HOW TO RESEARCH AND WRITE A SYNOPSIS OR TERM PAPER
Before writing, it is necessary to read and take notes. But how do you pick a topic and find suitable reference material?
Science writing falls into several categories:
1. Popular science (e.g. Time magazine, New York Times)
2. Web pages e.g. Google search, Wikipedia
3. Textbook (e.g. Biology, the science of life)
4. Reviews (e.g. Scientific American, Annual Reviews)
5. Primary source (e.g. articles and letters in Science, Nature, …)
Of these, the first three categories could help in choosing a topic of interest. If literature references are cited in the paper you are reading, as in the 4th and 5th categories above, it could be cited as a reference in your writing for an upper division science course.
Annotation. Authors of research papers generally take a reader’s background knowledge for granted. In some cases, you may have to acquire such background knowledge, fill in gaps, or establish that you have the necessary foundation. Reading research papers helps you to circumscribe the required body of knowledge. Just getting through the introduction of a research paper may be slow going. You should therefore write detailed notes as you read.
One way to circumscribe the field of molecular biology using primary source journal articles is to keep a first-rate textbook like Stryer’s Biochemistry or Alberts’ Molecular Biology of the Cell at hand as a reference. Whenever you encounter something which needs explanation, annotate (make a note) on your copy of the paper. Look up the key words in the index of Stryer. If you don’t find what you are looking for, try again with a different first word. Continue through the paper in this way, referring to the textbook for explanation as necessary.
Annotation (taking notes on your reading) will be helpful for both instructional and diagnostic purposes. The purpose of annotation is to clarify, explain or reference a statement. To be effective, each note should be your explanation for a specific phrase or concept in the paper. The most important and least familiar of the points made in the paper should be marked and explained. The key words and phrases in an article are those that seem important. The index of a textbook is alphabetical with headings and subheadings. Note the page numbers and read the pages in the text. It is easier to use the Index than the Table of Contents because it is alphabetical by topic.
Annotation is a useful study skill, regardless of whether the backup work it leads to is all new, all review, or in between. As review, it informs you of what you already know and prepares you to delve into the Results and Discussion of the paper with more understanding. As new learning, it informs you of the complexity and boundaries of the field. We will practice annotation together as a sample exercise. Don’t be alarmed by the time required for close reading of primary source material. It is a learned skill which improves with general and specialized knowledge, experience and practice.
References. Every scientific paper has literature References. In some journals, the Reference section may be used to explain or describe the Methods as well as to refer to the literature. A recent development is the SOM (Supplemental Online Material), which can in the extreme case expand a one page paper to 30 pages! We will see examples of SOM in our close reading of recent journal articles.
In researching a term paper, start with a recent paper so that the references will be up-to-date and comprehensive. Use the reference section and read the relevant articles referred to in the text. You will know that you have circumscribed the subject when most of the important references in a paper you are reading are ones you have already read.
Methods. Editors and publishers use fine print to “bury” the methods and thereby save space. Cell and Nature put the Methods at the end of the paper, just before References. Science puts Methods in Figure Legends and Notes. For a while, The Journal of Biological Chemistry used a Miniprint section following References which was so small, you had to use a magnifying glass to read it! Some journals put detailed methods in SOM.
Methods are Important! You can’t understand results unless you know how the experiments were done. Methods in molecular biology are complex and sophisticated. Authors assume that you would not be reading the work if you didn’t already know most of the concepts behind the methods. Joining this scientific elite requires hard work. Start now by explaining any method you mention in your writing.
Internet resources and avoiding plagiarism. These days, most of the background you need to know for term paper research can be found on Wikipedia or elsewhere on the Net. On the whole, the information available there is accurate and well written. How to produce original science writing when so much has already been well written? First of all, replace the information you obtain from web pages with proper science references. It is all right to download and paste in figures, as long as you cite the source in the text and reference section of your paper, but copying and pasting text, including figure legends, is unacceptable. Direct quotations from papers should not be used, even with proper referencing. Downloading text is unacceptable. Paraphrase, don’t plagiarize!
