Interdisciplinary Biochemistry Graduate Program | Analysis of Biochemical Literature
B502 | 1295 | DiMarchi, R.


1.	Description

Critical evaluation of the biochemical literature, using selected
papers as examples; development of written and oral communication
skills in the context of literature analysis.

2.	Logistics

A 1.5 credit hour semester-long class that meets once a week for 1.5
hours in the Fall semester. Required for all incoming Biochemistry
graduate students.  The course will be open to interested students
from departments that participate in the interdisciplinary
Biochemistry program.  Is not eligible for credit toward a minor in
Biochemistry.

Instructors:  Organized by one faculty coordinator from the
Biochemistry program.  The coordinator is encouraged to allow
colleagues with specific areas of expertise to participate.  This is
intended to allow broader, less formal interaction between the
faculty and students, and to allow a spectrum of research topics to
be covered from the areas of Biochemistry, Structural Biology, and
Molecular Biology.

3.	Prerequisites

Graduate status and concurrent enrollment in B501 or consent of
instructor.

4.	Objectives

Philosophy and Goals:  This course is intended to bring together the
graduate students in Biochemistry as a small group with one faculty
member who will lead the students through a critical analysis of
recent or classical papers.  The primary course goal will be to
identify and reinforce the analytical skills required to dissect a
scientific publication.  This will be accomplished using an ongoing
dialog that assesses the specific conclusions drawn from experiments
and the validity of the experimental approach.  A class discussion
might involve offering alternative strategies for addressing the same
problem experimentally, the degree of certainty that different
approaches might provide towards reaching a conclusion, or attempting
to provide alternative explanations that account for the data.  Where
competing labs have addressed the same research question, a
comparison of two experimental approaches might be informative to
illustrate the elements that comprise a convincing paper.

	A second major goal is to establish and reinforce the
importance of concise writing skills.  Because opportunities for
longer writing assignments are expected to arise later in the
curriculum, the focus in this course will be on writing short,
precise assignments.  The student will be asked to analyze, edit, or
re-write specific sentences or paragraphs present in published work.
Criteria for success might vary, depending on the assignment, but
could include addressing the following elements of scientific writing:

1.	Could the written unit be described more concisely?
2.	Could the writing be reorganized to make the meaning clearer?
3.	Does the excessive use of scientific jargon obscure the
argument?	

While the major goals of this course are outlined above,
opportunities for enhancing presentation or professional skills
should not be omitted. For example, it is envisioned that asking the
students to take turns in leading a class discussion about the
assigned papers represents an opportunity to polish presentation
skills.  One student might be assigned to make overheads of each
figure in an assigned paper, or to construct explanatory figures for
complex experiments.  The class presentation might then involve a
systematic explanation of each figure.  Such a systematic treatment
would include explaining the axes on plots, explaining the
visualization methods used to identify a specific result, or any
experimental features vital to understanding an experiment.

Major skills targeted:

I.	Analytical skills
A.	Defining the major questions addressed in each paper
B.	Assessing whether the published conclusions are supported by
the data
C.	Assessing conflicts in interpretation among similar papers
D.	Suggesting additional experiments or alternative
interpretations to resolve such conflicts

II.	Writing skills
A.	Concise presentation of individual ideas (sentence
construction)
B.	Distillation of a scientific argument (paragraph or abstract
construction)
C.	Summaries that critique a paper or set of papers (papers of 1-
3 pages)

Minor skills targeted:

III.	Presentation skills
A.	Preparing and delivering two 30 minute summaries of assigned
papers
1.	understanding components essential for topic introduction and
explanation
2.	constructing explanatory figures
3.	explaining details in published features

IV.	Other skills
A.	Understanding what information belongs in a paper and where
B.	The ability to critique figures, tables and legends
C.	Comparison of journal styles and content

5.	Grading and course assignments

Assignments:  One paper will be assigned each week, unless a more
substantial outside writing assignment is required.  Depending on the
enrollment, students will be required to prepare two presentations
that summarize the paper under consideration and initiate class
discussion.  The faculty coordinator will begin the course with an
example presentation and analysis.  Students will be expected to
carefully read each assigned paper prior to the class meeting, and to
contribute in a thoughtful way to the discussions each week.  The
student giving the presentation will also be expected to review the
supporting literature and answer questions that arise.  At the
discretion of the coordinator, students will be asked to analyze and
offer written revisions of specific sentences, paragraphs or
abstracts with an eye towards precision in content using minimal text.


Basis for Grading:  Each coordinator will decide on the scheme for
grading.  The elements deemed most important to formulate grades
include each studentís analytical and writing skills.  Frequent class
participation is to be expected and encouraged, and will also
comprise part of the grade.  Contributions to the class that are less
frequent but thoughtful are considered to be an acceptable level of
participation.

6.	Textbook

	None.  Readings will be taken from the primary literature.

7.	Course topics

	Course topics will vary, but will be taken from the
biochemical literature.