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Open Access Publications from the University of California


The investigations that led to the founding of Scripps Institution of Oceanography (SIO) began as summer marine biological studies conducted by UC Professor William E. Ritter beginning in 1892. In 1903, Ritter and a group of San Diegans established SIO. The scientific scope of SIO's research has grown to encompass physical, chemical, geological, and geophysical studies of the oceans, earth and atmosphere as well as biological research.

Scripps Institution of Oceanography

There are 1112 publications in this collection, published between 1911 and 2019.
Bulletin of the Scripps Institution of Oceanography (23)

External and internal characters, horizontal and vertical distributions, luminescence, and food of the dwarf pelagic shark, Euprotomicrus bispinatus

The object of this paper is to coordinate and expand knowledge of Euprotomicrus bispinatus (Quoy and Caimard, 1824), the pigmy shark : a most remarkable creature, which until recent years had been known for a century and a quarter on the basis of very few, casual observations at sea and of 8 museum specimens. As a result of increasing emphasis on high-seas research we now have data on 37 specimens, and a much richer fund of information on the species.

The pigmy shark is a strange creature, defying most concepts of a shark. In the first place it is tiny: the largest known example spans only 265 mm (10 ½ in.) in total length and weighs less than 70 grams (about 234 ounces) ! Males mature at 170 mm, females at 233 mm or less. Its terete body and wee gill openings remind one of a lamprey. Its essentially diphycercal tail, with large, rounded dorsal and ventral caudal-fin lobes and horizontal termination of the spinal column, little resembles the long-drawn-out, upturned heterocercal tail that is ordinarily associated with a shark. In this, and in some other respects, the appearance of this shark is almost embryonic. Its skeleton is almost devoid of calcification (apparently an adaptation for neutral buoyancy). Its vertebrae are unexpectedly few for a shark, and in radiographs lookr strangely like those of a bony fish. The teeth are strikingly unlike in the two jaws.

This little shark has been taken only at the sea surface, almost exclusively in the vast, relatively sterile central water masses of the world ocean. Its thousands of tiny light organs can combine to produce a bright blue-green glow. We now learn that it undertakes vertical migrations to considerable depth, where it feeds on bathypelagic squids and fishes.

Systematics, distribution, and abundance of the epiplanktonic squid (Cephalopoda, Decapoda) larvae of the California Current, April, 1954- March, 1957

Our knowledge of the biology of oceanic cephalopods is extremely limited. The population sizes, distribution patterns, breeding seasons, life histories, and growth rates are virtually unknown. In view of the fact that these organisms are undoubtedly abundant and ecologically important, both as predators and prey, this state of ignorance is unfortunate. Part of the reason for this lack is attributable to the great difficulty of adequately sampling the adults. The larvae and some juveniles, however, can be caught, in the types of plankton nets and trawls generally in use. Therefore the possibility exists that the times and places of spawning, and the developmental history of many species, may be determined from zooplankton surveys. Using this approach presupposes that a sufficiently extensive area is surveyed and that the sampling is intensive in both space and time. It is also necessary that enough specimens of the adults and intermediate-sized ranges be available for accurate identification of the larvae. This is best done by tracing the morphological changes through progressively smaller individuals. The Marine Life Research Group at Scripps Institution of Oceanography (SIO) has available a very large collection of zooplankton samples taken by the California Cooperative Oceanic Fisheries Investigations (CalCOFI) in the California Current. This program has surveyed a large portion of this current system by monthly cruises for a period of ten years. It is from these samples that the data in this report are derived.

Season of attachment and rate of growth of sedentary marine organisms at the pier of the Scripps Institution of Oceanography, La Jolla, California

This paper reports the studies in progress during the past four and one-half years on the organisms, particularly invertebrates, which attached themselves to submerged blocks throughout the year.

