Description of Assignment:
This description was written to address students directly.
Guide to the research paper (BY360)
You will prepare a 8-12 page research paper on a topic in
prokaryotic biology. This project will be graded in three
stages, detailed below. As explained in class,
Stage 1: Choose a general topic.
I have compiled a list of minireviews from the journals published
by the American Society for Microbiology. Choose one of these
as your starting material. The minireview you choose determines
the topic for your paper, so choose wisely! Send me an e-mail
explaining your choice. The e-mail must be received by Saturday
morning, so the safest course is sending it to me on Friday
afternoon. PDF files of the complete articles can be found
online, through www.asm.org.
An example of a minireview is "Shedding Light on Anaerobic
Benzene Ring Degradation: a Process Unique to Prokaryotes?"
CAROLINE S. HARWOOD AND JANE GIBSON, JOURNAL OF BACTERIOLOGY,
Jan. 1997, p. 301-309. Accessed online at http://jb.asm.org/minireviews.shtml
on 2 January, 2004. I won't give any points to students who
turn this assignment in late.
Stage 2: Choose two papers to critique.
The author of the minireview will likely refer to many publications.
Choose one research paper referenced in the minireview. By
their very nature, however, minireviews are a little "behind
the times" simply by virtue of the time delay involved
in writing and publication. Your second research paper should
be published more recently than the minireview, and related
somehow to the first paper you choose. It might be, for example,
written by the same last author, or written about a closely
related phenomenon. E-mail me the citations on Friday, January
30. Be advised that Tutt library does not subscribe to every
journal. Tutt does subscribe to Nature, PNAS and Science;
furthermore ASM publications (e.g. J. Bacteriology, Infection
and Immunity, and Applied and Environmental Microbiology)
are available free after 6 months. You can use the search
engines on the Tutt library web pages to ascertain whether
other journal articles are available. An example of a paper
discussed in the Harwood & Gibson review is Gibson, J.,
M. Dispensa, G. C. Fogg, D. T. Evans, and C. S. Harwood. 1994.
4-Hydroxybenzoate-coenzyme A ligase from Rhodopseudomonas
palustris: purification, gene sequence, and role in anaerobic
degradation. J. Bacteriol. 176:634-641. This paper is published
in the Journal of Bacteriology, which is available in print
at the library (the paper is too old to be found online as
a PDF file).
To find a related research article published more recently,
I used Medline through Tutt library and searched for the senior
author, Harwood CS. Here are some of the articles I found:
Both Pelletier & Harwood 1998 and Egland and Harwood,
1999 look like they would be relevant as well as freely available
through Tutt. I won't give any points to students who turn
this assignment in late.
Stage 3: Write a paper summarizing and critiquing the two
You will write a paper with three main goals. The first goal
is to summarize the background relevant to the research papers
you have chosen. Much of this material will likely be available
in the minireview. Strive to make connections to coursework.
This introductory material may take 2-3 pages and use figures.
The second goal is to summarize the experimental results presented
in each of the two papers. This material will likely take
3-5 pages, not counting figures. Describe the techniques used.
Excerpt key figures and describe the findings. Summarize the
authors' interpretations of their data, usually found in the
"discussion" section of publications. The third
goal is to critique the work. This goal is the most difficult
and will likely take 3-5 pages of text. What hypotheses were
the authors testing in the data presented in the figures?
Did the experiment performed really test that hypothesis?
Did the authors use appropriate controls in all of their work?
Are there alternative explanations of the data that the authors
do not discuss or that they disfavor? Are there experiments
the authors could have done to make a stronger case for their
conclusions? Are any of their conclusions based on weak evidence?
The critique should also compare and contrast the two papers.
Did they ask similar questions or use similar techniques?
Do they come to the same, or different conclusions? Did they
test related hypotheses?
I will deduct 20 points from papers that are turned in after
5:00 p.m. I will not accept any paper after noon on Wednesday,
The paper should be 8-12 pages long, with 4-6 additional pages
for all of the figures and the works cited. [Note: if an article
is available as an html full-text document, high-quality figure
images can usually be captured directly from the web site.]
Use 12 point font and double-spacing, with one inch margins
on all sides. In MS-Word, use the "view header and footer"
function to add a page number and your name to the bottom
of each page. Make sure that you cite your materials properly,
and avoid plagiarism! Review the CC plagiarism guidelines
before submitting your paper - professors are honor-bound
to report any hints of plagiarism. If you directly excerpt
a figure and include its legend, you must tell me that you
have quoted the source! Refer to the lab manual's "Format
for Scientific Papers" section for instructions on any
figures or tables and the references section of the research