Your scientific writing will be checked for originality using SafeAssign through Blackboard. When you submit to SafeAssign as a draft, your paper will not be added to the database. That way, you can submit it repeatedly with revisions to eliminate patches that are lacking in originality. Only the final version will be stored in the database. Only a version that passes SafeAssign will be scored, and a final submitted version that does not pass SafeAssign provides a basis for a report to the Office of Academic Affairs as an infraction on academic integrity, which typically will receive a ‘0’ for the assignment as the penalty.
PARTS OF A SCIENTIFIC PAPER
Authors and Affiliations
Write briefly in your own words the purpose of each of these parts.
TERM PAPER RESEARCH
Back to References. When researching a term paper, use a good science library. Start with PubMed!. PubMed is an online database for biochemistry and molecular biology literature searching. PubMed can be accessed through the National Library of Medicine website at the National Center for Biotechnology Information (http:\\www.ncbi.nlm.nih.gov/). When the site opens up, click on PubMed. Then click on the colored rectangle (dialog box) and enter the key words or author (last name followed by initials, no punctuation) for your search. Then click on Search. After the search is done, you can click on the titles to see and print abstracts. Some full length papers are also available online (open access). You can click on Related Papers to see additional references. Internet access can be obtained at various places at York College; ask at the library or see your instructor.
A variety of primary source journals should be consulted, including Nature, Science, Proceedings of the National Academy of Sciences, Molecular and Cellular Biology, Cell, Nucleic Acids Research, Journal of Molecular Biology and The Journal of Biological Chemistry. We have some of these journals in the York College library. Besides, York College subscribes to a literature service such as Science Direct, and additional papers that are not included in the online collection can be obtained electronically through Interlibrary Loan. Look through the shelf copy of each of these journals weekly and bring interesting topics and titles to class.
The easiest way to research a term paper is to start with a recent primary source or review article (key paper) on your chosen topic. Then, turn to the reference section of the key paper every time you read an important bit of information with a text reference citation. Include these references in your notes and state what they are about. Follow up by collecting, reading and annotating the relevant references. You will have circumscribed a body of primary source information when you see the same references appearing over and over again. Then you should be ready to write your term paper based on your notes.
Every paper needs a focus, which should emerge from your literature survey although you may not know what it is when you start. Focus also means that you should provide depth based on closely reading several solid research articles. Depth is more important than breadth. Avoid general topics like “prospects for gene therapy”; instead, zero in on a specific topic such as “Recent progress and prospects for treatment of Duchene’s Muscular Dystrophy by gene therapy”. The paper should be shaped like a funnel. Start with a broad summary and quickly bring the paper to a narrow focus.
Google Scholar is another useful source for references. It has a user-friendly dialog window where you can type in key words, author names, etc. The articles come up with the number of times they’ve been cited since publication, and the papers that cited a key reference can be useful for updating a research topic. One of the most useful features is ‘Cite’, which allows you to copy the reference and paste it into your reference section. Use APA style.
Referencing in a Term Paper. Your term paper needs text reference citations and a reference section. A text reference citation should appear every time you cite published non-textbook information. Don’t quote; paraphrase and reference! The format for a text reference citation is last name only (author, year), (author and author, year) or (author et al., year), depending on number of authors (one, two, three or more). One acceptable format for a reference in the reference section is:
First author (last name, first initial), later authors (first initial, last name). Year. Title. Journal. Volume: First page – last page.
You will encounter variations, but this one is both readable and informative. The title should be included because it tells you and other readers what the cited work is about.
Headings in a term paper. Your term paper should be subdivided by a title, headings and subheadings, much like a journal article. But because it is a library research paper, not a laboratory research paper, the headings would not be Methods, Results and Discussion. Instead you should have an Abstract, Introduction and further headings determined by a natural division of the subject you are reviewing, determined by content.