Biological Platforms for Environmental Sensor technologies and their uses as indicators of the marine environment, Seward, Alaska, September 19-21, 2007: workshop proceedings

The Alliance for Coastal Technologies (ACT) Workshop entitled, "Biological Platforms as Sensor Technologies and their Use as Indicators for the Marine Environment" was held in Seward, Alaska, September 19 - 21,2007. The workshop was co-hosted by the University of Alaska Fairbanks (UAF) and the Alaska SeaLife Center (ASLC). The workshop was attended by 25 participants representing a wide range of research scientists, managers, and manufacturers who develop and deploy sensory equipment using aquatic vertebrates as the mode of transport. Eight recommendations were made by participants at the conclusion of the workshop and are presented here without prioritization: 1. Encourage research toward development of energy scavenging devices of suitable sizes for use in remote sensing packages attached to marine animals. 2. Encourage funding sources for development of new sensor technologies and animal-borne tags. 3. Develop animal-borne environmental sensor platforms that offer more combined systems and improved data recovery methodologies, and expand the geographic scope of complementary fixed sensor arrays. 4. Engage the oceanographic community by: a. Offering a mini workshop at an AGU ocean sciences conference for people interested in developing an ocean carbon program that utilizes animal-borne sensor technology. b. Outreach to chemical oceanographers. 5. Min v2d6.sheepserver.net e and merge technologies from other disciplines that may be applied to marine sensors (e.g. biomedical field). 6. Encourage the NOAA Permitting Office to: a. Make a more predictable, reliable, and consistent permitting system for using animal platforms. b. Establish an evaluation process. c. Adhere to established standards. 7. Promote the expanded use of calibrated hydrophones as part of existing animal platforms. 8. Encourage the Integrated Ocean Observing System (IOOS) to promote animal tracking as effective samplers of the marine environment, and use of animals as ocean sensor technology platforms. [PDF contains 20 pages]

Evaluating approaches and technologies for monitoring organic contaminants in the aquatic environment, Ann Arbor, MI, July 21-23, 2006: workshop proceedings

The Alliance for Coastal Technologies (ACT) convened a workshop on Evaluating Approaches and Technologies for Monitoring Organic Contaminants in the Aquatic Environment in Ann Arbor, MI on July 21-23, 2006. The primary objectives of this workshop were to: 1) identify the priority management information needs relative to organic contaminant loading; 2) explore the most appropriate approaches to estimating mass loading; and 3) evaluate the current status of the sensor technology. To meet these objectives, a mixture of leading research scientists, resource managers, and industry representatives were brought together for a focused two-day workshop. The workshop featured four plenary talks followed by breakout sessions in which arranged groups of participants where charged to respond to a series of focused discussion questions. At present, there are major concerns about the inadequacies in approaches and technologies for quantifying mass emissions and detection of organic contaminants for protecting municipal water supplies and receiving waters. Managers use estimates of land-based contaminant loadings to rivers, lakes, and oceans to assess relative risk among various contaminant sources, determine compliance with regulatory standards, and define progress in source reduction. However, accurately quantifying contaminant loading remains a major challenge. Loading occurs over a range of hydrologic conditions, requiring measurement technologies that can accommodate a broad range of ambient conditions. In addition, in situ chemical sensors that provide a means for acquiring continuous concentration measurements are still under development, particularly for organic contaminants that typically occur at low concentrations. Better approaches and strategies for estimating contaminant loading, including evaluations of both sampling design and sensor technologies, need to be identified. The following general recommendations were made in an effort to advance future organic contaminant monitoring: 1. Improve the understanding of material balance in aquatic systems and the relationship between potential surrogate measures (e.g., DOC, chlorophyll, particle size distribution) and target constituents. 2. Develop continuous real-time sensors to be used by managers as screening measures and triggers for more intensive monitoring. 3. Pursue surrogate measures and indicators of organic pollutant contamination, such as CDOM, turbidity, or non-equilibrium partitioning. 4. Develop continuous field-deployable sensors for PCBs, PAHs, pyrethroids, and emerging contaminants of concern and develop strategies that couple sampling approaches with tools that incorporate sensor synergy (i.e., measure appropriate surrogates along with the dissolved organics to allow full mass emission estimation).[PDF contains 20 pages]

Application of Drifting Buoy Technologies for Coastal Watershed and Ecosystem, Ann Arbor, Michigan, June 5-7,2005: workshop proceedings

