Meetings When/Where:
Tuesday 4:00-5:50.
Room: CNS 163
Text:
Writing Papers in the Biological Sciences, Victoria E. McMillan, St. Martin
Press
Attendance:
Attendance is mandatory! Failure to attend class without a valid
excuse will result in a lowering of your grade.
Two unexcused
absences will
result in failure.
Grading:
Oral
presentations (2):
25% each
Written assignments (4):
10%
each
Participation
and
attendance: 10%
Class
Schedule:
9/04/07:
Organisational meeting; Presention of Library Search Techniques.
*Assignment #1: Literature search – due September 11
*Reading
assignment: Chapters 1 and 4
9/11/07:
General
organization of research papers. How to organize an oral
presentation. The instructor gives an example. Please bring a copy for
2 articles (see instructions on p.2 of this syllabus)
9/18/07:
Student presentations I ( max of 3 pairs presenting) . 20
min for each presentation
9/25/07:
Student presentations I (max of 3 pairs presenting) . 20 min for
each presentation
10/2/07: Data
presentation: Figures and Tables.
Computer programs for graphs.
*Assignment #2: Creating Figures and Graphs – due October 16
(or Oct. 23 for those presenting on Oct 16).
*Reading
assignment: Chapters 2 – 3, and 10
10/9/07:
Student
presentations II (max of 4 students presenting)
10/16/07:
Student
presentations II (max of 4 students presenting)
10/23/07: Student
presentations
II (max of 4 students presenting )
*Assignment
#3: Critical
evaluation of a paper – due October 30
…………….
12/11/07-12/13/07:
Students attend one
session of 302 (Research in Biology) presentations
*Assignment
#4: Critical evaluation of 302
presentations – due Dec. 16th
Written
Assignments
Assignment
#1: Literature Search
*Part 1. Using the computerized search
engines
available on the library home page, use one or more the databases
listed on the
course handout, or browse the databases yourself. You
will find that if your use more than one
database, you will find more papers, although many of the same papers
will
appear with different databases. In
general, it’s a good idea to use more than one database, since each has
their
own specific limitations.
·
Find ten
research papers on the genetics of bipolar
disorder.
While you may include some review articles on this list, at least 7 of the papers must be primary
research articles.
·
Hand in: a
typed list of ten articles
using correct citations: authors, year of publication, title, journal name, volume, and pages
·
Choose
two articles for your 1st presentation (in pair). Do not take
review papers. Bring those articles on Sept 12 so that I can evaluate
their suitability for our class.
*Part
2. Go to the
NCBI home
page, the public access point to many resources (http://www.ncbi.nlm.nih.gov/). A quick glance at this page shows that NCBI
contains far more
than just the sequence repository. It is a rich source of
information on all aspects of genetics
and genomics. All of the divisions are searchable and
information ranging from gene sequences, to the position of a locus on
a human chromosome,
to direct access to the scientific
literature dealing with a particular gene, is
immediately accessible. Click on ‘PubMed’.
PubMed is the NCBI gateway to the biomedical research
literature. It
is a searchable database
and information can be retrieved based on combinations of
parameters such as author, subject key words, or organism. A complex
query can be
entered and a list of publications
matching it will be returned. For instance, we could
enter a simple search by author. If we entered Hartwell
LH (one of the winners of the 2001 Nobel Prize in Medicine)
and pressed ‘Go’,
PubMed would return a list of his current publications. Give it a try.
The list of Hartwell's publications is 5 pages
long. Only the top and therefore most recent papers are displayed on
the first
page. Each paper is linked to its abstract and sometimes the
full text of the articles.
·
Find ten
research papers on the genetics of mental disorders (depression,
schizophrenia, ADHD etc...) . While you may include some review
articles on
this
list, at least 7 of the papers must
be primary research articles.
·
Hand in: a
typed list of ten articles using
correct citations: authors, year of publication, title, journal name, volume, and pages.
·
Choose
two articles for your 2d presentation (individual). Do not take review
papers. Bring those articles on Sept 12 so that I can evaluate their
suitability for our class.
Assignment #2: Creating Figures and
Graphs
An
essential component of any research paper is the presentation of the
data
collected in the Results section. For
this assignment, you will be given some “raw data” from a hypothetical
study. You need to organize the data
into a logical format for presentation in a paper.
