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Glossary of Terms

This glossary describes the vocabulary used by CMOP and the CMOP community. Click one of the letters below to be taken to the list of all terms beginning with that letter.

A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W


Acoustic Doppler Current Profiler (ADCP)
A current measuring instrument using sound – usually at high frequencies (e.g., >100 kHz).  The sound is reflected by suspended particles (sediment, plankton, bubbles), and current speed is calculated from the Doppler shift of the reflected sound, assuming that the particles are moving passively with the water. Time gating circuitry uses differences in acoustic travel time to divide the water column  into range intervals, called bins. Bins let one plot a profile of current speed and direction throughout the water column. ADCPs can be mounted on (or towed from) a ship, and can also be mounted on a buoy or on the bottom. Bottom-mounted systems can be used in shipping channels without getting in the way.

Adjective describing (a) an organism that requires free oxygen, or (b) an environment containing free oxygen.

Affiliated Tribes of Northwest Indians
An association of native-American tribes which live in the PNW (q.v.). Participates in CMOP, particularly in various educational efforts.

Adjective describing (a) an organism that requires free oxygen, or (b) an environment containing free oxygen. Anaerobic organisms can be OBLIGATE anaerobes (cannot survive in the presence of free oxygen) or FACULTATIVE anaerobes (can survive in the presence of free oxygen but may not like it).

Anticipatory science
A new scientific paradigm being advanced by CMOP, in which one seeks to predict environmental changes, and to steer them through human actions. See “reactive science”.

APL (also APL-UW) – Applied Physics Laboratory
Acronym for the Applied Physics Laboratory of the University of Washington at Seattle. A research unit (not a department or college) within UW. APL specializes in oceanic, acoustic, and arctic research. APL is a major partner in CMOP.

Acronym for Apprenticeships in Science and Engineering. A program that places high-school students in 8-week summer programs as interns, working with scientists and engineers. CMOP participates in this program, which is run by SATURDAY Academy (q.v.)

An organism that synthesizes organic molecules from inorganic starting materials through photosynthesis or chemosynthesis. Autotrophs ultimately provide all the energy for all heterotrophic (q.v.) organisms. See also chemosynthesis, photosynthesis; compare heterotroph

Acronym for Autonomous Underwater Vehicle – an instrumented research vehicle such as a glider (q.v.) which is self-contained (= autonomous) as to power and guidance. AUVs may store data internally, and send it to a receiver either via sonar or by surfacing and using a satellite radio link. When in contact with a command station, many AUVs can be reprogrammed to change their observational program, based on data to date.  Similar to but not the same as an UUV – Unmanned Underwater Vehicle, q.v.

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Single-celled microorganisms without nuclei.

Bathymetric map 
A map of the bottom of the ocean, with water depths indicated by contours that join points of equal water depth.

Adjective meaning on or associated with the bottom. Benthic organisms such as clams live on or in the bottom: benthic currents flow along the bottom.

The study of how organisms are distributed in time and space, usually but not necessarily on large scales.

Bottom node
Instrument packages designed to be placed on the bottom of the Columbia River and its estuary, with no physical connection to the surface or shore. They carry observational instruments and also act as acoustic relay stations for data from other more distant instruments.

Adjective describing water that is neither completely fresh nor completely salt-water. A mixture of fresh and salt waters such as occurs in estuaries.

The tendency of a body or fluid to rise when it is less dense than its surroundings.

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Campaign (also campaign science)
A marine sciences research cruise -or series of cruises- in which the various participating research programs (usually highly multidisciplinary) are integrated to address a particular overarching hypothesis or observational need. Differs from a traditional research cruise in having a very high degree of focus and cooperation on studying a single problem.

Carbon fixation
The process of extracting carbon from environmental CO2 and using it to make plant materials, including both structural products (e.g., cellulose) and energy-storage substances (e.g., starches, sugars, lipids). Usually done primarily via photosynthesis (q.v.).

Cascadia Subduction Zone
See CSZ (below)

Colored dissolved organic matter (CDOM) is the optically measurable component of the dissolved organic matter in water. Much CDOM is relatively chemically inert and can often be used to track movements of water parcels.

Charter (scientific)
Each major project or sub-project within CMOP is covered by a Charter which describes the overall goals of the project, and describes both how the program will be undertaken, and the program’s strategic fit to CMOP’s overall goals.

