Oceanography 443 - Class discussions and participation

Goals

One of the most important aspects of any research project is a thorough and critical review of the literature. In order to facilitate this, we have put together a suggested reading list, many articles of which are available through library reserve, including some downloadable from electronic reserve. Additionally, we will be discussing several articles in class; these articles were chosen not only to familiarize you with regional features, but also to help you approach scientific claims and arguments critically. It is not sufficient for something to have been published for us to believe it. Instead we need to ask some basic questions: What methods were used? What assumptions were made? Are conclusions supported by the available data and consistent with known facts? (In short, every paper demands that we ask the question, "Do I believe this -- and if so, why?") Reviewing the literature is also an opportunity to identify questions that interest you and methods of possible use to you. A literature review functions as a first ‘gauntlet’ through which to test your own ideas and challenge the ideas of others. Finally, if you review the literature well, you are not likely to spend valuable resources (time and money) reinventing the wheel or repeating someone else’s mistakes. Specific papers that we will discuss together in class include the following:

Chavez, F. P. and R. C. Brusca. 1991. The Galapagos Islands and their relation to oceanographic processes in the tropical Pacific. In GALAPAGOS MARINE INVERTEBRATES, pp. 9-33. M. J. James (ed.). Plenum Press, NY.

Feldman, G., D. Clark and D. Halpern. 1984. Satellite color observations of the phytoplankton distribution in the eastern equatorial Pacific during the 1982-1983 El Nino. Science 226: 1069-1071.

Feldman, G. 1986. Patterns of phytoplankton production around the Galapagos Islands. In: TIDAL MIXING AND PLANKTON DYNAMICS, pp. 77-106. M. J. Bowman and C. M. Yentsch (eds.). Springer-Verlag, NY.

Martin, J. H. and 43 other authors. 1994. Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean. Nature 371: 123-129.

All of these papers have been put on hard-copy and electronic reserve. An additional paper that you may care to take a look at is Kessler's review of circulation in the Equatorial Pacific, though we may not have time to discuss it in class.

Methods

One of the best ways to do a literature search is by looking at the references cited in the papers you've already read. For example, Chavez and Brusca (1991; above) cite ~95 papers at the end of their chapter, the vast majority specifically pertaining to the Galapagos. These references are obviously a good place to start a literature review. One shortcoming of such an approach, however, is that the references are necessarily dated -- Chavez and Brusca, for example, don't cite work accomplished after 1991. Thus, it is also helpful to do a database search, as described below. Beware that databases too have their shortcomings, frequently missing important and relevant papers either because they use slightly different terminology than your search criteria, or because they were published in a time span or in a journal that the database doesn't cover. Finally, note that expert help in library research can be found by making an appointment at the Natural Sciences Library Research Labs (543-1244) for one-on-one assistance with a librarian.

Introduction to Literature Searching

A number of databases having information on current and past scientific articles are available from the UW Libraries Information Gateway. These databases can also be accessed and used on the World Wide Web through the Fisheries-Oceanography Library Homepage:

http://www.lib.washington.edu/Fish

The UW Libraries, including the Fish-Ocean Library, have computer access to these databases (via WEBSPIRS) and they can be accessed from any computer with a web connection and a UW IP address.

The database most often used for oceanography, fisheries, and related articles is:

Aquatic Sciences and Fisheries Abstracts, 1978-(AFSA)

The most recent papers published in a wide range of fields are listed in:

Current Contents Search, 1996-

You should search the above two databases articles relevant to your project. Try AFSA first; it includes current articles too. Additionally, here are some other databases you might want to try if you don’t find what you need in AFSA or Current Contents:

Life Sciences Collection, 1982-(especially useful for biological/zoological subjects)

GeoRef, 1786-(earth sciences and geology)

GeoBase, 1980-(geography, ecology, earth, and marine sciences)

BIOSIS, 1975-(life sciences, ecology, zoology, and microbiology)

Good books and articles can be found elsewhere in the Libraries’ online resources, so don’t limit your searches exclusively to the databases.