This includes a labeled figure, graph, or table.
It also includes a title for
the figure and a figure legend. You
should examine the general experimental
questions and results and determine, in your own mind, the best way to
present
this data.
·
Hand in:
Figures/tables/graphs with appropriate titles and labels and a
typed
legend for each.
Assignment
#3: Critical
Evaluation of a Student research paper
You
will be provided with a research paper, written by an anonymous, former
(already graduated) undergraduate, to read and critique.
Although the topic of the paper will probably
be unfamiliar, the expectation is that there will be enough information
in the
Introduction to allow you to understand the rest of the paper. Assume, for this assignment, that you are a
faculty member who has been asked to review this paper.
Grade
the paper with a justification for your grade.
Provide
comments on the paper. Some points
to consider when evaluating the paper are:
·
Are all the
necessary parts to a
scientific paper included?
·
Is the
material correctly organized?
(i.e. Is there material in the results
section that should be in the
discussion section)
·
Is the
introduction sufficient to allow
you to understand the paper?
·
Are the
figures clearly labeled and
understandable?
·
Are the
figure legends sufficient to
describe the experiments?
·
Are the
materials and methods sufficient
to reproduce the experiments?
·
Are the
conclusions/interpretations
appropriate?
·
What about
spelling and/or grammatical
errors?
·
Hand in (1)
the original paper, with your
corrections and grade, (2) a typed sheet of comments on the quality and
organization of the paper, and (3) suggestions for improvements
Assignment
#4: Critical Evaluation of 302
Presentations
During
the last week of classes, students doing 302 research this semester
will
present their talks to the department. You
are required to attend one of
these sessions. As your assignment, you
need to write up a critique on two
of the talks presented. For this
critique, you need to think about:
·
Was enough
background presented to
understand the research?
·
Was the talk
well organized?
·
Did they
speak clearly?
·
Were the
slides/overheads readable?
·
Did you
understand the general methods
used?
·
Was the data
presentation clear?
·
Did the
conclusions follow the results
well (i.e., did their conclusions make sense based on the data they
presented)
Oral
Presentations
Each
student will give two oral presentations on a primary research paper.
For the
first paper, students will work in pair on papers that must be
chosen
from the attached list. For the second paper, students will work individually
and can either take one of the papers from the list attached, or select
themselves their paper (provided that this second paper is approved by
me one
week prior to the presentation and that it fits with the theme of the
section).
At least one of the presentations must
use the software “PowerPoint”.
If you
are interested in choosing yourself the
second paper you present, the library has links to several electronic
databases
for searching for papers. The two most
appropriate databases for this topic would be PubMed and Science Direct. PubMed contains an index of all the major
biological and medical journals, whereas Science Direct is a listing of
all
journals published by the major publishing house, Elsevier Science. The advantage to Science Direct is that it
provides access to many articles directly.
Thus, you can download a PDF of the article from your computer. I suggest trying there first, simply because
you’ll have greater success actually getting copies of the papers. However, many of the journals indexed in
PubMed may also allow direct access to PDF files, especially if the
paper is
more than a year old.
In
general, the presentation should last approximately 15 min.
Within this time period, you need to give a
general introduction (so that people understand the topic, the question
being
asked, and the relevance), enough methods to understand what they did,
an
overview of the important results, and a discussion of what these
results mean
and how the study adds to our overall understanding of the topic.
Most research papers will contain more
information than you need to present.
In
many cases, the types of information that you can exclude are minute
details of
the methods and occasionally, some of the results (control experiments
to show
that their technique works, for example).
The first task for you as the presenter – and in many cases the
harder
task – is to determine what information you need to discuss and what
you can
leave out.
Each student in the class
will evaluate the presentations of their peers (see attached sheet).
These evaluations will be summarized and
given to the presenter, along with my evaluation and a grade.
Peer evaluations are NOT used in determining
the grade.
More
guidelines for Presentations
Presentations
should be about 15‑20 minutes long. Visual aids (i.e. overhead
transparencies)
are encouraged (essential?), as is use of the blackboard. If you wish
to use
PowerPoint, the computer and projector will be available. <>
Make sure your visual aids are readable by people in the back of the
room. If
it's a figure from a paper, consider enlarging the figure and then
making an
overhead of just the figure or graph. If it's a table, maybe
you should
underline the important data points in red so the audience knows where
to look,
or if necessary, rewrite the table including only the important
information.