Chlorophyll is a family of green pigments found in most plants, algae, and cyanobacteria. Chlorophyll is the major pigment used for photosynthesis, which process enables the organism to capture energy from sunlight.

Shortened acronym for the National Science Foundation-funded Science and Technology Center for Coastal Margin Observation and Prediction. CMOP sits within the Institute of Environmental Health at Oregon Health and Science University.

CMOP1 is the first five years of the Center’s program (2006-2011): CMOP2 is the second five years. Primary funding for both comes from the National Science Foundation, plus 30% matching by partner institutions.

Acronym for a research program funded by NSF to study the Oregon coastline.

Coastal forcing
The natural processes (e.g. winds, waves, tides, etc) that drive (a) changes in the shape of coastlines, and (b) changes in currents (e.g., speed, direction).

A compound word blending “collaboration” with “laboratory”: CMOP’s unique new approach to coastal margin science. Each collaboratory is an ad-hoc, carefully designed and integrated assemblage of information, methods and people aimed at a specific scientific problem or goal. More formally, a collaboratory is “… a networked integration of sensors, platforms, models, data, analyses and social processes that enables diverse stakeholders to understand, sustain and operate coastal margins, without geographic, disciplinary or geographical barriers.”

Columbia River Climatological Atlas
The "Columbia River Climatological Atlas" is a core CMOP scientific project, designed to offer insights into multiple scales of variability of the contemporary Columbia River coastal margin, via statistics of an extensive set of indicators. The term "climatological" does not refer merely to atmospheric conditions, but rather encompasses the entire breadth and variety of environmental conditions and factors, over some considerable span of time, which span depends on both the nature of a factor's variability, and the availability of historical observations. The focus of the Atlas is on indicators for the estuary and plume, but indicators of external forcing are also included for context. Due to their diversity, indicators have different data sources and levels of reliability. Data can come from observations, simulations, or analyses.

Competitive funding pool
A program planned for CMOP2 (q.v.) in which a pool of money is set aside to fund (a) small, cutting-edge or high-risk exploratory projects unlikely to be funded elsewhere, and (b) small enabling grants to meet emergencies or unexpected needs in funded research projects.

An electrical property of seawater which depends on the amount of dissolved materials (primarily NaCl). Measures of conductivity can be used (with other variables) to calculate seawater’s salinity.

Acronym for Columbia River.

Acronym for Columbia River Estuary.

Acronym for Columbia River Coastal Margin – the primary area of CMOP’s research focus and activities. Includes the lower reaches of the Columbia River itself, plus the River’s estuary, and also adjacent ocean shoreline and/or oceanic waters beyond the estuary but which are still affected by the River’s flow and outputs.

Acronym for Columbia River Inter-Tribal Fish Commission. Participates in CMOP.

Acronym for Cascadia Subduction Zone – the Pacific Northwest sub-region (both offshore and continental) within which plate tectonics carries the sea floor downwards, beneath North America (= subduction). The region has many active volcanoes, relatively frequent earthquakes, the potential for having the largest earthquakes in North America, and includes the Columbia River, its estuary, and considerable coastal land.

Acronym for an electronic instrument which measures simultaneously Conductivity, Temperature, and Depth (as pressure). Those measures together can be used to calculate both the salinity and density of seawater. The instrument is lowered or towed on a conducting cable, and often includes an acoustic depth-sounder to measure either depth below the surface or height above bottom. A winch-lowered CTD provides detailed vertical profiles of properties: a towed CTD measures horizontal variations in properties, and by being simultaneously cycled up/down can provide vertical data as well. Some CTDs have batteries and computers that allow them to be self-recording so they can be moored in one spot to make measurements for days or months.

Cyber technology
Computing-sciences technology in the widest sense (i.e., both equipment and programming). Within CMOP the term usually (but not always) refers to the non-hardware aspects… programming, information storing and distribution, modeling, etc.

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Density interface
The surface where two fluids of different densities meet. An extreme example is the air-sea interface, where the density difference is over 1000x. Interfaces occur between water masses, particularly when one overlies another to produce the horizontal layering which is common in the ocean.

The vertical distance from a specified location to the sea floor.

