Scientific statistics and graphics on the Macintosh

The personal computer has become commonplace on the desk of most scientists. As hardware costs have plummeted, software capabilities have expanded enormously, permitting the scientist to examine extremely large datasets in novel ways. Advances in networking now permit rapid transfer of large datasets, which can often be used unchanged from one machine to the next. In spite of these significant advances, many scientists still use their personal computers only for word processing or e-mail, or as "dumb terminals". Many are simply unaware of the richness of software now available to statistically analyze and display scientific data in highly innovative ways. This paper presents several examples drawn from actual climate data analysis that illustrate some novel and practical features of several widely-used software packages for Macintosh computers.

Paciano II: the report of a conversation on whaling and science, 1-3 March 2008 (Paciano, Umbria)

In 2006 the UK-based charity, Global Ocean, with local support from the Third Millennium Foundation, convened a Conversation among specialists about the problems facing the conservation of whales. Called "A consultation on whaling", this gathering was held in the ancient village of Paciano, in Umbria near the border with Tuscany, 15 – 17 October 2006. There were 15 participants from 11 countries. Dr Kees Lankester served as moderator. The outcome was an Aide Memoire which served to guide the participants in the run-up to the 2007 meeting of the International Whaling Commission (IWC), held in Anchorage, Alaska, in June. One point of agreement was that a second consultation should be held in the months following the Anchorage meeting, involving some but not necessarily all of the participants in the first, but concentrating this time on scientific issues – especially those encountered in the Scientific Committee of the IWC –with particular attention to informing a wider public about those scientific activities in relation to the problems confronting the IWC and the views of scientists about them. This document is the report of that Conversation, referred to as Paciano II. The moderator was Dr Giuseppe Notarbartolo di Sciara and the Report was written by Kieran Mulvaney in consultation with all participants, and with reference to an Aide Memoire prepared by the Rapporteur, Dr Russell Leaper. The sponsor and organisers have agreed with the general sentiment expressed by participants in Paciano II that further such conversations should be held at roughly yearly intervals and they will try to satisfy that desire. Although these future gatherings would be concerned with the living ocean they would not necessarily be restricted in future to consideration of whales and whaling. Discussions are on-going for selection of a theme which is of both scientific interest and practical concern for conservation of marine life and management of the uses of ocean space. (Document has 18 pages)

Paciano II: a report of a conversation on whaling and science, 1-3 March 2008

In 2006 the UK-based charity, Global Ocean, with local support from the Third Millennium Foundation, convened a Conversation among specialists about the problems facing the conservation of whales. Called "A consultation on whaling", this gathering was held in the ancient village of Paciano, in Umbria near the border with Tuscany, 15 – 17 October 2006. There were 15 participants from 11 countries. Dr Kees Lankester served as moderator. The outcome was an Aide Memoire which served to guide the participants in the run-up to the 2007 meeting of the International Whaling Commission (IWC), held in Anchorage, Alaska, in June. One point of agreement was that a second consultation should be held in the months following the Anchorage meeting, involving some but not necessarily all of the participants in the first, but concentrating this time on scientific issues – especially those encountered in the Scientific Committee of the IWC –with particular attention to informing a wider public about those scientific activities in relation to the problems confronting the IWC and the views of scientists about them. This document is the report of that Conversation, referred to as Paciano II. The moderator was Dr Giuseppe Notarbartolo di Sciara and the Report was written by Kieran Mulvaney in consultation with all participants, and with reference to an Aide Memoire prepared by the Rapporteur, Dr Russell Leaper. The sponsor and organisers have agreed with the general sentiment expressed by participants in Paciano II that further such conversations should be held at roughly yearly intervals and they will try to satisfy that desire. Although these future gatherings would be concerned with the living ocean they would not necessarily be restricted in future to consideration of whales and whaling. Discussions are on-going for selection of a theme which is of both scientific interest and practical concern for conservation of marine life and management of the uses of ocean space. (19 page document)

Stock assessment of loggerhead and leatherback sea turtles and An assessment of the impact of the pelagic longline fishery on the loggerhead and leatherback sea turtles of the Western North Atlantic