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Coastal Morphology Group (12)

Shorerise and Bar-Berm Profiles on Ocean Beaches

A beach equilibrium model is developed that treats the outer (shorerise) portion of the profile independently from that of the inner (bar-berm) portion. The two portions are matched at the breakpoint-bar. The partitioning of the profile in this way is consistent with the different forcing modes on either side of the breakpoint. This formulation utilizes beach profile data not previously available. It is shown that both portions of the profile are well fitted by curves of the form h=Ax/sup m/, where h is positive downward and x is the positive offshore coordinate. Surprisingly, the value of m approximately=0.4 is nearly the same for shorerise and bar-berm and does not change significantly with seasonal beach changes (summer/winter). The principal difference between seasonal profiles is that in winter (higher waves) the breakpoint-bar is deeper and farther offshore while the berm crest is displaced landward. Thus the changes in seasonal equilibria are manifested by simple, self-similar displacements of the bar-berm and shorerise curves as a consequence of changes in surf zone width and O(1) variations in the factor A.

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IMR Reference (2)

Physical Oceanography Of The Region Near Point Arguello

Various investigators have described the California Current system,. Since then various small-scale studies have been made over the area, but the Point Arguello area had not received particular attention until work in January 1964. The Point Arguello area is an especially interesting part of the California Current because it is characterized by a remarkable and systematic seasonal reversal in flow.

Fish life in the kelp beds and the effects of kelp harvesting

This final report is the result of research during the five and one-half year period from September 1948 to March 1954. Throughout the investigation the apparent decline of sport fish was causing sport fishermen great concern. Among other factors, kelp harvesting was blamed for the poor catch of the sportsman. More than a year after the beginning of this investigation, the Kelco Company approached the Scripps Institution of Oceanography of the University of California, with the request that the problems of kelp cutting in relation to the fish supply be attacked by the University under a fellowship grant, by unprejudiced research. The Company wanted to determine whether the kelp operations were adversely affect­ing fishing, and if so, how harvesting methods might be altered to prevent this.

The first phase of the program was concerned with observation and identification. Thousands of hours were spent above and below the surface observing the organisms in their own environment. Extensive use was made of scuba diving equipment for observations, collection, and placing of equipment. Underwater photography was developed to a point where many observations could be recorded.

The second phase of the program was to appraise the effects of kelp harvesting on fish life. Because of the lack of pertinent published data on the ecology of the inshore waters, it was necessary to investigate not only the beds of the main commercial kelp (Macrocystis pyrifera), but also many other regions, in order to obtain comparative data. Such areas included bays, rocky areas below the levels where kelp grows, rocky areas with no kelp, the surf zones, sandy areas, and regions outside the West Coast range of Macrocystis. Kelp beds were studied as far north as Monterey and as far south as the San Benito Islands, Baja California. Diving observations in the kelp were made at Monterey, Morro Bay, Goleta, Santa Barbara, Point Dume, Palos Verdes, Newport, Laguna, Dana Point, San Clemente, Del Mar, Solana Beach, La Jolla, Point Loma, Ensenada, Punta San Carlos, Punta Blanca, Punta Santa Rosalia, and numerous other points along the mainland; also at San Miguel, Santa Rosa, Santa Cruz, Anacapa, Santa Catalina, Coronado, San Martin, and San Benito Islands. Intensive studies of the problem were carried out in Orange and San Diego Counties, with special concentra­tion on the nearby La Jolla kelp beds.

One portion of the La Jolla kelp beds was left uncut as a control. Little difference has been noted in the fish life within the bed as contrasted with harvested beds. The kelp itself became more sparse, probably because of reduced light penetration through the heavy canopy that developed tem­porarily. In the 1952-53 winter season much of the kelp was de­stroyed by storms. These studies yielded a vast amount of information bearing not only on the kelp problem but also on the life ways of the fishes.

As a result of these long and thorough studies, it is concluded that kelp harvesting, as cutrrently practiced, has no seriously detrimental effects on fishing. The various claims as to the ways in which kelp harvesting was supposed to destroy fish life and to decrease the fish catch were completely investi­gated and found to be in error. Spawning and nursery grounds of fish are not being destroyed. Sufficient cover and food are always available during and after harvesting. The kelp beds are not destroyed by harvesting methods. Harvesters do not frighten sportfish from an area.