Microscopic unicellular or colonial algae of the class Bacillarieae. They have a silicified (glassy) cell wall called a test, which persists after death. Masses of such tests form kieselguhr (loose or porous diatomite). Diatoms occur abundantly in fresh and salt waters, in soil, and as fossils. They form a large part of the phytoplankton (q.v.) in most aquatic systems.

In hydrology, discharge is the volume rate of water flow, including any suspended solids (i.e. sediment), dissolved chemical species and/or biologic material (i.e. diatoms). The units are volume (or mass) per unit time per unit area at right angle to the flow (e.g., m3/sec/m2)

Dissolved oxygen (“DO”, pronounced as two words, “dee oh”)
A measure of oxygen contained in the water, usually given as (a) ml of oxygen/l of water, (b) % saturation at the water’s temperature and pressure, or (c) mg of oxygen/l of water. Adequate dissolved oxygen is critical to most aquatic organisms (see aerobic). Oxygen concentration is an important indicator of environmental health in most aquatic systems.

DNA microarrays
Devices for studying bacterial assemblages, using details of their genetic (DNA) composition.

Acronym for Department Of Geology and Mineral Industries (of Oregon).

Downward movement of surface water caused by onshore (Ekman) transport, converging currents, or when water becomes more dense than the surrounding water.

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Acronym for External Advisory Board. A small group of scientists, administrators and educators from outside CMOP, which meets at least annually to assess progress and advise as to possible needs for changes of direction or emphasis.

Acronym for the Division of Environmental and Biomolecular Systems at Oregon Health and Science University. EBS is the home administrative unit of OHSU, within which CMOP resides.

Acronym for “Ecology of Harmful Algal Blooms”, a 5-year multi-disciplinary project to study the physiology, toxicology, ecology and oceanography of toxic Pseudo-nitzschia species off the Pacific Northwest coast. Run by the NOAA Northwest Fisheries Science Center in Seattle.

An evolved ecological unit consisting of one or more communities of organisms and their environment(s).

Acronym for “Events and Gradient Regions”. Descriptive of the overarching CMOP hypothesis (1) that specific environmental EVENTS are important determinants of the structure and functioning of the Columbia River Coastal Margin’s ecosystems, and (2) that SPECIFIC AREAS WHICH HAVE STRONG GRADIENTS in various environmental parameters are likewise critical to both structure and function of those systems. Hence E-GRs are, generically, a major focus of CMOP research. More formally, ‘events’ are usually mesoscale phenomena with strong temporal signatures (e.g., coastal upwelling, algal blooms, formation of hypoxic regions), and ‘gradient regions’ are predominantly spatial features associated with strong gradients of function (e.g., river-to-ocean salinity gradients, fronts associated with plumes, and estuarine turbidity maxima).

Acronym for “Eulerian-Lagrangian CIRCulation” – a mathematical model used within CMOP to study circulation of water in estuaries and other coastal environments.

Enabling Technologies
A wide variety of technologies seen as critical to advancing CMOP science, each of which either does not exist and needs to be developed, or does exist but needs improvement and/or modifications to achieve CMOP research goals. Examples include bottom nodes and the Sigma Profiler (both of which q.v.)

Endangered Species Act
Complex federal legislation, and regulations that flow from it, intended to protect endangered species and their habitat.

Endocrine disrupting compounds
Chemicals (usually man-made) which are designed for various uses, eventually wind up in both fresh and salt-water, and which interfere with the proper functioning of various organisms’ endocrine systems (or the systems’ products). Examples include steroids and hormones in cattle-feed, which can pass through the animal’s digestive tract unused and unmodified, thence into drain-water or sewage system and on into the environment generally. An item of study within CMOP.

Environmental genomics
A field of science in which the genetic makeup of individuals or (more often) populations is/are studied and related to environmental parameters and to the organisms’ responses to changes in those parameters.

Acronym for Environmental Observation and Forecasting System. EOFS is used to study and predict the spatial and temporal variability of the Lower Columbia River. It is a project within CMOP that seeks to characterize and predict complex circulation and mixing processes in a system encompassing the lower river, the estuary and the ocean near the estuary.

Acronym for “Estuary and Ocean Systems”, a new curricular track within the Environmental Science and Engineering program at OHSU. Makes strong use of CMOP.

Acronym for Environmental Protection Agency – the federal agency charged with implementing and enforcing federal environmental regulations.

