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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 1827 publications in this collection, published between 1908 and 2022.
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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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 Technical Memorandum (4)

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.

Site Surveys in the North Pacific and Bering Sea from ANTIPODE Expedition

ANTIPODE Legs II and III, from San Francisco to Adak and Adak to Tokyorespectively were conducted by the R/V MELVILLE between 6 July and 19 August1970. Deep Sea Drilling Project (DSDP) site surveys were conducted in conjunctionwith seismic refraction anisotropy surveys at most stations. This report willsummarize just the site surveys while the refraction data will be published elsewhere.  The chief scientist for both legs was George G. Shor, Jr.

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.

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Other Scholarly Work (37)

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

A Surface Recovery Technique for Deep Moored Vertical Arrays

A surface recovery technique was developed for the retrieval of a vertically oriented array which had been anchored at a depth of 4550 meters. The array was severed within 100 meters of the bottom in order to retrieve two faulty anchor releases as well as the scientific instrumentation.

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Scripps Institution of Oceanography Technical Report (146)

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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SIO Reference (215)

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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