The Alliance for Coastal Technologies (ACT) Partner University of Michigan convened a workshop on the Applications of Drifting Buoy Technologies for Coastal Watershed and Ecosystem Modeling in Ann Arbor, Michigan on June 5 to 7,2005. The objectives of the workshop were to: (1) educate potential users (managers and scientists) about the current capabilities and uses of drifting buoy technologies; (2) provide an opportunity for users (managers and scientists) to experience first hand the deployment and retrieval of various drifting buoys, as well as experience the capabilities of the buoys' technologies; (3) engage manufacturers with scientists and managers in discussions on drifting buoys' capabilities and their requirements to promote further applications of these systems; (4) promote a dialogue about realistic advantages and limitations of current drifting buoy technologies; and (5) develop a set of key recommendations for advancing both the capabilities and uses of drifting buoy technologies for coastal watershed and ecosystem modeling. To achieve these goals, representatives from research, academia, industry, and resource management were invited to participate in this workshop. Attendees obtained "hands on" experience as they participated in the deployment and retrieval of various drifting buoy systems on Big Portage Lake, a 644 acre lake northwest of Ann Arbor. Working groups then convened for discussions on current commercial usages and environmental monitoring approaches including; user requirements for drifting buoys, current status of drifting buoy systems and enabling technologies, and the challenges and strategies for bringing new drifting buoys "on-line". The following general recommendations were made to: 1). organize a testing program of drifting buoys for marketing their capabilities to resource managers and users. 2). develop a fact sheet to highlight the utility of drifting buoys. 3). facilitate technology transfer for advancements in drifter buoys that may be occurring through military funding and development in order to enhance their technical capability for environmental applications. (pdf contains 18 pages)

20th annual meeting of the WEFTA Working Group on Analytical Methods in Fish and Fishery Products and 3rd annual meeting of the WEFTA Working Group on Microbiology. A retrospect on 20 years

After 20 annual meetings it is worth to have a look back and to see how it has started. There has been very little collaboration on research projects between member institutes under the auspices of WEFTA, co-operation in more neutral areas of common interest was developed at an early stage. The area which has proved very fruitful is methodology. It was agreed that probably the best way to make progress was to arrange meetings at each laboratory in turn where experienced, practising scientists could describe in detail how they carried out analyses. In this way, difficulties could be demonstrated or uncovered, and the accuracy, precision, efficiency and cost of the methods used in different laboratories could be compared.

Workshop on climate change and salmon production, Vancouver, March 26-27, 1998: technical report

The Workshop on Climate Change and Salmon Production was held in Vancouver, Canada, 26-27 March 1998. The Workshop was organized and sponsored by the North Pacific Anadromous Fish Commission (NPAFC). Each Party to the Commission designated one scientist to the Workshop Steering Committee. Each member of the Steering Committee chaired one half-day session of the Workshop. All necessary arrangements were made by the NPAFC Secretariat in cooperation with the Steering Committee and the Canadian Party to the Commission. (PDF contains 60 pages) Over 70 scientists, industry representatives and fisheries officials attended the Workshop. There were 20 presentations of scientific papers followed by the discussion sessions. Extended abstracts are included in this Technical Report, which also contains opening address by the Chairman of the Steering Committee and short review of the Workshop by the Coordinator. The material presented in the Technical Report has not been peer reviewed and does not necessarily reflect the views of either the NPAFC or the Parties. The material has been edited by the technical editor for clarity and publication purposes only. Items in this Report should not be cited except as personal communication and with the author's permission.

Preliminary economic evaluation of 10 metre (LOA) shallow draft vessel in daily fishery, off Imo River, Cross River State

Scientists from the Institute with the collaboration of Food and Agricultural Organisation (FAO), Rome designed and built a 10-m (LOA) shallow draft vessel. The prototype vessel was tried at Uta-Ewa, Ikot Abasi, Cross River State. The paper deals with the preliminary economic analysis of the performance of prototype vessel. An analysis of the annual return has shown that 43.66% of the annual gross income was paid to labour; 15.91% was spent on repairs and replacements; 7.76% on fuel and lubricants; 24.38% on maintenance costs and the return of investment, 6.2%. This low return of investment is attributable to high percentage of labour costs as well as low fishing intensity

Commercial production of natural freshwater fish food

A review is made of some of the methods that can be used for mass cultivation of natural fish food and the types of organisms that are cultured, which include various algae and zooplankton. Some examples are given of successful case histories in the mass cultivation of natural fish food in order to stimulate the interest of Nigerian scientists on research activities of live fish food for use by fish farmers in the country

Aerodynamic characteristics research on wide-speed range waverider configuration

Waverider generated from a given flow field has a high lift-to-drag ratio because of attached bow shock on leading edge. However, leading edge blunt and off-design condition can make bow shock off leading edge and have unfavorable influence on aerodynamic characteristics. So these two problems have always been concerned as important engineering science issues by aeronautical engineering scientists. In this paper, through respectively using low speed and high speed waverider design principles, a wide-speed rang vehicle is designed, which can level takeoff and accelerate to hypersonic speed for cruise. In addition, sharp leading edge is blunted to alleviated aeroheating. Theoretical study and wind tunnel test show that this vehicle has good aerodynamic performance in wide-speed range of subsonic, transonic, supersonic and hypersonic speeds.