Semi-enclosed coastal body of water which has a free connection with the open sea (the ‘mouth’ of the estuary) and where fresh water from land (usually the mouths of rivers) is mixed with seawater. Most have tides and cyclical fluctuations in salinity. In many estuaries, the fresh river water is blocked from streaming freely into the open ocean by surrounding mainland, peninsulas, barrier islands, fringing salt marshes, and other features. The mixing of fresh and salt water, plus the nutrients in the fresh water, create unique environments that often have very high biological productivity and unique (often highly diverse) communities.

Acronym for Environmental Sample Processor.

Acronym for Estuarine Turbidity Maximum. Turbidity (q.v.) is a measure of the cloudiness of water (e.g., from suspended sediment or from phytoplankton). In many estuaries (including the Columbia’s) there is a maximum of turbidity at some depth. The intensity, depth, movements and composition of the turbidity maximum can be important ecologically – e.g., by carrying various materials about, or by restricting the amount of light). The ETM is an important item of study within CMOP.

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Field campaigns
Large-scale, usually multidisciplinary scientific research conducted in the field. See “campaign science” above.

A device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light.

Fluvial systems
River systems, usually taken to include a defined region’s rivers and tributaries and the watershed feeding them. The Columbia River and its tributaries and their watershed(s) constitute one large-scale fluvial system.

Federal Columbia River Power System
The federally-constructed collection of dams and their appurtenances which uses the flow of the Columbia River to generate electrical power, which is then distributed via connections to the national power grid. One major dam in the system is the Bonneville Dam on the lower Columbia River. Collectively these dams, and how they impound or release water (or distribute it for irrigation) are a major anthropogenic driver of ecological structure and function in the Columbia River and its estuary.
The process in which a photon is absorbed by a molecule and shortly thereafter (10-11 to 10-8s later) another photon of greater wavelength is emitted by that molecule.

Acronym for Fast Methane Analyzer. An instrument to rapidly measure the concentration of methane (CH4) in seawater. Especially useful for studying some microbiological populations and processes.

Food chain
A sequence of feeding relationships describing how energy is transferred from primary producers to various levels of consumers. Such energy flow is usually more complex than is implied by the “chain” concept, and the flow is more properly described as a “food web”.

Framing hypothesis
A high-level hypothesis used to state general principles and/or propositions. Not usually presented as a formal, technically testable scientific hypothesis. One such framing hypothesis might be, e.g., “Events and gradient regions [E-GRs – q.v.] are important controllers of the Columbia River’s ecological functions.”

Acronym for a family of mathematical models used in CMOP research and elsewhere.

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A variety of AUV (Autonomous Underwater Vehicle, q.v.), usually relatively small (e.g., human-sized), which is launched from a platform (usually a ship). Gliders use changes in buoyancy and usually changes in angle of attack instead of motors to provide propulsive force. Gliders can carry a wide variety of instruments, and can undertake an extraordinarily wide range of observational programs. Many can send data to a receiver either acoustically or via satellite radio link, and can be reprogrammed during such contacts. Extensively used in CMOP.

“Genes-to-climate” (“gene-to-climate thinking”)
Shorthand for one major CMOP goal, namely to study and understand many aspects of the CRCM on scales from that of genes (microscopic physical scales, and usually short time scales) to scales on which climate changes (broad areas and extended periods, usually decades or longer). It is a major goal of CMOP to be able to integrate observations, modeling and prediction across many variables and across that broad span of time and space scales.

Grand Challenge (CMOP’s)
CMOP’s declared Grand Challenge is to serve as a catalyst for better (fully integrated) understanding of the effects of both climate and human activities on coastal margins. Part of the Challenge is to then use that understanding to positively affect outcomes of those factors (and changes in them) on environmental sustainability, economic development, and public health.

“Great water bodies”
A category (and list by name) of large, ecologically and economically important water bodies within the USA. Examples include the Great Lakes, Chesapeake Bay, and the Columbia River Estuary. The category and list were created by the EPA (q.v.).

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Acronym for Harmful Algal Bloom. A category of explosive growth of micro-organisms which in high concentration are poisonous or otherwise harmful to other species (e.g., by using up all the oxygen). Red tides are an example.

Half-baked talks
A series of occasional informal “brown-bag lunch” talks by CMOP investigators and/or visitors, presenting research results or seeking input about ideas and problems.