On September 7, 2000 the National Marine Fisheries Service announced that it was reinitiating consultation under Section 7 of the Endangered Species Act on pelagic fisheries for swordfish, sharks, tunas, and billfish. 1 Bycatch of a protected sea turtle species is considered a take under the Endangered Species Act (PL93-205). On June 30, 2000 NMFS completed a Biological Opinion on an amendment to the Highly Migratory Pelagic Fisheries Management Plan that concluded that the continued operation of the pelagic longline fishery was likely to jeopardize the continued existence of loggerhead and leatherback sea turtles.2 Since that Biological Opinion was issued NMFS concluded that further analyses of observer data and additional population modeling of loggerhead sea turtles was needed to determine more precisely the impact of the pelagic longline fishery on turtles. 3,4 Hence, the reinitiation of consultation. The documents that follow constitute the scientific review and synthesis of information pertaining to the narrowly defined reinitiation of consultation: the impact of the pelagic longline fishery on loggerhead and leatherback sea turtles The document is in 3 parts, plus 5 appendices. Part I is a stock assessment of loggerhead sea turtles of the Western North Atlantic. Part II is a stock assessment of leatherback sea turtles of the Western North Atlantic. Part III is an assessment of the impact of the pelagic longline fishery on loggerhead and leatherback sea turtles of the Western North Atlantic. These documents were prepared by the NMFS Southeast Fisheries Science Center staff and academic colleagues at Duke University and Dalhousie University. Personnel involved from the SEFSC include Joanne Braun-McNeill, Lisa Csuzdi, Craig Brown, Jean Cramer, Sheryan Epperly, Steve Turner, Wendy Teas, Nancy Thompson, Wayne Witzell, Cynthia Yeung, and also Jeff Schmid under contract from the University or Miami. Our academic colleagues, Ransom Myers, Keith Bowen, and Leah Gerber from Dalhousie University and Larry Crowder and Melissa Snover from Duke University, also recipients of a Pew Charitable Trust Grant for a Comprehensive Study of the Ecological Impacts of the Worldwide Pelagic Longline Industry, made significant contributions to the quantitative analyses and we are very grateful for their collaboration. We appreciate the reviews of the stock definition sections on loggerheads and leatherbacks by Brian Bowen, University of Florida, and Peter Dutton, National Marine Fisheries Service Southwest Fisheries Science Center, respectively, and the comments of the NMFS Center of Independent Experts reviewers Robert Mohn, Ian Poiner, and YouGan Wang on the entire document. We also wish to acknowledge all the unpublished data used herein which were contributed by many researchers, especially the coordinators and volunteers of the nesting beach surveys and the sea turtle stranding and salvage network and the contributors to the Cooperative Marine Turtle Tagging Program. (PDF contains 349 pages)

Multi-species and multi-interest management: An ecosystem approach to market squid (Loligo opalescens) harvest in California

Market squid (Loligo opalescens) plays a vital role in the California ecosystem and serves as a major link in the food chain as both a predator and prey species. For over a century, market squid has also been harvested off the California coast from Monterey to San Pedro. Expanding global markets, coupled with a decline in squid product from other parts of the world, in recent years has fueled rapid expansion of the virtually unregulated California fishery. Lack of regulatory management, in combination with dramatic increases in fishing effort and landings, has raised numerous concerns from the scientific, fishing, and regulatory communities. In an effort to address these concerns, the National Oceanic and Atmospheric Administration’s (NOAA) Channel Islands National Marine Sanctuary (CINMS) hosted a panel discussion at the October 1997 California Cooperative Oceanic and Fisheries Investigations (CalCOFI) Conference; it focused on ecosystem management implications for the burgeoning market squid fishery. Both panel and audience members addressed issues such as: the direct and indirect effects of commercial harvesting upon squid biomass; the effects of harvest and the role of squid in the broader marine community; the effects of environmental variation on squid population dynamics; the sustainability of the fishery from the point of view of both scientists and the fishers themselves; and the conservation management options for what is currently an open access and unregulated fishery. Herein are the key points of the ecosystem management panel discussion in the form of a preface, an executive summary, and transcript. (PDF contains 33 pages.)