Whales and Sonar: Environmental Exemptions for the Navy's Mid-Frequency Active Sonar Training.

Mid-frequency active (MFA) sonar emits pulses of sound from an underwater transmitter to help determine the size, distance, and speed of objects. The sound waves bounce off objects and reflect back to underwater acoustic receivers as an echo. MFA sonar has been used since World War II, and the Navy indicates it is the only reliable way to track submarines, especially more recently designed submarines that operate more quietly, making them more difficult to detect. Scientists have asserted that sonar may harm certain marine mammals under certain conditions, especially beaked whales. Depending on the exposure, they believe that sonar may damage the ears of the mammals, causing hemorrhaging and/or disorientation. The Navy agrees that the sonar may harm some marine mammals, but says it has taken protective measures so that animals are not harmed. (PDF contains 20 pages)

Sentence comprehension before and after 1970: Topics, debates and techniques

[EN] Language Down the Garden Path traces the lines of research that grew out of Bever's classic paper. Leading scientists review over 40 years of debates on the factors at play in language comprehension, production, and acquisition (the role of prediction, grammar, working memory, prosody, abstractness, syntax and semantics mapping); the current status of universals and narrow syntax; and virtually every topic relevant in psycholinguistics since 1970. Written in an accessible and engaging style, the book will appeal to all those interested in understanding the questions that shaped, and are still shaping, this field and the ways in which linguists, cognitive scientists, psychologists, and neuroscientists are seeking to answer them.

Habitat enhancing marine structures: Creating habitat in urban waters

Although maritime regions support a large portion of the world’s human population, their value as habitat for other species is overlooked. Urban structures that are built in the marine environment are not designed or managed for the habitat they provide, and are built without considering the communities of marine organisms that could colonize them (Clynick et al., 2008). However, the urban waterfront may be capable of supporting a significant proportion of regional aquatic biodiversity (Duffy-Anderson et al., 2003). While urban shorelines will never return to their original condition, some scientists think that the habitat quality of urban waterfronts could be significantly improved through further research and some design modifications, and that many opportunities exist to make these modifications (Russel et al., 1983, Goff, 2008). Habitat enhancing marine structures (or HEMS) are a potentially promising approach to address the impact of cities on marine organisms including habitat fragmentation and degradation. HEMS are a type of habitat improvement project that are ecologically engineered to improve the habitat quality of urban marine structures such as bulkheads and docks for marine organisms. More specifically, HEMS attempt to improve or enhance the physical habitat that organisms depend on for survival in the inter- and sub-tidal waterfronts of densely populated areas. HEMS projects are targeted at areas where human-made structures cannot be significantly altered or removed. While these techniques can be used in suburban or rural areas restoration or removal is preferred in these settings, and HEMS are resorted to only if removal of the human-made structure is not an option. Recent research supports the use of HEMS projects. Researchers have examined the communities found on urban structures including docks, bulkheads, and breakwaters. Complete community shifts have been observed where the natural shoreline was sandy, silty, or muddy. There is also evidence of declines in community composition, ecosystem functioning, and increases in non-native species abundances in assemblages on urban marine structures. Researchers have identified two key differences between these substrates including the slope (seawalls are vertical; rocky shores contain multiple slopes) and microhabitat availability (seawalls have very little; rocky shores contain many different types). In response, researchers have suggested designing and building seawalls with gentler slopes or a combination of horizontal and vertical surfaces. Researchers have also suggested incorporating microhabitat, including cavities designed to retain water during low tide, crevices, and other analogous features (Chapman, 2003; Moreira et al., 2006) (PDF contains 4 pages)

Adapting to climate change: Combining economics and geomorphology in coastal policy