An organism which cannot synthesize organic compounds, and which fulfils its energy requirements by feeding on other organisms (e.g., via predation, parasitism) or on nonliving organic matter (e.g., organic detritus).

The output of a mathematical model when the model begins with available data and present knowledge of a system’s state or function, and works backwards to calculate the system’s condition at some past time from which data have not been given to the model. One then compares the model’s estimate of that condition with actual data collected at the time under consideration. The precision and accuracy of “hindcast vs real data” provide a measure of the skill of the model.

Hypotheses: high-level; CMOP
CMOP’s science is predicated on these three major hypotheses: (1) Events and Gradient Regions (E-GRs, q.v.) play a major role in the ecological function and productivity of coastal margins, with microbial communities as essential mediators: (2) Variability and changes in E-GRs are largely controlled by climate and human activities; (3) E-GRs may contain effective “sentinels” (q.v. – essentially indicator or predictor variables, usually biological and often microbial) for the response of coastal margins to climatic and anthropogenic forcing.

A condition in which dissolved oxygen is below the level necessary to sustain most animal life, generally < 2mg/l [milligrams/liter] (i.e., < 2 ppm [parts per million])

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Internal waves
Waves that occur not at the surface of the water but rather at some depth. Although internal waves can be quite large (10s of m in amplitude), they move slowly and have little surface manifestation. Internal waves can occur when there is an interface between waters of different densities – i.e., layering. Internal waves are common, and can break as do surface waves. The break is entirely subsurface, and can cause vertical mixing that can bring plant nutrients upwards into sunlit depths.

Acronym for Integrated Ocean Observing System, a program within NOAA (National Oceanic and Atmospheric Administration).

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Acronym for Knowledge Transfer, a catchall term for a major function within CMOP. KT involves data analysis, distribution of data and results by various means (e.g., via the WWW, through peer-reviewed publications, by helping develop better scientific curricula for K-12 [q.v.] courses, teaching at many levels, bringing together parties who share common interests, and the like). KT also includes locating, and then making available, unusual or unexpected types of data (e.g., Native American ecological knowledge), and promoting connections between knowledge sources and potential users.

Shorthand for “kindergarten through twelfth grade”.

The human ages from kindergarten through indeterminate old-age. Used in discussing educational needs of the population in toto, and both plans and efforts to address those needs

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Acronym for an estuarine research program funded by NSF. Not part of CMOP.

Acronym for Long-Term Ecological Research. A program within NSF which funds integrated, large-scale, long-term (e.g., 10 yrs or more) ecological research. Such efforts are called “LTERs” and each focuses on a specific ecosystem (e.g., desert, savannah, fresh-water, etc.). Similar in many ways to the STC program of which CMOP is a part.

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Acronym for Math Science Partnership, a program funded via the Oregon Department of Education (ODE). CMOP participates in MSP.

Max[imum] fluorescence (fm)
Fluorescence is the emission of light by a substance that has absorbed radiation (usually visible light) of a different wavelength than that emitted. Fm is defined as the maximum quantum efficiency of photosystem-II.

Acronym for Monterey Bay Aquarium and Research Institution.

From Greek, meaning literally “methane eating”. A form of chemo-autotrophy. The process by which some microorganisms gain metabolic energy by consuming methane (CH4).

A microscopically visible organism of diameter (~) .01 to .001 mm; usually single-celled. Individual Bacteria and Archaea are microbes.

Modeling benchmark
Any known reference against which a mathematical model’s output (predictions; hindcasts [q.v.]) can be compared.  Used in assessing modeling skill (q.v.).

Modeling skill
The degree to which a mathematical model of a process is both accurate and precise in its predictions (or in its hindcasts, q.v.).

Myrionecta rubra
A ciliate micro-organism commonly found in the Columbia River and its estuary. The species can form intense blooms, and is under investigation by CMOP researchers as a possible biological “sentinel” (q.v.)

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Acronym for Native American Youth and Family Center.

Acronym for Northwest Association of Networked Ocean Observing Systems.  An integrated network of regional ocean observing programs or systems in the Pacific NorthWest, in which CMOP participates. NANOOS is part of IOOS (International Ocean Observing System).
Neap tide
Tides with the smallest height difference between high tide and low tide, usually occurring during the moon's quarters. Compare with spring tide.

