work with nomenclaturalists to improve the effectiveness of biological nomenclature, if they are to ensure that it will fulfil both their requirements in the 21st century. The prospects for systematics are bleak if it fails to consummate the dual responsibilities of scientific endeavour and user requirements     

Photon-correlation spectroscopy of proteins

The works in the field of photon-correlation spectroscopy of proteins are considered from the field origination until the 2001 year inclusive. The certain part of the quoted references is presented by the works of the authors. The survey includes the photon-correlation spectroscopy physical principles, the methods of technical realization, the optical schemes optimization, the algorithms of the obtained information processing. The numerous examples are given for the structural-dynamics problems solution by the photon-correlation spectroscopy method. Bibliography contains 165 references.     

Evolution of neurodegeneration

A number of neurodegenerative diseases principally affect humans as they age and are characterized by the loss of?specific groups of neurons in different brain regions. Although these disorders are generally sporadic, it is now clear that many of them have a substantial genetic component. As genes are the raw material with which evolution works, we might benefit from understanding these genes in an evolutionary framework. Here, I will discuss how we can understand whether evolution has shaped genes involved in neurodegeneration and the implications for practical issues, such as our choice of model systems for studying these diseases, and more theoretical concerns, such as the level of selection against these phenotypes.     

中国植物分类学者的历史与现状

中国植物资源丰富, 长期以来被外国人所关注和研究。直到1916年, 中国植物分类学者才开始独立研究本国植物, 并经历了从民国时期开始自立、到1949年后自主完成《中国高等植物图鉴》《中国植物志》等国家级和相对完整的地方植物志以及中外合作完成英文版的国家植物志Flora of China、再到21世纪新一代学者每年更新《中国生物物种名录》并且开始主导国际性植物分类学研究工作等3个主要时期。统计表明, 超过3,000位中国学者参与过植物命名或植物名称处理等命名相关工作, 近些年更是达到每年新增100人左右的新高。但这种繁荣局面与中国植物分类学的衰退状况彼此矛盾。为了解释这个矛盾, 结合对历史回顾的深入分析说明, 真正能够反映分类学发展程度的量化指标应当是“活跃”分类学者数目。这个数目在21世纪停滞不前, 表明当今的分类学人才队伍建设仍存在不少问题, 特别是新分类群的发表与系统学研究脱节, 对分子系统学证据的应用仍有不足, 以及科研评价体系偏重于论文影响因子等。本文因此提出了当今分类学者应该具备的6条技能标准: (1)具有科学精神和全球视野; (2)掌握学科内知识; (3)掌握学科外知识; (4)具备野外工作技能; (5)具备标本馆和实验室工作技能; (6)掌握文献和数据库检索技能。     

Genome-wide mRNA profiling: impact on compound evaluation and target identification in anti-bacterial research

Array-based mRNA profiling offers a variety of opportunities to address different issues relevant to anti-bacterial research. The technique can be used to investigate the mode of action of antibiotics, bacterial resistance mechanisms and virulence factors, and to identify novel targets. This review discusses recent developments of this highly innovative field of technology with respect to technical requirements and experimental design. Several applications are described in which bacterial mRNA profiling has already been successfully performed, illustrating how the generation of large numbers of diverse datasets can be used as a powerful tool for evaluating anti-bacterial compounds and consequent counteracting mechanisms in the cell.     

Morphometrics of a neotropical sandfly subspecies, Lutzomyia carrerai thula

In spite of obvious and frequently observed morphological variation in geographic populations of sand flies, taxonomists are reluctant to create subspecies. In doing so they avoid confusion caused by the accumulation of new taxa, but they also obscure natural processes, some of them related to probable species emergence. We investigated here how far the partitioning of size, shape and form could be a relevant technique for exploring early evolutionary processes. We used a typical case of species, subspecies and cryptic species among three related taxa: Lutzomyia carrerai, its subspecies L. carrerai thula and L. yucumensis, a cryptic species of L. carrerai. Univariate and multivariate metric analyses showed global size differences, even between sympatric taxa (L. carrerai and L. yucumensis). When allometric effects were discounted, the subspecies L. c. thula still disclosed important differences from its putative type species, more pronounced than those existing between the two cryptic species, L. yucumensis and L. carrerai. A similar result was obtained after removing isometric size. These analyses question the validity of L. carrerai thula as a subspecies, and show that morphometrics may be a useful tool for separating simple geographic variation from evolutionary divergence.     

Fish haematology-A bibliography

Over 900 references have been documented concerning Fish Haematology. This bibliography, it is hoped, will be of assistance to research workers particularly in their preliminary library search.     

Evolution and self-assembly of protocells

Cells define the minimal building blocks of life. How cellular life emerged and evolved implies to cross the boundary between living and nonliving matter. Here we explore this problem by presenting several relevant components of the whole picture involving chemistry, physics and natural selection. Available evidence suggests that the basic logic of life can be understood and eventually translated into synthetic forms of cellular life. A simple, physically sound model of information-free protocell replication suggests that the basic logic of how to couple metabolism and container can be more relevant than the specific set of parameters used, thus indicating that the emergence of cells might have been easier than we would expect.