Each
presentation should include:
• an introduction that describes
the
background information that is necessary to understand the research.
Specifically, what is the general topic (i.e.
the alterations in DNA repair proteins which result in phenotypes
associated
with cancer), and what was known of this problem when the paper was
written? Please start
simply.
While you have struggled through this paper several times, remember
that no one
else in the room has ever seen it. What general topic does the paper
deal with?
For example: "this paper concerns effects of mutations in genes for
nucleotide excision repair upon development of cancer in mice." To introduce
the audience
to the topic, please use a figure from a course text (or another simple
diagram
that is likely to be familiar to students) in your introduction. This
will
encourage you to (a) think about the general area of the research, and
how
these experiments fit into the material that students in this course
have
learned; and (b) to begin your talk as simply as possible.
•
an explanation of the hypothesis, or
question being addressed?
•
a description of the experiments
performed. What methods were used? This is likely to
require some explanation of specific experimental details. For
unfamiliar
techniques, it may be helpful to explain the possible
outcomes of the experiment (for example, if the hypothesis
is correct that a DNA repair protein binds to a specific DNA sequence,
then
when the fragment of DNA is incubated with the protein, a shift in the
mobility
of the fragment should be seen upon electrophoresis.). Were appropriate
controls used? Be sure to explain them.
•
an explanation of the observed results. Do not confuse
results
with interpretation. Results are what is clearly observed or measured.
Interpretation is the explanation, or what the authors believe is
happening. Take time to explain the results clearly; remember
no one else in the room has ever seen this paper before. If you are
explaining
a gel, explain what is loaded in each lane. If you are explaining a
graph, be
sure to explain what on is on the x‑axis, y‑axis, etc. If explaining a
photograph, give some context (i.e. "this is a photograph of a cell,
stained with antibodies that recognize...").
•
what are the interpretations or
conclusions of the work?Again, place
the paper
in context: what is the significance to the overall area of research,
to our
understanding of general biological or biomedical problems? This is
perhaps the
most important part of the talk from the perspective of the listener;
after
hearing complex experiments, what is the bottom line? It is important
for you
as a speaker/teacher to step back from
the specifics of the experiment to explain the conclusion in
understandable,
simple terms. I strongly recommend using
a simple figure with which students are likely to be familiar. This
will help
to put things in context, and to relate it back to the course material.
‑ examples: no: This suggests that a low level of
XPA in the testis tumour cell lines is sufficient to explain their poor
ability
to remove cisplatin adducts from DNA and may be a major reason for the
high
cisplatin sensitivity of testis tumors..
yes: Why do mutations in XPA lead to
an increase in cisplatin sensitivity of testis tumors? XPA is required
to
remove this type of DNA damage and failure to remove this damage
results in
death of the tumor cells.
Were the authors able to answer the questions
originally posed? Are
there problems in
the logic or interpretation? (some authors will try to gloss over
these). What new
questions
have been raised by the results and/or interpretation?
• any general conclusions or comments? non‑scientific
comments
are ok [but not required] here; for example, ethical or economic
concerns; what this might mean for
society, etc.)
General
suggestions on
presentations
•
You may use notes, but please do not
read your notes.
•
You may not be able to
cover all the experiments that were performed in the paper. For longer
papers,
you will have to limit your talk to only some of the experiments
• Use straightforward language, that is
understandable. If you need to use new terms, explain them.
The whole talk should be in English that will be
understood by a tired, restless audience. There is no point in
preparing and
delivering a talk that your audience will not understand.
• Explain
new terms. If you use a term that no one has heard before,
explain what it means, and write it on the board (or on an overhead or
slide).
• Use the
board, to
write new terms, or to make simple drawings.
• If you find
outlines
useful in helping you to follow lectures, consider using an outline to
help
students follow your talk.
• Tables help
to summarize
data. For example, imagine cells treated with drug A for 2 hours, 6
hours, and
24 hours, and drug B for 2 firs, 6 firs and 24 firs. Keeping all the
results
straight would be greatly helped by presenting it as a table:
|
|
2 firs
|
6 hrs
|
24 hrs
|
|
Drug A
|
|
|
|
|
Drug B
|
|
|
|