The University of Washington carries most academic/scientific journals, and the Fisheries-Oceanography Library has most oceanography, fisheries, and marine science related publications. The latest issues of journals are displayed unbound in racks, and the volumes of older issues are shelved by call number. You can find out which library carries the publication(s) you want and its call number by using the UW Libraries Catalog. There is a link to the catalog on the Fish-Ocean Homepage and Information Gateway. Publications/sources of articles can include journals, conference proceedings, books, etc. All publications that the UW carries should, however, be on file in the UW Libraries catalog by title of journal, series title, etc. Ask staff for assistance if you are having difficulty finding materials.

You will almost always need the full title of a journal to find it in the UW Libraries catalog. Unfortunately, most science databases still use the abbreviated titles of journals in their records. If it is not possible to decipher the full title, you may ask your instructor or TA, or (better yet) look it up in the book CASSI: Chemical Abstracts Service Source Index located in the reference stack of the Fish-Ocean Library. CASSI contains full titles of almost all scientific journals, listed in alphabetical order by the abbreviated title. The bolded part of the title is its standard abbreviation. Another source for complete titles is a website named "All That JAS: Journal Abbreviation Sources" (www.public.iastate.edu/~cyberstacks/JAS.htm).

Next is an example of searching for and obtaining an article. This can serve as a review/reminder of the skills you developed in Ocean 442. If you are unfamiliar with using the databases, do the example on a computer to learn the process. For more help on how to construct searches, valid search statements, etc., click the 'Help' button in the search window. Librarians are always available for additional assistance.

EXAMPLE: Searching for articles about red tides in our area

1. OPEN THE DATABASE

Open the World Wide Web to the Fish-Ocean Library Homepage: http://lib.washington.edu/Fish

Click on Databases & Catalogs (under "Find It") or "Journal Databases, A-Z;"
Scroll down to Aquatic Sciences and Fisheries Abstracts, 1978- and click on it;
Wait.....the search window appears.

2. SEARCH FOR ARTICLES

Leave search set for 'Words Anywhere'
Type red tide* (* means that any string of characters with this root will be searched);
Leave search set for 'Any Year' - Don't click on any of the five languages listed;
Click the 'Search' button. Wait…..
Search - Results: 2157 Records appears. This is too many to look through!

You will need to limit the search, but first let’s see what types of articles have been found about red tides in order to determine how to move around in the display window.

The most recent articles are displayed first, 10 at a time, and the records appear in the following format:

The title of the article

The author(s) of the article

SO The source of the article, usually: journal name (abbreviated)

Publication year, volume, number, and pages

Language

The Abstract of the article

Subject headings

The Abstract number

*LHM

Local Holdings (call number and library location)

Scroll down through the record using the scroll button on the right side of the screen. (Note that many of the articles are in languages other than English).
Click on 'Next' to display the next 10 articles
Click on 'Previous' to return to the first 10 articles
Now go back to the Search window and construct a more limited search:
Click on 'Back to Search' button to get back to the Search window.
Leave it set on 'Words Anywhere'
Type in the search box: red tide* and Puget Sound
Click on the box for 'English' to limit the search to English articles
Leave it set for 'Any Year'
Click on 'Search' button. Wait.....
Search-Results: 6 Records. This is a reasonable number!
Records are displayed automatically for most recently executed search.

3. FIND THE LIBRARY HOLDINGS

All the Webspirs databases include a field labeled *LHM, or Local Holdings. Here is where you can find out what library has the journal or book indicated in the SO (source) field, and what the call number is. If the message "Local holdings could not be determined" appears in the *LHM field, then you should consult the UW Libraries Web catalog. If the source is a book, for example, or conference proceedings published as a book, then Webspirs can’t determine whether or not the UW Libraries owns the item. When searching the catalog for these kinds of items, try searching in the Title box or the Keywords box. When the library has an electronic subscription to a journal, the link is provided in the LHM field.

All that remains is to take down the call number and go get the volume from the stacks. After you’ve read the article (or maybe only the Abstract), you’ll know whether you’ve ferreted out valuable information from among the seemingly limitless information in the stacks (congratulations!) or whether you have to go back to AFSA and the other databases and search some more.

4. URLs TO SEARCH BY

UW Libraries Information Gateway

http://www.lib.washington.edu

Fisheries-Oceanography Library

http://www.lib.washington.edu/fish

UW Libraries Catalog

http://catalog.lib.washington.edu/search~

Remember, Library staff are always available and willing to answer your questions. For expert one-on-one assistance in researching a specific topic, you can make an appointment with one of the librarians in the Natural Sciences Library.