A salt or ester of nitric acid, containing the group NO3. Nitrates dissolve very easily in water and are important plant nutrients hence an important component of the nitrogen cycle.

A diatomic noble (“inert”) gas. Organic nitrogen can take many forms in water, including the major plant nutrients nitrate, nitrite, and ammonia, which all promote plant growth. Ammonia concentrations below 0.3 mg/L significantly limit plant and algae populations. Conversely, overabundance of those nutrients can help cause disastrous overgrowth of plants and algae, leading to eutrophication.

Acronym for National Oceanic and Atmospheric Administration, a major federal research and regulatory agency.

NOAA Northwest Fisheries Science Center
A research facility of NOAA, located in Seattle. A participant in CMOP.

Northwest Fisheries Science Center (see NOAA Northwest Fisheries Science Center)

Acronym for North West Indian College (Bellingham WA), a native-American school. A CMOP participant, primarily for educational efforts.

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Acronym for Oregon Department of Education (see MSP).

Acronym for Oregon Health and Science University – the major site and lead institutional partner in CMOP

The Ocean Observing Initiative, a research program within the National Science Foundation

Open data policy
CMOP’s policy with regards to accessing CMOP data. The concept is to make data (all forms) readily and easily available to a wide variety of interested parties (not just to CMOP’s partners and participants), as quickly as possible consistent with quality control.

Acronym for Oregon State University – a major CMOP partner institution.

Oxygen saturation ("O2 sat")
A relative measure of the amount of oxygen dissolved in the water, usually given as % of the equilibrium concentration with air, at a given temperature, pressure and salinity.

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Partial pressure of carbon dioxide gas

Acronym for Polymerase Chain Reaction. A process (and investigatory tool) for studying various aspects of the genetics, or of the metabolic functioning, of organisms.

Adjective meaning “open-ocean” in the sense of far from land (and usually in deep water). Compare to ‘neritic’ – meaning relatively near-shore (and usually in shallow water).

A measure of how acidic or basic a solution is. Defined as the negative log (base 10) of the hydrogen-ion concentration of a solution. A pH of 7.0 is precisely neutral (neither acid nor base). The pH of seawater plays an important role in the ocean's carbon cycle and there is overwhelming evidence of ongoing ocean acidification traceable to anthropogenic CO2 emissions.

The process by which green plants use energy from the sun to combine water and carbon dioxide, thereby producing both fixed carbon (carbohydrates) and free oxygen.

Small (usually microscopic) photosynthetic organisms that float or drift with water motions. They are the base of the open-ocean (pelagic) food web, and can also be very important in both shallow-water (near-shore) marine environments and in fresh-water systems.

Pioneer Array
A part of CMOP’s SATURN (q.v.) collaboratory (q.v.). SATURN consists of, inter alia, (a) relatively long-term permanent observational systems (called “endurance stations” [q.v.] e.g., buoys, shore sites, bottom-mounted instruments) and (b) systems that are either mobile or used only intermittently (or both): the mobile/intermittent systems provide a larger-scale context for the more voluminous but single-site data from endurance stations. These latter (b) are called “Pioneer Arrays” in specific contrast to endurance stations.

Plume (of the Columbia River)
The fresh-water outflow from the Columbia River’s mouth into the Pacific Ocean.

Acronym for Pacific North West – the region of the USA containing the entire Columbia River, its tributaries and watershed and estuary, and the major CMOP states of OR and WA.

Acronym for Pacific North-West Center for Human Health and Ocean Studies, a program based at the University of Washington.

Primary productivity
The rate at which organic matter is produced by autotrophic organisms (q.v.), using energy captured from the environment in the form of light or chemical energy. Most marine primary productivity is done by pelagic (open-ocean) phytoplankton, not by nearshore benthic plants. Usually expressed as “grams of carbon fixed per unit area [or volume] per unit time” (e.g., grams/m2/hr), but more properly expressed as “grams of C fixed per unit time per gram of photosynthetic biomass”. The total such productivity in a region or system is called “gross primary productivity”. Some fraction of gross productivity is used up by the primary producers themselves: the remainder is “net” productivity. Net marine primary productivity is the amount of photosynthetically-fixed organic material available to support higher trophic levels – i.e., herbivores and carnivores.

Acronym for Primarily Undergraduate Institutions. Colleges and universities that have small or non-existent graduate programs, and whose strong emphasis is therefore on undergraduate education. Several PUIs are partners in CMOP.

