Syllabus Biology 299 Dr. Art Conway Fall ... - Faculty.rmc.edu

Syllabus
Biology 299
Dr. Art Conway
Fall Semester
Copley 127 and Pannill Honors House
2004 Office Hours 12-1 PM Wed (C127)
Wed 1:40 - 2:40
and 12-1 PM Mon and Fri (PHH)
Copley 104 Office 752-3720 (ext 3720)
Home 746-2475(leave message)
office email aconway@rmc.edu
home email caconway@vcu.org
Objectives
1. By the end of this course, each student will have learned the basic skills necessary for
literature searching, analyzing scientific data, and writing professional reports in a style
acceptable to a journal in the student's field.
2. By the end of this course, each student will have selected a research advisor, designed a
research project, surveyed the literature relevant to the project, and written a proposal which
is acceptable to the faculty of the biology department.
Textbooks
1. Ambrose, H. W. III; Ambrose, K. P. A handbook of biological investigation. 6th ed. Winston-
Salem: Hunter Textbooks, Inc.; 2002.
2. Grinnell, F. The scientific attitude. 2nd ed. New York: The Guilford Press; 1992.
3. McMillan, V. E. Writing papers in the biological sciences. 3rd ed. New York: St. Martin's
Press; 2001.
Disability Accommodations
The Americans with Disabilities Act of 1990 and other Federal laws require Randolph-Macon College
to provide a “reasonable accommodation” to any individual who advises us of a physical,
psychological, or learning disability. If you have a physical, psychological, or learning disability that
requires an accommodation, you must first register with the Office for Disability Support Services,
located in the Higgins Academic Center. Please arrange a meeting with the course instructor to
discuss your needs and how to register for support services.

Class Schedule
Date Session Assignment
Sept 8
Overview of the course
15 What is research? Read A&A Ch 1,2
Designing a research project G Intro, Chs 1-4,7,8
McM Intro, Ch 2
Exercise 1 handouts
Hand in Ex 1
22 Library research techniques Read library
research handouts,
A&A Chs 9-10
McM Ch 1
Hand in Ex 2
29 Ethics in research Read G Chs 5,6
Hand in Ex 3
Oct 6 Research project design Read A&A Chs 1,6
McM Ch 2
Hand in Ex 4
13 The Title, Introduction, Read McM Chs1, 4-6
Materials and Methods A&A Chs 9-11,13
Literature Cited Hand in Ex 5
20 Data analysis Read A&A Chs 2-8
(discuss Ex 5) McM Ch 2
Hand in Ex 6
27 The Results Section Read McM Chs 1, 3, 4
(discuss Ex 6) A&A Chs 10-13
Hand in Ex 7
Nov 3 Discussion Section Read McM Ch 1, 4
(discuss Ex 7) A&A Chs 10-11,13
Hand in Ex 8
10 The Abstract Read McM Ch 4, 10
Verbal presentation A&A Chs 10-13
techniques
Hand in Ex 9 and
(discuss Ex 8)
rough draft of
entire proposal
17 Student presentations
24 Thanksgiving Break
Dec 1 Student presentations
10 Proposals are due in Dr. Martin's office by 5 PM

Requirements for Biology 299
1. Each student must attend all weekly meetings of Biology 299 (unless excused by the
Instructor(s)) and participate fully in class discussions of readings and exercises.
2. Each student must submit all of the written exercises assigned during Biol. 299. These will be
graded by the instructor(s).
3. Each student must select a Research Advisor who is a faculty member in the Biology
Department. The student should select his or her Research Advisor during the first three weeks
of the semester in which Biology 299 is taken and must meet regularly with the Research Advisor
while designing the student's research project and writing the formal research proposal. The
student must give the RESEARCH ADVISOR'S EVALUATION form at the end of this document
to the Research Advisor when the Advisor is chosen.
4. Each student must prepare a formal research proposal for the project which the student plans to
do in Biology 300 or Biology 497-498 or Biology 487-488. This paper must follow typical
guidelines for preparation of proposals for research (the format is appended). The paper must be
completed and turned in to the departmental office by 5 P.M. of the last day of regular classes in
the semester in which Biol. 299 is taken. The APPLICATION FOR ADMISSION TO A BIOLOGY
RESEARCH COURSE form at the end of this document must be the first page on the proposal.
5. Each student must prepare and present a seminar describing his/her proposed project. This will
be presented to the Biology 299 class during the last 2 weeks of the semester.
6. Each student must attend all seminar presentations by students in biology research courses (Biol
300, 488, 498) which are given during the semester the student is registered for Biology 299.
Students with classes which conflict with seminar presentations will be excused from those
seminars but must notify the instructor(s) in charge of Biology 299 in writing.
7. Any student who wishes to do an off-campus project must submit the APPLICATION TO DO AN
OFF-CAMPUS BIOLOGY RESEARCH COURSE (appended to this document) to the
Chairperson of the Biology Department no later than the ninth week of the semester prior to the
semester in which the project will be done.