EXAMPLE OF SEARCH OUTPUT

Usage is subject to the terms and conditions of the subscription and License Agreement and the applicable Copyright and intellectual property protection as dictated by the appropriate laws of your country and/or International Convention.

Factors controlling paralytic shellfish poisoning (PSP) in Puget Sound, Washington

Rensel,-J

83. Annu. Meet. of the Natl. Shellfisheries Assoc. Special Symp. : Harmful Phytoplanktonic and Shellfish Interaction, Portland, OR (USA), 30 May-3 Jun 1993

J.-SHELLFISH-RES. 1993 vol. 12, no. 2, pp. 371-376

*LHM

See records of latest issues received--http://catalog.lib.washington.edu/record=b2022341

Location: Fisheries-Oceanography Reserve

-- Call number: 639.406 N213p

-- LIB HAS: v. 45-70, no.2. (1954-1980.)

Location: Microforms Newspapers

-- Call number: Microcards

-- LIB HAS: 1952-1955, 1958-1960

See records of latest issues received – http://catalog/lib.washington.edu/record=b2057706

Location: Fisheries-Oceanography General Stacks

-- Call number: SH365.A1 J37

-- LIB HAS: v.1-(June 1981-)

-- UNBOUND ISSUES ON RESERVE

English

PSP has spread throughout much of Puget Sound, Washington since the mid 1970s. Now all but parts of southern Puget Sound and all of central and southern Hood Canal are periodically affected by PSP. There are important sport and commercial shellfish beds in these areas that could be threatened by further expansion of PSP. The initial spread of PSP has been traced to major physical events, but the lack of PSP in most of southern Puget Sound and all of central and southern Hood Canal has not been investigated. Monitoring and preliminary experimental data suggest that the low concentration of surface and subsurface (10 m) nitrogen in the unaffected areas prevents the growth of Alexandrium catenella. Increased nitrogen discharge from rapid urbanization and non-point sources could lead to PSP problems in areas presently unaffected by PSP, unless preventive measures are taken.