How is climate change affecting our coastal environment? How can coastal communities adapt to sea level rise and increased storm risk? These questions have garnered tremendous interest from scientists and policy makers alike, as the dynamic coastal environment is particularly vulnerable to the impacts of climate change. Over half the world population lives and works in a coastal zone less than 120 miles wide, thereby being continuously affected by the changes in the coastal environment [6]. Housing markets are directly influenced by the physical processes that govern coastal systems. Beach towns like Oak Island in North Carolina (NC) face severe erosion, and the tax assesed value of one coastal property fell by 93% in 2007 [9]. With almost ninety percent of the sandy beaches in the US facing moderate to severe erosion [8], coastal communities often intervene to stabilize the shoreline and hold back the sea in order to protect coastal property and infrastructure. Beach nourishment, which is the process of rebuilding a beach by periodically replacing an eroding section of the beach with sand dredged from another location, is a policy for erosion control in many parts of the US Atlantic and Pacific coasts [3]. Beach nourishment projects in the United States are primarily federally funded and implemented by the Army Corps of Engineers (ACE) after a benefit-cost analysis. Benefits from beach nourishment include reduction in storm damage and recreational benefits from a wider beach. Costs would include the expected cost of construction, present value of periodic maintenance, and any external cost such as the environmental cost associated with a nourishment project (NOAA). Federal appropriations for nourishment totaled $787 million from 1995 to 2002 [10]. Human interventions to stabilize shorelines and physical coastal dynamics are strongly coupled. The value of the beach, in the form of storm protection and recreation amenities, is at least partly capitalized into property values. These beach values ultimately influence the benefit-cost analysis in support of shoreline stabilization policy, which, in turn, affects the shoreline dynamics. This paper explores the policy implications of this circularity. With a better understanding of the physical-economic feedbacks, policy makers can more effectively design climate change adaptation strategies. (PDF contains 4 pages)

Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

Eliciting and using stakeholder input to guide Puget Sound nearshore restoration decisionmaking

The goal of the Puget Sound Nearshore Ecosystem Restoration Project (PSNERP) is to improve system-wide functionality of nearshorei ecosystem processes. To achieve that goal, PSNERP plans to strategically restore nearshore sites throughout Puget Sound. PSNERP scientists are assessing changes to the nearshore, and will recommend an environmentally strategic restoration portfolio. Yet, PSNERP also needs stakeholder input to design a socially strategic portfolio. This research investigates the values and preferences of stakeholders in the Whidbey Sub-Basin of Puget Sound to help PSNERP be both socially and environmentally strategic. This investigation may be repeated in the six other Puget Sound Sub-Basins. The results will guide restoration portfolio design and future stakeholder involvement activities. This study examines four areas of stakeholder values and preferences: 1) beliefs about the causes, solutions, and severity of nearshore problems; 2) priorities for nearshore features, shoreforms, developments, and restoration objectives; 3) thoughts about ecosystem servicesiii and trade-offs among them; and 4) visions of a future, restored Puget Sound nearshore and the role of science in attaining this vision. The study is framed by two hypotheses from the Advocacy Coalition Framework (ACF), which suggests that groups of policy advocates form around shared “policy core beliefs” which can transcend traditional categories of stakeholders.(PDF contains 3 pages)

Using climate extension to assist coastal decision-makers with climate adaptation

Coastal managers need accessible, trusted, tailored resources to help them interpret climate information, identify vulnerabilities, and apply climate information to decisions about adaptation on regional and local levels. For decades, climate scientists have studied the impacts that short term natural climate variability and long term climate change will have on coastal systems. For example, recent estimates based on Intergovernmental Panel on Climate Change (IPCC) warming scenarios suggest that global sea levels may rise 0.5 to 1.4 meters above 1990 levels by 2100 (Rahmstorf 2007; Grinsted, Moore, and Jevrejeva 2009). Many low-lying coastal ecosystems and communities will experience more frequent salt water intrusion events, more frequent coastal flooding, and accelerated erosion rates before they experience significant inundation. These changes will affect the ways coastal managers make decisions, such as timing surface and groundwater withdrawals, replacing infrastructure, and planning for changing land use on local and regional levels. Despite the advantages, managers’ use of scientific information about climate variability and change remains limited in environmental decision-making (Dow and Carbone 2007). Traditional methods scientists use to disseminate climate information, like peer-reviewed journal articles and presentations at conferences, are inappropriate to fill decision-makers’ needs for applying accessible, relevant climate information to decision-making. General guides that help managers scope out vulnerabilities and risks are becoming more common; for example, Snover et al. (2007) outlines a basic process for local and state governments to assess climate change vulnerability and preparedness. However, there are few tools available to support more specific decision-making needs. A recent survey of coastal managers in California suggests that boundary institutions can help to fill the gaps between climate science and coastal decision-making community (Tribbia and Moser 2008). The National Sea Grant College Program, the National Oceanic and Atmospheric Administration's (NOAA) university-based program for supporting research and outreach on coastal resource use and conservation, is one such institution working to bridge these gaps through outreach. Over 80% of Sea Grant’s 32 programs are addressing climate issues, and over 60% of programs increased their climate outreach programming between 2006 and 2008 (National Sea Grant Office 2008). One way that Sea Grant is working to assist coastal decision-makers with using climate information is by developing effective methods for coastal climate extension. The purpose of this paper is to discuss climate extension methodologies on regional scales, using the Carolinas Coastal Climate Outreach Initiative (CCCOI) as an example of Sea Grant’s growing capacities for climate outreach and extension. (PDF contains 3 pages)