Major Assignments In Biology 299
1. Choose a research project and a Research Advisor.
This should be done within the first 2 weeks of classes. Students should begin talking to faculty
immediately and should choose a Research Advisor by the end of the third week of classes.
Biology 299 is designed to help students design a research project which can be done in a 1 or 2
semester period. The full benefit of this course will not be realized unless the project is designed
as the course progresses. Our experience has been that students who wait until late in the
course to choose a project usually end up with a poor literature search, a poorly designed project,
and a poorly written proposal. These problems can be eliminated by deciding on a project at the
start of the semester and then refining the design of the project as the semester progresses. This
should also eliminate a time crunch at the end of the semester.
2. Do a complete literature search on the project area.
A complete literature search should consist primarily of references to original scientific journal
articles, with a few other general references as needed. A typical literature search should include
from 25 to several hundred journal articles. The criterion used to judge the literature search is its
completeness, not the total number. References on organisms similar to the species which will
be used in the project should be included, and references to similar biological phenomena in
unrelated organisms may also be useful. The literature search should be completed by
midsemester or shortly thereafter to allow sufficient time for writing a proposal.
3. Write a formal research proposal for submission to the biology department.
This proposal will be evaluated by the department as part of the student's grade in 299, but
presentation of an acceptable proposal to the department is also one of the prerequisites for
enrollment in Biology 300, 487-488, or 497-498. Students who fail to provide a proposal which
the department approves will not be allowed to take a research course until an acceptable
proposal is submitted.
The student should submit preliminary drafts of the proposal to the Research Advisor and to other
faculty members for comments. At least 1 week should be allowed for each rough draft
submission. The extent and the usefulness of the faculty comments will be increased if the
student produces a well organized paper before submitting it for comments. The usefulness of
faculty comments is also increased if the faculty member is allowed adequate time to read the
paper numerous times.

Grading
1. Weekly Seminar Grade - 60% of final grade
Homework exercises will be graded, and those grades will be averaged at the end of the
semester. The Research Advisor's grade is averaged with the exercises. The mean exercise
grade adjusted for attendance becomes the seminar grade.
Attendance is required at all classes in Biol. 299. Absences approved by the instructor are not
counted when computing attendance. Each unapproved absence will lower the weekly seminar
grade 5%.
Class participation will be used to determine the letter grade for any student whose course
grade falls within 0.5% of a letter grade boundary. Above average participation will raise the
course grade by up to 0.5%, average participation will cause no change in the grade, and below
average participation will lower the course grade by up to 0.5%.
2. Formal Proposal - 40% of final grade
The proposal will be graded by the Biology Department faculty. Each faculty member assigns a
grade to the proposal and these grades are then averaged to produce the paper grade. The
paper grade will be lowered by 1 letter grade (10%) for every calendar day (or part of a day) that
it is late. The paper grade will also be lowered if the required format for the proposal is not
followed exactly.
3. Final Grade
Final grades will be assigned using the following scale.
100 - 97.0% = A+
96.99 - 93.0% = A
92.99 - 90.0% = A-
89.99 - 87.0% = B+
86.99 - 83.0% = B
82.99 - 80.0% = B-
79.99 - 77.0% = C+
76.99 - 73.0% = C
72.99 - 70.0% = C-
69.99 - 67.0% = D+
66.99 - 63.0% = D
62.99 - 60.0% = D-

The Written Proposal
1. The paper should be written in a style acceptable to a granting agency in the area of research.
Unless permission is granted by the instructor(s)of Biology 299 and the student's Research
Advisor, the proposal must follow the format below. The format follows the recommendations of
the CBE Style Manual (1).
2. The paper must be typed and double spaced.
3. Each section must begin on a new page.
4. The title page must be the APPLICATION FOR ADMISSION TO A BIOLOGY RESEARCH
COURSE form which is appended to this document.
Introduction
1. Survey the existing knowledge which pertains to your proposed project. This means finding more
than 1 or 2 review articles. You are expected to thoroughly review all of the past literature.
Effective strategies will be covered in class.
2. Describe what your project is designed to determine and why it is meaningful (i.e. why should you
do it?). The objective(s) of the project must be VERY clearly stated in the form of information to
be obtained or hypotheses to be tested.
3. Use present tense for information which extends beyond a single reported experiment.
4. Use past tense to refer to results of specific previous experiments.
5. Use future tense to refer to your proposed work.
Materials and Methods
1. Describe what you plan to do in enough detail to allow evaluation of the effectiveness and
practicality of the experimental design and the proposed methods. Published methods which will
be followed exactly may be cited without describing them.
2. Any modifications of published methods or new methods must be described fully.
3. Use future tense.
Project Budget
1. This section should consist of a listing of the supplies and materials needed for the project. The
listing should include the approximate cost of each major item and the suggested source for each
unusual item.
2. Field projects must include an estimate of total vehicle mileage which will be needed for collecting
trips, etc. during the study.
3. This section may be organized as a table.