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[an error occurred while processing this directive] Introduction Goals, Logistics and Assignments Instructors Students Course Schedule Proposal Guidelines Research Vessels Related Links Measurements and Equipment Student message board E-Submit	Oceanography 443, Fall 2005 Design of Oceanographic Field Experiments Class discussions and participation Goals One of the most important aspects of any research project is a thorough and critical review of the literature. In order to facilitate this, we have put together a suggested reading list, many articles of which are available through library reserve, including some downloadable from electronic reserve. Additionally, we will be discussing several articles in class; these articles were chosen not only to familiarize you with regional features, but also to help you approach scientific claims and arguments critically. It is not sufficient for something to have been published for us to believe it. Instead we need to ask some basic questions: What methods were used? What assumptions were made? Are conclusions supported by the available data and consistent with known facts? (In short, every paper demands that we ask the question, "Do I believe this -- and if so, why?") Reviewing the literature is also an opportunity to identify questions that interest you and methods of possible use to you. A literature review functions as a first ‘gauntlet’ through which to test your own ideas and challenge the ideas of others. Finally, if you review the literature well, you are not likely to spend valuable resources (time and money) reinventing the wheel or repeating someone else’s mistakes. Specific papers that we will discuss together in class include the following: Chavez, F. P. and R. C. Brusca. 1991. The Galapagos Islands and their relation to oceanographic processes in the tropical Pacific. In GALAPAGOS MARINE INVERTEBRATES, pp. 9-33. M. J. James (ed.). Plenum Press, NY. Feldman, G., D. Clark and D. Halpern. 1984. Satellite color observations of the phytoplankton distribution in the eastern equatorial Pacific during the 1982-1983 El Nino. Science 226: 1069-1071. Feldman, G. 1986. Patterns of phytoplankton production around the Galapagos Islands. In: TIDAL MIXING AND PLANKTON DYNAMICS, pp. 77-106. M. J. Bowman and C. M. Yentsch (eds.). Springer-Verlag, NY. Martin, J. H. and 43 other authors. 1994. Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean. Nature 371: 123-129. All of these papers have been put on hard-copy and electronic reserve. An additional paper that you may care to take a look at is Kessler's review of circulation in the Equatorial Pacific, though we may not have time to discuss it in class. Methods One of the best ways to do a literature search is by looking at the references cited in the papers you've already read. For example, Chavez and Brusca (1991; above) cite ~95 papers at the end of their chapter, the vast majority specifically pertaining to the Galapagos. These references are obviously a good place to start a literature review. One shortcoming of such an approach, however, is that the references are necessarily dated -- Chavez and Brusca, for example, don't cite work accomplished after 1991. Thus, it is also helpful to do a database search, as described below. Beware that databases too have their shortcomings, frequently missing important and relevant papers either because they use slightly different terminology than your search criteria, or because they were published in a time span or in a journal that the database doesn't cover. Finally, note that expert help in library research can be found by making an appointment at the Natural Sciences Library Research Labs (543-1244) for one-on-one assistance with a librarian. Introduction to Literature Searching A number of databases having information on current and past scientific articles are available from the UW Libraries Information Gateway. These databases can also be accessed and used on the World Wide Web through the Fisheries-Oceanography Library Homepage: http://www.lib.washington.edu/Fish The UW Libraries, including the Fish-Ocean Library, have computer access to these databases (via WEBSPIRS) and they can be accessed from any computer with a web connection and a UW IP address. The database most often used for oceanography, fisheries, and related articles is: Aquatic Sciences and Fisheries Abstracts, 1978-(AFSA) The most recent papers published in a wide range of fields are listed in: Current Contents Search, 1996- You should search the above two databases articles relevant to your project. Try AFSA first; it includes current articles too. Additionally, here are some other databases you might want to try if you don’t find what you need in AFSA or Current Contents: Life Sciences Collection, 1982-(especially useful for biological/zoological subjects) GeoRef, 1786-(earth sciences and geology) GeoBase, 1980-(geography, ecology, earth, and marine sciences) BIOSIS, 1975-(life sciences, ecology, zoology, and microbiology) Good books and articles can be found elsewhere in the Libraries’ online resources, so don’t limit your searches exclusively to the databases. The University of Washington carries most academic/scientific journals, and the Fisheries-Oceanography Library has most oceanography, fisheries, and marine science related publications. The latest issues of journals are displayed unbound in racks, and the volumes of older issues are shelved by call number. You can find out which library carries the publication(s) you want and its call number by using the UW Libraries Catalog. There is a link to the catalog on the Fish-Ocean Homepage and Information Gateway. Publications/sources of articles can include journals, conference proceedings, books, etc. All publications that the UW carries should, however, be on file in the UW Libraries catalog by title of journal, series title, etc. Ask staff for assistance if you are having difficulty finding materials. You will almost always need the full title of a journal to find it in the UW Libraries catalog. Unfortunately, most science databases still use the abbreviated titles of journals in their records. If it is not possible to decipher the full title, you may ask your instructor or TA, or (better yet) look it up in the book CASSI: Chemical Abstracts Service Source Index located in the reference stack of the Fish-Ocean