Integrated Sensor Systems for Vessels of Opportunity, National Oceanographic Centre, Southampton, UK, October 10-12,2006 : workshop proceedings

The use of self-contained, low-maintenance sensor systems installed on commercial vessels is becoming an important monitoring and scientific tool in many regions around the world. These systems integrate data from meteorological and water quality sensors with GPS data into a data stream that is automatically transferred from ship to shore. To begin linking some of this developing expertise, the Alliance for Coastal Technologies (ACT) and the European Coastal and Ocean Observing Technology (ECOOT) organized a workshop on this topic in Southampton, United Kingdom, October 10-12, 2006. The participants included technology users, technology developers, and shipping representatives. They collaborated to identify sensors currently employed on integrated systems, users of this data, limitations associated with these systems, and ways to overcome these limitations. The group also identified additional technologies that could be employed on future systems and examined whether standard architectures and data protocols for integrated systems should be established. Participants at the workshop defined 17 different parameters currently being measured by integrated systems. They identified that diverse user groups utilize information from these systems from resource management agencies, such as the Environmental Protection Agency (EPA), to local tourism groups and educational organizations. Among the limitations identified were instrument compatibility and interoperability, data quality control and quality assurance, and sensor calibration andlor maintenance frequency. Standardization of these integrated systems was viewed to be both advantageous and disadvantageous; while participants believed that standardization could be beneficial on many levels, they also felt that users may be hesitant to purchase a suite of instruments from a single manufacturer; and that a "plug and play" system including sensors from multiple manufactures may be difficult to achieve. A priority recommendation and conclusion for the general integrated sensor system community was to provide vessel operators with real-time access to relevant data (e.g., ambient temperature and salinity to increase efficiency of water treatment systems and meteorological data for increased vessel safety and operating efficiency) for broader system value. Simplified data displays are also required for education and public outreach/awareness. Other key recommendations were to encourage the use of integrated sensor packages within observing systems such as 100s and EuroGOOS, identify additional customers of sensor system data, and publish results of previous work in peer-reviewed journals to increase agency and scientific awareness and confidence in the technology. Priority recommendations and conclusions for ACT entailed highlighting the value of integrated sensor systems for vessels of opportunity through articles in the popular press, and marine science. [PDF contains 28 pages]

Cruise report: regional assessment of ecosystem condition and stressor impacts along the northeastern Gulf of Mexico shelf; NOAA Ship Nancy Foster NF-10-09-RACOW (August 13-21, 2010)

This cruise report is a summary of a field survey conducted along the continental shelf of the northeastern Gulf of Mexico (GOM), encompassing 70,062 square kilometers of productive marine habitats located between the Mississippi Delta and Tampa Bay, August 13–21, 2010 on NOAA Ship Nancy Foster Cruise NF-10-09-RACOW. Synoptic sampling of multiple ecological indicators was conducted at each of 50 stations throughout these waters using a random probabilistic sampling design. At each station samples were collected for the analysis of benthic community structure and composition; concentrations of chemical contaminants (metals, pesticides, TPHs, PAHs, PCBs, PBDEs) in sediments and target demersal biota; sediment toxicity; nutrient and chlorophyll levels in the water column; and other basic habitat characteristics such as depth, salinity, temperature, dissolved oxygen, turbidity, pH, CDOM fluorescence, sediment grain size, and organic carbon content. Discrete water samples were collected just below the sea surface, in addition to any deeper subsurface depths where there was an occurrence of suspicious CDOM fluorescence signals, and analyzed for total BTEX/TPH and carcinogenic PAHs using immunoassay test kits. Other indicators of potential value from a human-dimension perspective were also recorded, including presence of any vessels, oil rigs, surface trash, visual oil sheens in sediments or water, marine mammals, or noxious/oily sediment odors. The overall purpose of the survey was to collect data to assess the status of ecosystem condition and potential stressor impacts throughout the region, based on these various indicators and corresponding management thresholds, and to provide this information as a baseline for determining how such conditions may be changing with time. In addition to the original project goals, both the scientific scope and general location of this project are relevant to addressing potential ecological impacts of the Deepwater Horizon oil spill. While sample analysis is still ongoing, a few preliminary results and observations are reported here. A final report will be completed once all data have been processed.