For several decades California has experienced a tremendous increase in population. Cities have grown where deserts and foothills were the homes of deer, rabbits, ground squirrels, ground owls, doves,and quail. In most places these animals have largely disappeared, and with them the intertidal mollusks — Pismo clams, butter clams, abalone, and many other species. The shore fishes such as corbina and spotfin croaker are less common in the individual fisherman's catch. Over kelp beds where a man might have fished alone a decade or two ago, we may see 50 sport boats with a total of 1000 anglers. Thus, even though the annual catch may be the same as or higher than 10 or 20 years ago, the catch per fisherman is much lower.

The kelp industries have arisen indirectly from our social-economic needs for new raw materials to fill new markets. They have become established in our economy and are essential for the production of certain new products. As is typical of modern, young industries, they have conducted research to determine the maximum sustained yield. The industry naturally has no desire to destroy kelp.

The sportfishing industry is large and provides recreation, necessary for our nation's health, to thousands of persons. With the addition of thou­sands of newcomers to sportfishing and the reduction of catch per unit of effort, it is not difficult to understand the fishermen's concern over factors supposedly destroying their sport. It is necessary, however, to determine the real reason for the apparent decline of fish before any constructive action can be taken. It may be a problem of overfishing or of natural population fluctuations, but the blame cannot be laid to the kelp harvesting.

MPL Atmospheric Group (3)

Development of Extinction Imagers for the Determination of Atmospheric Optical Extinction

The primary goals of this project for JTO and ONR (Grant N00014-07-1-1060) were to further develop Extinction Imagers for use in the ocean environment, and to extend the capabilities into the Short Wave IR (SWIR).  Extinction Imaging is a method for determining the effective extinction coefficient over an extended path using a sensor at one end of the path.  It uses calibrated imagers to acquire the relative radiance of a dark target near the other the end of the path and the horizon sky in the direction of the dark target.  It is completely passive and thus covert, and the hardware is robust and relatively inexpensive.  It uses rigorous equations, which determine the extinction coefficient from the measured apparent contrast of the radiance of the dark target with respect to the horizon sky. 


The project was very successful.  We found that the ocean surface could readily be used as a dark target in red and SWIR wavelengths.  Both the red and the SWIR measurement results were excellent for daytime.  Comparisons with standard instruments, as well as uncertainty analysis, indicated that extinction imagers provide better measurements of the atmospheric extinction losses over extended paths than other methods of which we are aware.


Our secondary goals were to address the night regime, and to address slanted paths above the horizontal.  Regarding night, we found that the visible sensor acquired excellent data, but the ocean surface was not a good dark target in our wavelengths.  Recommendations on the handling of night are given in the report.  Regarding the lines of sight above the horizon, we developed a slant path algorithm that determines beam transmittance.  It performed very well.  Recommendations are made regarding integration of these techniques for military applications.

MPL Report (1)
MPL Technical Memorandum (3)

The scientific research support potential of the submersible MARITALIA 3GST9

Marine Physical Laboratory Technical Memorandum 420. Deep submergence facilities are now considered to be a vitalcomponent of the U. S. Navy fleet and the National OceanographicLaboratory System facilities inventory. Scientific use of mannedsubmersible systems is now routinely applied to a broad range ofscientific disciplines. Advancements in deep submergencetechnologies continue to require evaluation and assessment for theirscientific support potential. This study report assesses the scientificsupport potential of a specific new diver lockout submersible, theMARITALIA (3GST9), that may be added to the U.S. Navy deepsubmergence facilities inventory.

Complete Solution Of The Bearings Only Approach Problem

In using the data available during the conduct of a bearings only approach two rather different procedures are usually followed.

One is to attempt the complete solution for range, course and speed by taking usually six bearings while maneuvering the submersible in a rather specialized way. The other methods involve the use usually of three bearings and an assumed range or speed to calculate the course and the speed or range (whichever was not assumed).

The purpose of this paper is to show that using four bearings it is first actually possible to solve the problem completely (range, course and speed solution) in a very general way, and second to give in detail several simple, direct methods for making such a solution without restricting the motion of the submersible.

