Research Project (150pts)

During the course of the semester you will do an experiment dealing with seed germination.  You are responsible for the design, implementation, funding, and completion of the experiment and related assignments, described below. You may work in pairs or individually.  If you work in pairs all written materials must be done individually.  That means written individually, interpreted individually, etc., i.e. do not turn in two copies of the same abstract, etc.  The purpose of the project is to give you experience in the process of science, particularly thesis research and preparation.  You will have problems to solve, so it is best to get started immediately.  Also, once your project is under way, you must bring in your seedlings or other proof of the reality of your project.  You will not receive full credit on your assignment unless you do so. 

Literature Search

                 We will be doing an orientation at the CSUSM library (http://library.csusm.edu/), to expose you to online search engines designed to search for academic journal articles.  Journal articles are required as part of your literature research related to the subject of your seed germination project. 

                Useful search engines include the following.  EBSCOHOST (Academic elite version) contains both scholarly and popular articles, and both abstracts and full text articles. SCIENCE DIRECT has full text peer reviewed articles.  IDEAL has both abstracts and full text articles.  FIRST SEARCH contains abstracts.  BASIC BIOSIS is composed of abstracts. All search engine abstracts or articles can be saved to disc or emailed to your home.

                Through the Palomar library peer reviewed, full-text journal articles at http://www.palomar.edu/library//OnlineDatabases/databases.htm .  Once through to the site, go to JSTOR, Ecology and Botany.

                Use key words such as seed, seedling, germination, growth, and the specific subjects you may be interested in to find relevant articles.  With most search engines using the word, AND, combines databases, whereas the word, OR, finds only those articles that contain all the elements of interest.  For example if you were interested in whether smoke triggers seed germination, searching SEED AND GERMINATION AND SMOKE would yield all articles that had the word seed in the title, germination in the title, and smoke in the title.  This would potentially be thousands of articles.  If you searched for SEED OR GERMINATION OR SMOKE the search would yield only those articles whose titles had the words seed, germination, and smoke in the same title.

                Articles may also be accessed through the National Agricultural Library at www.nal.usda.gov/ search.htm or the International Directory of Botany at www.helsinki.fi/kmus/botmenu.html.   If you are looking for books, useful Library of Congress call numbers are SB (Botany), and QK (Plant Physiology).

Step 1     20 pts                     Due Date: February 10

Step 1 will consist of the following three sections.  Each section should be separate, and titled as below.  Remember, all formal writings are done in the third person.

1.        Abstract:  Prepare an abstract of 100 words or less describing what you plan to do.  An abstract is a brief summary of the planned experiment.  The abstract should clearly state the hypothesis you are testing, how you are testing the hypothesis, and results (once obtained).

2.        Experimental Design:  explain the design and procedure of your experiment in as much detail as possible.  Also define the control group, test (experimental) group(s), independent variable, dependent variables, and controlled variables.  Include a timeline of when you expect to complete various parts of your experiment.  Use diagrams if helpful.  I need to understand what you are going to do, and how you are going to do it.

3.        Bibliography:  List at least three sources you consulted in researching your topic. Follow the bibliographic guidelines provided, explicitly.   Neither your textbook, nor I may be included as one of the minimum of three.

Step 2                     40pts                                      Due Date: March 17

Step 2 will consist of the following elements:

1.        Introduction to your research paper:
 The purpose of the introduction is to familiarize the reader with the general background of the project.  In our case, you will discuss the role of the seed in the flowering plant life cycle; seed structure; seedling growth and germination, and factors that affect seedling growth and germination including scarification; and the specific factors you are testing. Give examples of previous research that has influenced your test, or lends credibility to your test. The last sentence of your introduction should clearly state your hypothesis (The purpose of this exercise is to test the effect of                             on             ). 