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Acronym for Quinault Indian Nation, a tribe in the Pacific NorthWest which participates in various aspects of CMOP.

Quantum yield (fv/fm)
The quantum yield of a radiation-induced process is the number of times that a defined event (usually a step in photosynthesis) occurs per photon absorbed by the system. It is a measure of the efficiency with which absorbed light produces some effect.

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Reactive science
The most common form of environmental science today, in which one waits for and observes changes, then reacts to them after the fact. Compare to anticipatory science (q.v.), which is one important CMOP goal.

Research roadmap
A set of detailed written presentations of research plans for CMOP, including all as-yet identified or planned projects, their timelines, leaders, and interrelationships. Shows how individual projects fit into an overall research strategy.

Research themes, CMOP
CMOP’s overall research plan is organized along these three themes: (1) Development and use of coastal margin collaboratories (see Collaboratories); (2) Coastal margin science – seeing how the physical, biological and chemical conditions and processes vary both naturally and due to human activities; (3) Sensors and platform – developing and/or improving the sensors and platform needed to investigate the conditions and processes in (2) above.

Acronym for Research Experience for Undergraduates. A national effort in which CMOP participates, seeking to provide opportunities for undergraduates to actively participate in scientific research, either in academia or in industry.

Acronym for Research Integration Group – an administrative and planning group within CMOP which helps plan, integrate, and direct the overall CMOP research program. 

Acronym for a research program funded by NSF to study river plumes, primarily where rivers empty into salt-water.

Nickname for ‘river radar”, a light-weight, unmanned, robust radar system being developed within CMOP. Used to radar-reflectivity of the water surface and from that to infer water-wave spectra, currents, tidal flows, and perhaps internal wave activity. Versions are being considered that use conventional, synthetic aperture, and Doppler radars.

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Acronym for Science & Engineering. Usually refers to education, research, or employment.
Number of grams of dissolved matter per thousand grams of water (in the ocean, this is mostly NaCl). Usually expressed in parts per thousand by weight (ppt, or ‰). Ocean water averages ~35 ‰, or 3.5% dissolved matter by weight.

Saturday Academy
Both a tax-exempt organization (501c3: located in Portland OR) and an educational program for both students and teachers. It offers exceptional opportunities for enriched learning by enlisting community professionals to share facilities, equipment and expertise through hands-on classes, workshops and internships. Since 1983, Saturday Academy has provided instruction to more than 110,000 students and teachers in urban, suburban and rural communities. A CMOP participant.

Acronym for Science And Technology University Research Network – the CMOP test-bed for the collaboratory concept, and central to CMOP’s investigations of the structure and functioning of the Columbia River system.

Scattering coefficient
The fractional decrease in intensity of a beam of electromagnetic radiation or particles per unit distance traversed, which results from scattering rather than absorption. Values are from 0 to 1.

Scientific blueprint
A written description or recipe used as guidance or explanation of how to best do a scientific procedure, or how best to phrase and investigate a scientific hypothesis.

Acronym for a 3-dimensional mathematical model of water movements. Used in CMOP’s hydrographic and other research involving flows (tides, currents).

An environmental parameter which can give advance warning of environmental changes. Many sentinels are biological, e.g., presence/absence of a species; changes in abundance or function of a species; changes in structure and function of an entire community or of an important assemblage such as microbes. Other sentinels may be physico/chemical (e.g., changes in dissolved nutrients, or in stream flow rates). Identifying and investigating candidate sentinels is a major CMOP research focus.

Acronym for SATURN Implementation Group – an administrative and planning group within CMOP which helps direct the development and use of the SATURN (q.v.) collaboratory (q.v.).

Sigma Profiler
A physically simple, robust, bottom-mounted system which can provide vertical profiles of salinity by interpreting electrical signals broadcast and received by the device. Developed under CMOP funding.

Acronym for Science Implementation Plan, a document that NSF requires be prepared by each Science and Technology Center, such as CMOP. Gives details on the organization of the Center’s research efforts, e.g., how and when the various scientific plans within the proposal will actually be implemented.

Acronym for Science and Math Investigative Learning Experiences, a program at Oregon State University for K-12 (q.v.) students, in which CMOP participates.