Library. CASSI contains full titles of almost all scientific journals, listed in alphabetical order by the abbreviated title. The bolded part of the title is its standard abbreviation. Another source for complete titles is a website named "All That JAS: Journal Abbreviation Sources" (www.public.iastate.edu/~cyberstacks/JAS.htm). Next is an example of searching for and obtaining an article. This can serve as a review/reminder of the skills you developed in Ocean 442. If you are unfamiliar with using the databases, do the example on a computer to learn the process. For more help on how to construct searches, valid search statements, etc., click the 'Help' button in the search window. Librarians are always available for additional assistance. EXAMPLE: Searching for articles about red tides in our area 1. OPEN THE DATABASE Open the World Wide Web to the Fish-Ocean Library Homepage: http://lib.washington.edu/Fish Click on Databases & Catalogs (under "Find It") or "Journal Databases, A-Z;" Scroll down to Aquatic Sciences and Fisheries Abstracts, 1978- and click on it; Wait.....the search window appears. 2. SEARCH FOR ARTICLES Leave search set for 'Words Anywhere' Type red tide* (* means that any string of characters with this root will be searched); Leave search set for 'Any Year' - Don't click on any of the five languages listed; Click the 'Search' button. Wait….. Search - Results: 2157 Records appears. This is too many to look through! You will need to limit the search, but first let’s see what types of articles have been found about red tides in order to determine how to move around in the display window. The most recent articles are displayed first, 10 at a time, and the records appear in the following format: TI The title of the article AU The author(s) of the article SO The source of the article, usually: journal name (abbreviated) Publication year, volume, number, and pages LA Language AB The Abstract of the article DE Subject headings AN The Abstract number LHM Local Holdings (call number and library location) Scroll down through the record using the scroll button on the right side of the screen. (Note that many of the articles are in languages other than English). Click on 'Next'* to display the next 10 articles Click on 'Previous' to return to the first 10 articles Now go back to the Search window and construct a more limited search: Click on 'Back to Search' button to get back to the Search window. Leave it set on 'Words Anywhere' Type in the search box: *red tide and Puget Sound Click on the box for 'English' to limit the search to English articles Leave it set for 'Any Year' Click on 'Search' button. Wait..... Search-Results: 6 Records*. This is a reasonable number! Records are displayed automatically for most recently executed search. 3. FIND THE LIBRARY HOLDINGS All the Webspirs databases include a field labeled LHM, or Local Holdings. Here is where you can find out what library has the journal or book indicated in the SO (source) field, and what the call number is. If the message "Local holdings could not be determined" appears in the LHM field, then you should consult the UW Libraries Web catalog. If the source is a book, for example, or conference proceedings published as a book, then Webspirs can’t determine whether or not the UW Libraries owns the item. When searching the catalog for these kinds of items, try searching in the Title box or the Keywords box. When the library has an electronic subscription to a journal, the link is provided in the LHM field. All that remains is to take down the call number and go get the volume from the stacks. After you’ve read the article (or maybe only the Abstract), you’ll know whether you’ve ferreted out valuable information from among the seemingly limitless information in the stacks (congratulations!) or whether you have to go back to AFSA and the other databases and search some more. 4. URLs TO SEARCH BY UW Libraries Information Gateway http://www.lib.washington.edu Fisheries-Oceanography Library http://www.lib.washington.edu/fish UW Libraries Catalog http://catalog.lib.washington.edu/search~ Remember, Library staff are always available and willing to answer your questions. For expert one-on-one assistance in researching a specific topic, you can make an appointment with one of the librarians in the Natural Sciences Library. EXAMPLE OF SEARCH OUTPUT Usage is subject to the terms and conditions of the subscription and License Agreement and the applicable Copyright and intellectual property protection as dictated by the appropriate laws of your country and/or International Convention. Copyright Information TI Factors controlling paralytic shellfish poisoning (PSP) in Puget Sound, Washington AU Rensel,-J CO 83. Annu. Meet. of the Natl. Shellfisheries Assoc. Special Symp. : Harmful Phytoplanktonic and Shellfish Interaction, Portland, OR (USA), 30 May-3 Jun 1993 SO J.-SHELLFISH-RES. 1993 vol. 12, no. 2, pp. 371-376 LHM See records of latest issues received--http://catalog.lib.washington.edu/record=b2022341 Location: Fisheries-Oceanography Reserve -- Call number: 639.406 N213p -- LIB HAS: v. 45-70, no.2. (1954-1980.) Location: Microforms Newspapers -- Call number: Microcards -- LIB HAS: 1952-1955, 1958-1960 See records of latest issues received – http://catalog/lib.washington.edu/record=b2057706 Location: Fisheries-Oceanography General Stacks -- Call number: SH365.A1 J37 -- LIB HAS: v.1-(June 1981-) -- UNBOUND ISSUES ON RESERVE LA English AB PSP has spread throughout much of Puget Sound, Washington since the mid 1970s. Now all but parts of southern Puget Sound and all of central and southern Hood Canal are periodically affected by PSP. There are important sport and commercial shellfish beds in these areas that could be threatened by further expansion of PSP. The initial spread of PSP has been traced to major physical events, but the lack of PSP in most of southern Puget Sound and all of central and southern Hood Canal has not been investigated. Monitoring and preliminary experimental data suggest that the low concentration of surface and subsurface (10 m) nitrogen in the unaffected areas prevents the growth of Alexandrium catenella. Increased nitrogen discharge from rapid urbanization and non-point sources could lead to PSP problems in areas presently unaffected by PSP, unless preventive measures are taken. AN 3560829 Back to Record Display
Last modified: 9/29/2005 5:12 PM