In the text of your paper you must cite all information that was not your own original research.  Citing gives credit to sources of information that are not your own original research.  In reality, virtually every sentence of the introduction can be cited.  It is best to have as many sources as possible, and never go more than a paragraph without a citation, i.e. the last sentence of the paragraph should always be cited.  Some examples of citing are listed below.  Let’s say you found information on seed structure from a botany book by C. Rodriguez, PhD., published in 2001.  You could cite as follows:

The radish seed is a dicot, meaning the embryo has two cotyledons (Rodriguez, 2001).
The radish seed is a dicot, meaning the embryo has two cotyledons¹.
The radish seed is a dicot, meaning the embryo has two cotyledons (1).

In each example the source is cited inside of the period.  If you cited by last name, the Literature Cited page (see below) would list sources in alphabetical order and they should not be numbered.  In the examples in which a number is used, the sources are numbered and listed on the Literature Cited page, in the order in which they are first used.  You may cite Rodriguez many more times, but he would always be cited as “1” because he was the first source cited.  The introduction will be freely cited.  If you are not sure whether to cite information or not--then CITE! The introduction, and all parts of this thesis, should be written in the third person.
 

2.        Literature Cited
All literature cited in the introduction should be listed on a separate page, strictly adhering to the bibliographic format provided.  Consult with me early if you have citations that do not fit the format provided or if you are confused.  If you do not specifically refer to a source in your introduction, you may not list it as “Literature Cited,” because you did not cite it in your paper.  You must cite a minimum of six sources, at least three of them peer reviewed journal articles.  Neither your textbook, nor I can be one of your six citations.

Step 3                     90pts                                      Due Date: April 26

Step 3 is your Research Paper to be organized as below.  The paper should be written in the third person.  Factors that will be considered in grading include: presentation; quality of writing; properly citing and listing citations; effective use of diagrams, charts, tables, etc.; and proper and effective statistical analysis to include a randomization analysis or other “goodness of fit” test to include confidence levels.  The paper should be a minimum of 1500 words excluding data, and at least six references should be cited excluding your textbook or me, with at least 3 coming from peer reviewed journal articles.  I prefer the papers be stapled, and not in a binder of any kind. You must also show proof that you did the experiment.  You may bring in the seedlings when you are finished, bring in a picture, etc.  Failure to show proof will lead to a 20% penalty on your paper.

A.                  Title page (include the following): Project title; by (your name); Biology 201; Dept. of Life Sciences, Palomar College, 1140 W. Mission Rd., San Marcos, Ca. 92069-1487; Due Date.

B.                   Blank page: (put a handwritten word count on this page in pencil, i.e. the number of words excluding tables and data).

C.                   Your paper--the parts of the paper will be continuous, one part with another.  Space appropriately and label the different parts of the paper.  The paper should be organized as below.  The words in bold print are required headings.

1.                  You should begin with the title again near the top of the page, and your name as the author listed a couple of spaces beneath the title.  Skip a few more spaces.

2.                    Abstract. The abstract should be 100 words or less.  A brief summary of your experiment to include what you were testing, how you did it, and results.  Write in past tense, third person.

3.                    Introduction:  Described previously.  Modify and improve the introduction, if necessary.

4.                    Materials and Methods:  A detailed description of your experimental design, materials used, and the step-by-step process involved in your experiment.  The reader should be able to duplicate your set-up (and results) by carefully following your procedure.  Use diagrams as necessary.

5.                    Results:  Describe the data generated in your experiment.  Use tables, charts, or graphs where appropriate.

6.                    Discussion:  This is where you statistically analyze your results and discuss their relevance to your hypothesis.  Charts, graphs, and tables may be useful.  You want the reader to clearly understand what your results mean.  You must apply Randomization, t-test, chi-square, or other relevant statistical analysis to your data, and determine whether differences in control and experimental data sets show a significant difference.  Explain the steps in your statistical analysis, and be very explicit.  Clearly state whether you accept or reject the null and alternate hypotheses (be sure to define them, as well). The reader should clearly understand what your results mean, and whether you accept, reject, or have modified your hypothesis.  Use charts or graphs where appropriate.