Naga Report (7)

Physical Oceanography of the Southeast Asian waters

This book is the outcome of my analysis of all available knowledge of the Southeast Asian Waters. It is hoped that workers in the region, whether in oceanography or other branches of science may find it a source of information and a stimulus to undertake further research in these waters. Some chapters in this book are summaries and condensations of already known facts, but others offer new ideas and interpretations, particularly those chapters on monsoon circulations and their dynamics, on deep circulation and its relation to surface circulation, on the energy exchange between sea and atmosphere, and on the quantitative description of the exchange of water in the deep sea basins.

The physical oceanography of the Gulf of Thailand, Naga Expedition; Bathythermograph (BT) temperature observations in the Timor sea, Naga Expedition, Cruise S11

The Research Vessel Stranger of the Scripps Institution of Oceanography, University of California, San Diego, was engaged in the Naga Expedition in the Gulf of Thailand and the South China Sea during the period of October, 1959, to December, 1960. The expedition was jointly sponsored by the Governments of South Viet Nam, Thailand and the United States of America. It had a two-fold purpose; to collect oceanographic, biological and fisheries data and material and to train scientists and technicians from Thailand and South Viet Nam in oceanography and marine biology. This report is a description of the oceanographic environment in the Gulf of Thailand derived from oceanographic and meteorological data collected for the most part on six cruises in the Gulf between October, 1959, and December, 1960. The cruise plans for the Gulf of Thailand were designed to investigate systematically the distribution and variability of the physical properties of the Gulf waters. The station plan consisted of stations located 30 to 40 miles apart on five parallel lines running perpendicular to the east and west coasts of the Gulf. The lines were 60 to 90 miles apart. Figure 1 is a composite plan for the five Gulf cruises which made complete hydrographic measurements. The stations were numbered chronologically on each cruise. Thus, stations at approximately the same location have different numbers on each of the cruises. Within the limits of navigation the primary stations on each line were at the same location on each cruise. The following physical oceanographic data were collected at each station; reversing thermometer temperatures, salinity and oxygen determinations at standard levels—0, 10, 20, 30 and 50 m—as depth allowed and bathythermograph (BT) temperature observations. The latter were also taken midway between regular stations and at intervals parallel to shore between station lines. Meteorological observations, including wind, air temperature and sea condition, were taken at the time of each BT. Station data and a description of the physical and chemical methods may be found in Faughn, NAGA report, volume 1. The R. V. Stranger of the Scripps Institution of Oceanography carried out an extensive geophysical survey of the Timor Sea between March 29 and April 24,1961, (van Andel and Veevers, 1967) following the completion of the major oceanographic observational programs in the Gulf of Thailand and the South China Sea. During the survey, closely spaced bathythermograph (BT) temperature and wind velocity observations were made. Observed wind velocities, vertical temperature sections along the cruise tracks and horizontal distributions of temperature at standard depth levels based on BT data are the subject of this report. These observations provide a detailed description of the temperature structure of the Timor Sea and complement the more general one given by Wytrki (1961).

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SIO Reference (212)

Temporal metric spaces in radiative transfter theory. III. Characteristic spheroids and ellipsoids

SIO Reference 59-10. The main emphasis of this paper is on the development of a new set of concepts in radiative transfer theory which may eventually broaden its scope of applicability and draw it closer to the discipline of topological dynamics - the mathematics of future physics.

Historical Logbook Databases from California's Commercial Passenger Fishing Vessel (Partyboat) Fishery, 1936-1997

Commercial passenger fishing vessel (CPFV, or ‘partyboat’) logbook data have only been available to the public as two-page reports summarizing sport catch by port area for the calendar year. Electronic records of individual trip logs have been maintained by the Department since 1980, but trip-specific logbook records contain confidential information (vessel-specific) and are not available to the general public. From 1936 to 1978, however, the Department maintained an archive of reports (hard copy sheets) which summarize total monthly CPFV catch and effort for California Department of Fish and Game statistical areas (‘blocks’). These data are the subject of this report.