Juvenile salmon that are enroute downstream from where they hatched, headed for the ocean where they will live for several years, grow to sexual maturity, and then return to spawn where they were hatched.

Acronym for Senior Management Team – a high-level group within CMOP’s administrative structure. Meets twice monthly (and ad-hoc when needed) to provide guidance and advice to the Director.

Spring tide
Tides with the greatest range between highs and lows, usually occurring during the full or new moons. Compare with neap tide.

Acronym for Science and Technology Center. Also a program within the National Science Foundation which funds competitively evaluated, integrated attacks on large-scale, important scientific and/or technological problems. CMOP is an STC (the only one ever funded to study the coastal margin). Each STC is funded for an initial five years (usually at about $4,000,000 per year), with the possibility of one further five-year period, after which NSF’s overt support ceases, although the STC is expected to continue via other support.

Acronym for Science, Technology, Engineering and Math. Usually used in reference to education or jobs.

Acronym for a family of mathematical models used in CMOP research and elsewhere.

Super Sucker 
A  large ship-mounted underwater “vacuum-cleaner-like” device for removing invasive algae from coral reefs. See

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Thematic workshop
A program of intense, focused workshops, as proposed for CMOP2 (q.v.).

Themes, research, CMOP
See research themes.

Tidal bellows
The pumping action (of water) that can occur due to the interactions of tides and bottom topography. Often seen in estuaries, including the Columbia River’s, where it is an object of CMOP study. Can be very important ecologically, e.g., by mixing various water types, and by moving species, nutrients, pollutants, and oxygen about.

Adjective meaning that something (usually an environmental parameter) is changed by the tides.

Acronym for Teachers Translating Research into Practice. A CMOP program that seeks to close the gap between actual technical knowledge and how it is presented in the classroom, primarily in high-schools.

A measure of the degree to which the transparency of a fluid (e.g., water, air) is impaired due to suspended particulate matter. The suspended matter may absorb various wavelengths of light, whilst also scattering and/or absorbing light. The particles are usually too small to be seen individually by the naked human eyeball. Fluids containing visible suspended matter are said to be “turbid”.

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Acronym for University-National Oceanographic Laboratory System. An organization that handles the scheduling and logistics of the use of national oceanographic research facilities, including the national fleet of oceanographic research ships. Many such ships are located at, and operated by, various universities (under federal funding) – however, use of the facilities (e.g., ships, shore-based labs) is granted to anyone whose research is (a) funded by NSF, and (b) requires such facilities. The main large sea-going research ship used by CMOP is a UNOLS vessel operated by Oregon State University, a CMOP partner.

A rising of water toward the surface from below. Most common where a persistent wind blows parallel to a coastline such that the resultant wind-driven current moves water away from the coast: deeper water then moves upwards to replace that water which is being driven offshore. A common effect is to bring colder (and often nutrient-rich) water to the surface: this in turn often supports rapid algal growth and this in turn may support large fisheries (sardines, anchovies, krill). Over the open ocean, upwelling occurs wherever the wind circulation is cyclonic (CCW viewed from above), but is appreciable only in areas where that circulation is relatively permanent. It is also observable when and where the southern trade winds cross the equator.

Acronym for United States Geological Service, a federal research organization that participates in CMOP.

Acronym for University of Texas at El Paso.

Acronym for Unmanned Underwater Vehicle. Any propelled underwater vehicle that does not carry a human crew to operate it. Most UUVs are similar to but distinct from AUVs – Autonomous Underwater Vehicles (q.v.). A simple naval torpedo is an example of a UUV; if that torpedo also carries an internal system [such as sonar] which can investigate the vehicle’s status and the environment, and change the vehicle’s course without aid from the outside, it is also an AUV.

Acronym for the University of Washington (main campus Seattle). A major partner institution in CMOP.

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A vector quantity including both speed and direction.

Virtual Columbia River (also Virtual CR; Virtual CRCM)
A CMOP-developed, continually improved, detailed mathematical model of the structure and functioning of the Columbia River (and its Coastal Margin). The Virtual CR (or Virtual CRCM) is a major tool for studying, planning, describing and predicting the River’s behavior. Includes the estuary and beyond. Many aspects are available to the public via the CMOP website.

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Water column
A concept including the water from free surface (usually air) to the bottom.

Winch-based profiler
A system using a winch to lower and raise instruments attached to the winch’s cable.

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