7.                    Conclusion:  Briefly summarize your results and readdress your original hypothesis.  Were results as you expected?  Were there problems in experimental design?  Is further research needed?  What is the value of your experiment?  What might you have done differently, etc.

8.                    Literature Cited:  You will list all literature cited in your paper.  The Literature Cited page will be the last page of your paper--it will be separate from the rest of the paper.  List by author or number depending on your preference.  In the text of your paper you must cite all information that was not your own original research!   The introduction should be freely cited.  If you are not sure whether to cite information or not--then CITE!

Common Mistakes and Penalties

• A.                  Not showing proof of experiment (20points).

• B.                   Abstract more than 100 words (10points).

• C.                   Formatting errors on Literature Cited page (10 points per).

• D.                  Fewer than 3 peer reviewed journals (20 points).

• E.                   Fewer than six sources on Literature Cited page (20 points).

• F.                   Listing references on Literature Cited page, not cited in the thesis (10 points per).

• G.                   Citing references and not listing them on the Literature Cited page (10 points per).

• H.                  Writing in the first person.

• I.                     Improperly formatting thesis. (10 points min).

• J.                    Not clearly stating hypothesis (10 points).

• K.                  Not properly explaining rationale of statistical evaluation.

• L.                   Not explicitly defining steps in statistical evaluation.

• M.                 Not defining and addressing null and alternate hypotheses in discussion.

• N.                  Not stating or properly interpreting p value and confidence.

• O.                  Not addressing weaknesses/flaws of design and implementation in conclusion.

The format for your references is listed below:

 1. Journal article, one author.

 Smith, D.  2000.  Intestinal parasites.  Journal of Parasitology 1(4): 102-110.

 The 1 represents the journal volume, the (4) journal number in that volume, and 102-111 the page numbers of the article.

 2. Pamphlet or booklet published by local agency (two authors).

 Smith, D., and J. Jones.  2000.  Adolescent feeding patterns.  American Dietetic Assn.  Los

                Angeles, Ca.  34 pp.

Notice that if there is a second author, it is listed by first initial and then last name, and that if the citation is more than one line, the second line is indented with the first line left justified. 34 pp means 34 total pages.

3. A book (three authors)

Smith, D., J. Jones, and J. Johnson.  2000.  The bats of North San Diego County.  Oxford Univ. Press, London.  254 pp.

If there had been more than three authors list authors as: Smith, D., et al.  1996.  Books list total number of pages so the 254 pp is total pages.

 4. A scientific bulletin (no author).

 Evolutionary principle and you.  1998.  Bernice P. Bishop Museum. Honolulu Bull.  172 pp.

 Always attempt to cite by author.  If no author is known, cite by editor.  If no editor is known cite by title.

 5. Citing of "personal communications" with an expert in the field.

 Bray, Richard.  1999.  Personal communications.  Prof. of Biology.  Calif. State Univ.  San Marcos, Ca.

 6. One article within an encyclopedia.

Halstead, B. 2000.  Poisonous and dangerous marine animals.  pp. 105-115 in Encyclopedia of Marine              Invertebrates. Vol. 93  (C. Brown.  ed.).  Academic Press, New York.

An encyclopedia is not a credible source for formal papers, unless it is a scientific encyclopedia.    Encyclopedia Britannica is not a scientific encyclopedia.  The page numbers are those of the article.

7. One article within an encyclopedia--no author, editor unknown.

Barrier reef cnidarians.  2001. pp 200-210  in Encyclopedia of Marine Invertebrates Vol. 93(C. Brown.  ed.).  Academic Press, New York.

Note that the year of publication follows the title if no author or editor is known.

8. Book, listed by editor (if no author listed).

Key, R.E.  (ed.)  2000.  A naturalist's guide to Guam.   Guam Science Teacher's Assoc., Agama, Guam.    160 pp.

9. Internet articles:

Author.  Year.  Title.  <URL>

Jones, Jim.  2000.  Arctic ecosystems. <http://www.jones.coyote.edu.jimbo.eco/>