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Other Scholarly Work (12)

Hydrographic Atlas of the World Ocean Circulation Experiment (WOCE) Volume 4: Indian Ocean

The Hydrographic Programme of the international World Ocean Circulation Experiment (WOCE) was a comprehensive global hydrographic survey of physical and chemical properties, of unprecedented scope and quality, and represents the "state of the oceans" during the 1990s.   This PDF atlas is a copy of the published volume and contains full introductory text.  Web access: doi:10.21976/C61595

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Scripps Institution of Oceanography Technical Report (134)

Informatics and the Environmental Sciences

This report is on the topic of informatics and its relations to scientific research and data - rich, multi-faceted data that represent the earth and environmental systems. Data travel from field and laboratory into collections, repositories and archives. Just as data are a scientific resource, so too the work carried out with data and their organization is a resource for the environmental sciences.

Informatics is concerned with the stewardship of data, that is, with the tending of data and its flow, the design of information systems and their interfaces, and the growth of infrastructure given a distributed variety of data arenas. Enacted at the intersection of information science, environmental science and social science, informatics is evolving as we learn more about information environments and arrangements of human and technical systems. Five informatics ‘good practices’ are identified in this report:

Informatics Good Practices

1. Incorporate data problem formulation and data scoping early in the scientific planning process.

2. Recognize articulation, translation, negotiation and mediation as central to work with data.

3. Partner with appropriate information professionals for data work.

4. Create collaboration opportunities as well as coordination mechanisms for community work.

5. Recognize informatics as conducting research while carrying out information management.

The realm of informatics ranges across spatial, temporal, and organizational scales, weaving together diverse configurations, stretching over physical, digital and conceptual spaces. Many salient topics about data care remain to be discovered or investigated: data classification and provenance; data organization and modeling; data migration and data exchange; data assurance and quality control; data mediation and integration. Along with the development of roles for information professionals, we are learning about the dynamics of information environments, communities, and networks.

Informatics is happening. As we transition from use of ‘my data’ to ‘our data’, changes occur in data, collaborative, and scientific practices. Informatics provides new approaches and tools of interest to environmental scientists, information professionals, and social scientists alike.

I am an information manager privileged to work with several long-term, interdisciplinary projects within the Integrative Oceanography Division (IOD) at Scripps Institution of Oceanography and as an affiliate of the Science Studies Program at UCSD with its dynamic mix of communication, sociology, history and philosophy. Regarding my agenda with informatics, it is twofold: to be a responsible data steward and to partner with environmental science researchers by creating a contemporary information environment that supports concurrently the practice of information management and the inquiry of informatics research.

Seasonal Sand Level Changes on Southern California Beaches

Seasonal airborne and ground-based observations of sand level changes were made along the coast of southern California from 2001 to 2008. Hourly, high alongshore spatial resolution wave estimates from a network of wave buoys and a spectral refraction wave model complement the sand level change data. Water returns from the ocean surface were removed from the airborne lidar elevation observations with a new method using tide and wave data, which was validated with concurrent in situ surveys. The resultant sand levels show high alongshore variability in seasonal shoreline position change along the 120-km survey region. Alongshore variability in wave energy, geologic factors, and sand grain size are hypothesized to control the alongshore variability of the seasonal shoreline change magnitude.

Monthly or more frequent ground-based surveys at four selected focus sites show seasonal shoreline and bathymetry change, with winter shoreline erosion and offshore bar development, and summer shoreline accretion and the loss of the offshore bar. Analysis of surveys completed after a small beach nourishment at Torrey Pines Beach showed the presence of the nourishment through more than one full seasonal cycle.

Observations from Torrey Pines Beach show the dependence of shoreline change on the initial shoreline position and the wave forcing. The observations motivated the development of an equilibrium shoreline change model, which accurately reproduces the observations with four free parameters. With at least two years of monthly surveys or multiple years of appropriately-timed biannual observations used to determine the free parameters, the model accurately predicts withheld observations and is applied at the additional survey sites. Ongoing work includes applying the model at additional locations and investigating the relationship between the tuned parameters and geologic factors.