Scientific assessment of freshwater harmful algal blooms

In 2004, Congress reauthorized the Harmful Algal Bloom and Hypoxia Research and Control Act of 1998 with the Harmful Algal Bloom and Hypoxia Amendments Act (HABHRCA 2004). The 2004 legislation required the generation of five reports, including this "Scientific Assessment of Freshwater Harmful Algal Blooms." HABHRCA 2004 stipulates that this report 1) examine the causes, consequences, and economic costs of freshwater HABs, 2) establish priorities and guidelines for a research program on freshwater HABs, and 3) make recommendations to improve coordination among Federal agencies with respect to research on HABs in freshwater environments. This report is divided into five chapters: Chapter 1 provides the legislative background and process for developing the report, Chapter 2 describes the problem of freshwater and inland HABs in the United States, Chapter 3 outlines the current Federal efforts in freshwater and inland HAB research and response, Chapter 4 discusses the future research priorities, and Chapter 5 delineates opportunities for coordination to advance research efforts. The document is based, in large part, on the proceedings (Hudnell 2008) of the International Symposium on Cyanobacterial Harmful Algal Blooms, a meeting convened by EPA and sponsored by a variety of Federal agencies, to describe current scientific knowledge and identify priorities for future research on CyanoHABs. This report offers a plan for coordinating the important research that is currently ongoing in the United States and for guiding future research directions for Federal programs as well as for state, local, private, and academic institutions in order to maximize advancements. To this end, the Interagency Working Group on Harmful Algal Blooms, Hypoxia, and Human Health (IWG-4H) identifies seven priorities, all of equal weight, for freshwater HAB research and response. These priorities represent research areas where there is the greatest potential for progress in freshwater HAB research. This report does not attempt to assess the relative importance of freshwater HAB research compared to other research areas or other priorities for Federal or state investment.

Major and trace element analytical methods of the National Status and Trends Program: 2000-2006

This document contains analytical methods that detail the procedures for determining major and trace element concentrations in bivalve tissue and sediment samples collected as part of the National Status and Trends Program (NS&T) for the years 2000-2006. Previously published NOAA Technical Memoranda NOS ORCA 71 and 130 (Lauenstein and Cantillo, 1993; Lauenstein and Cantillo, 1998) detail trace element analyses for the years 1984-1992 and 1993-1996, respectively, and include ancillary, histopathology, and contaminant (organic and trace element) analytical methods. The methods presented in this document for trace element analysis were utilized by the NS&T Mussel Watch and Bioeffects Projects. The Mussel Watch Project has been monitoring contaminants in bivalves and sediment for over 20 years, and is the longest active contaminant monitoring program operating in U.S. costal waters. Approximately 280 Mussel Watch sites are monitored on biennial and decadal timescales using bivalve tissue and sediment, respectively. The Bioeffects Project applies the sediment quality approach, which uses sediment contamination measurements, toxicity tests and benthic macroinfauna quantification to characterize pollution in selected estuaries and coastal embayments. Contaminant assessment is a core function of both projects. Although only one contract laboratory was used by the NS&T Program during the specified time period, several analytical methods and instruments were employed. The specific analytical method, including instrumentation and detection limit, is noted for each measurement taken and can be found at http://NSandT.noaa.gov. The major and trace elements measured by the NS&T Program include: Al, Si, Cr, Mn, Fe, Ni, Cu, Zn, As, Se, Sn, Sb, Ag, Cd, Hg, Tl and Pb.

Fishes of Ceylon: a catalogue, key and bibliography

A knowledge of the specific composition of Ceylon fish fauna is essential to any programme of development of commercial fisheries, or the study of Ceylon's ichthyology and the need for cataloguing it has been keenly felt for many years. The need for cataloguing the whole of Ceylon's flora and fauna was stressed by the Natural Science Section of the Ceylon Association for the Advancement of Science during its 1952 annual sessions and it was then that the writer agreed to help satisfy this need by compiling an up-to-date check list of species of two families of fishes, the Clupeidae and the Carangidae, which are important in the beach seine fishery which he was studying at that time. In the course of this work it was decided to expand the check-list to make it comprehensive of all species of fish that have been recorded from Ceylon to date and to supply keys for their identification. This has involved a screening of the pioneer works of Bennet (1834) and Day (1878-1889) and the many subsequent references to Ceylon fish scattered through various scientific journals and other publications, some of them long out and now almost unobtainable.

Fisheries research component implementation status 1997 -2001 and workplans 2001-2003

The report covers the status of: the economic and ecological values of Lake Victoria; priority issues; the vision of the Fisheries Research Component; the objectives of the Fisheries Research Component under LVEMP to generate, package and disseminate scientific knowledge and build capacity.