Categorizing the Types of Surfing Breaks around Jetty Structures

Coastal modifications to control erosion, maintain navigation channels, and create harbors are often undertaken near surfing breaks. Surfing conditions can be improved by these activities, but they can also adversely affect existing surfing breaks. Jetties are coastal structures that on occasion improve surfing conditions. Even though there is an increasing volume of literature on the ways ordinary waves transform into surfing waves, the mechanics of surfing breaks around jetties has not been explored in detail. Four main types of surfing breaks that are created or enhanced by jetties have been identified. The types are dependent on the length of the jetty relative to surfzone width and the degree to which the ebb delta influences wave propagation. Case studies clearly show the behaviors of the different types of jetty breaks. Monochromatic wave refraction modeling of each site has identified the surfing break components that produce the surfing waves. Understanding the effects of a coastal structure on sediment transport, ecology, water quality, shoreline position, and recreation is important to minimize and mitigate any potential negative effects and to streamline coastal permitting. The effects on surfing conditions are being considered more often as the social and economic value of surfing to coastal communities is realized. This research helps to better predict the impact of jetty construction or alteration on surfing conditions.

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Underwater noise caused by snapping shrimp

Crangon (Alpheus) and Synalpheus are the two principal genera of noise-producing shrimp. These animals (not to be confused with commercial shrimp, which are noiseless) are about 3/4 inch to 1-1/2 inches long. They have one enlarged claw which produces a vigorous snap when closed. Over a large colony there is a continuous succession of snaps which causes an intense crackling noise resembling the burning of dry twigs. With increasing distance from the shrimp bed, the crackle merges into a sizzle or a hiss.

The Discrimination Of Transducers Against Reverberations

The directivity index which is currently used for characterizing the directional properties of transducers, refers primarily to their ability to radiate sound power. When transducers are used in echo ranging, the directivity index is, theoretically at least, of minor interest. Of greater interest is the ability of the transducer to discriminate between the echo from a target at which it is pointed, and the reverberation returned to it from this and other directions. This discrimination is measured by other quantities, called reverberation indices. One of these concerns volume, the other surface or bottom reverberation. The purpose of the present work was to study the relations between the three indices.

Conclusions drawn from a study of typical projector patterns are as follows:

1. The volume reverberation index and the surface reverberation index of a projector are linearly related to the directivity index, provided that the directivity pattern is reasonably similar to that of a circular piston in an infinite baffle. This condition is found in the echo-ranging projectors studied when they are operated at 24 kc without domes. However, the directivity index does not provide a reliable measure of the reverberation indices when the projector pattern has abnormally strong side lobes.

2. Neither projector housing studied has appreciable effect on reverberation indices.

3. The echo: reverberation ratio depends almost entirely on the shape of the main lobe of the composite directivity pattern between zero and -6 db. As a result, the reverberation indices of a transceiver can be determined by measuring the width of its directivity pattern at -6 db. Half of this angle will be termed the half-width of the pattern.

4. Since the reverberation indices can be so readily calculated from the half-width, it is recommended that this quantity be specified in describing a transducer. The directivity index usually, but not always, can be calculated from the half-width to within 3 db.

A Survey of Biological Underwater Noises Off the Coast of California and in Upper Puget Sound

UCDWR No. U100. This investigation was undertaken to obtain information onthe northward extension of crackling underwater noises characteristicof the coastal waters of Southern California and for the purpose ofobserving if there were any seasonal changes in background noises inthe Puget Sound area which had been visited previously in November1942. The regions visited include Santa Barbar.a, San Luis Obispo,Monterey and Eureka to Crescent City in California, and AdmiraltyInlet and the San Juan Archipelago in Puget Sound.The characteristic crackling noises produced by snappingshrimps were found only at Santa Barbara, San Luis Obispo, andMonterey. In the northern California and Puget Sound areas wherethese animals have not been reported the waters were relatively freefrom biological noises, only very weak crackling and piping soundswere detected. There was no noticeable seasonal change .in noiseconditions in the Puget Sound area.

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