A study on the piscifauna of the Idukki Reservoir and catchment area

From the area under report 17 species, 15 endemic and 2 exotic, of freshwater fish have been identified. Of these, 8 species are commonly found in the catches and are of fishery significance. The fact that small fish species which have no fishery importance also support life in other trophic levels of this ecosystem is well exemplified by the interaction of the birds and mammals with these species. A scientific management and monitoring of the reservoir waters as well as the remaining segments of forests are recommended to salvage the wild life and vegetation from a possible rapid deterioration within years.

Fishery resources: their exploitation, management and conservation in Africa

The beginning of the 20th century saw the discovery of Africa's vast natural resources. Not only did explorers "discover" lakes, rivers, forests and mountains but scientists and naturalists also "discovered what at that time were called new species of plants, fish and other animals. Thus scientific names were tagged to various species using the famed binomial nomenclature and immortalising the names of some of the people who first described those species. Africa of course abounds with thousands of different floral and faunal varieties and the early colonial scientists found the African environment lucrative fron the point of discovery of new species. This paper therefore attempts to descrihe the role science could only in the development and exploitation of one of Africa's renewable resources namely fisheries. This paper has attempted to expose the value of fish in human nutrition, provision of employment and uplifting of social and economic standards. The fishery resources of Africa are extensive and in the main not fully exploited. These resources like other natural resources are exhaustible although renewable. Efforts to exploit these resources must be encouraged but scientific planning and management of the resource is called for.

Evaluations of the pelagic resources in the Burundi waters of Lake Tanganyika and the evolution of the fisheries

The important pelagic fishery resources of northern Lake Tanganyika were identified after a preliminary scientific evaluation, and in Burundi, with governmental assistance they were rapidly developed and exploited more intensively until overfishing was thought to have occurred. At this point, legal measures were introduced in order to protect the resource by restricting fishing effort and maintaining the total yield near the apparent maximum sustained limit. Complementary biological research on the fish stocks did not accompany the rapid fishery development and now an intensive stock assessment programme has been launched by the Government and UNDP in order to define more precisely the available fish stocks and to consider, with the co-operation of the neighbouring lacustrine states, suitable ways of ensuring optimum levels of fish harvest from year to year.

Annual report 2005 - North Pacific Marine Science Organization (PICES). Fourteenth meeting, Vladivostok, Russia, September 29-October 9, 2005

Report of Opening Session (pdf 0.07 Mb) Report of Governing Council (pdf 0.2 Mb) Report of the Finance and Administration Committee (pdf 0.07 Mb) Reports of Science Board and Committees Science Board inter-sessional meeting (pdf 0.07 Mb) Science Board (pdf 0.1 Mb) Biological Oceanography Committee (pdf 0.2 Mb) Fishery Science Committee (pdf 0.04 Mb) Marine Environmental Quality Committee (pdf 0.06 Mb) MONITOR Technical Committee (pdf 0.05 Mb) Physical Oceanography and Climate Committee (pdf 0.06 Mb) Technical Committee on Data Exchange (pdf 0.04 Mb) Reports of Sections, Working and Study Groups Section on Ecology of harmful algal blooms in the North Pacific (pdf 0.03 Mb) Section on Carbon and Climate Working Group 18 on Mariculture in the 21st century - The intersection between ecology, socio-economics and production (pdf 0.06 Mb) Working Group 19 on Ecosystem-based management science and its application to the North Pacific (pdf 0.03 Mb) Reports of the Climate Change and Carrying Capacity Program Implementation Panel on the CCCC Program (pdf 0.04 Mb) CFAME Task Team (pdf 0.04 Mb) MODEL Task Team (pdf 0.04 Mb) Reports of Advisory Panels Advisory Panel on Iron Fertilization Experiment in the Subarctic Pacific Ocean (pdf 0.04 Mb) Advisory Panel on Marine Birds and Mammals (pdf 0.03 Mb) Advisory Panel on Micronekton Sampling Inter-Calibration experiment (pdf 0.05 Mb) Summary of Scientific Sessions and Workshops (pdf 0.2 Mb) Membership List (pdf 0.07 Mb) List of Participants (pdf 0.07 Mb) List of Acronyms (pdf 0.03 Mb)