Expected Results and Interpretation
1. Verbally describe all important expected results. You will probably have to base this on previous
studies on related organisms or on extrapolations from the current information using accepted
theories. You may find that there are several alternative possibilities. You should not get too "far
afield" in this section, but you must show that you understand the current status of the field and
that you have thought through the reasonable possibilities in terms of results.
2. Indicate clearly how the results will be analyzed. Be sure to include the statistical methods to be
used.
3. Explain why the information which you expect to obtain will be important to the area of biology
related to your research.
Literature Cited
1. Include only references actually cited in the text of the paper.
2. All items of information which are not results of the current study should be referenced as to
source in the text of the paper.
3. A typical Biology 299 proposal should contain 25 to 100 references.
4. DO NOT USE FOOT-NOTES EXCEPT TO DEFINE ABBREVIATIONS!
5. Acceptable formats for citations in the text of the paper are Author (#) and (#).
6. References in the Literature Cited section must be arranged alphabetically and numbered
sequentially. These numbers are used in the text to refer to the references. Consult the CBE
Style Manual (1) for detailed examples of Literature Cited entries. A few selected examples are
shown below.
Literature Cited
1. CBE Style Manual Committee. CBE style manual. 5th ed. Bethesda: Council of Biology Editors;
1983.
2. Caulfield, M. J.; Shaffer, D. A computer program for evaluation of ELISA data obtained using an
automated microtiter plate absorbance reader. J. Immunol. Methods 74:205-215; 1984.
3. Gardner, R. Origins and properties of trophoblast. In: Edwards, R. G.; Howe, C. W. S.; Johnson,
M. H., eds. Immunology of trophoblast. Cambridge: Cambridge University Press, 1975:43-65.

Figures
1. Photographs, drawings, and graphs should be located in the Figures section of the paper.
2. The Figures section of the paper should follow the Literature Cited section in the paper.
3. Each figure should be numbered with an Arabic numeral (1,2,3 etc.). Letters (a, b, c, etc.) may
be used to indicate parts of a multi-part figure.
4. The figures should be numbered in the order in which they are first referred to in the text of the
paper.
5. More than 1 figure may be placed on a page, but each page of figures MUST have margins of at
least 1 inch on the free sides of the page and 1.5 inches on the binding side of the page.
6. Photographs or drawings should be done to professional standards and clearly labeled.
7. Graphs should be done with professional materials (computer printer, black ink, tape, etc.) on
plain white paper.
8. A page of corresponding Figure Legends must be bound facing each page of figures.
9. Each Figure Legend must include the figure title and a brief description of the figure. When
appropriate, the figure legend should also include a list of abbreviations used in the figure,
probability values and the name of the test used to generate them, magnification of photographs,
and any other useful information. The reader should be able to interpret the figure using only the
Figure Legend plus the Materials and Methods section of the paper.
Tables
1. Tables should be placed in a separate Tables section which should follow the Figures section.
2. Tables should be numbered with Roman numerals (I, II, III, etc.) in the order in which they are
first referred to in the text of the paper.
3. More than 1 table may be placed on a page, but each page of tables must have margins of at
least 1 inch on all free sides and 1.5 inches on the bound side.
4. Tables must be typed or lettered on plain white paper.
5. Each page of tables must be accompanied by a facing page of Table Legends.
6. Each Table Legend must give the full title of the table, give a brief description of the table, and
define any abbreviations used. The reader should be able to interpret the table using only the
Table Legend plus the Materials and Methods section of the paper.

The Oral Presentation in Biology 299
1. Your oral presentation will be made to the Biology 299 class. You will have 5 minutes for your
oral presentation which will be followed by about 3 minutes of questions from the audience. This
is a shortened form of the format followed at most professional meetings in biology.
2. The oral presentation should follow the same basic format as the written proposal (see below).
3. All information should be presented in a logical sequence.
4. The oral presentation should include effective visual aids. Effective visual aids display data
patterns in easily understood ways and contain text which is large enough to be easily read from
the rear of the room. Refer back to the materials covering design of graphs and tables.
5. The oral presentation should be prepared in advance and practiced numerous times. Several of
those practice presentations should be made to your research advisor so that you can benefit
from his or her suggestions.
6. You should be able to give your talk with no more than occasional references to notes. You
should attempt to maintain good eye contact with the audience and should point out items on
your visual aids as you refer to them.
7. You should speak distinctly at a volume which can be easily heard at the rear of the room.
8. You should pace your talk so that you can comfortably complete it in the allotted 5 minutes
without rushing.
Title of the oral presentation
The title of the oral presentation should be the same as the title of the written proposal and should
allow a reader to determine what you propose to do in your experiment.
Introduction section of the oral presentation
1. Briefly summarize the existing knowledge which pertains to your project. This summary should
allow a general scientific audience to understand the reasoning behind your research project.
2. Use present tense for information which extends beyond a single reported experiment. Use past
tense to refer to results of specific previous experiments.
3. Clearly state the question or questions which your project is designed to answer.
4. Describe why your project is meaningful.

Materials and methods section of the oral presentation
1. Use future tense.
2. Summarize the methods which will be used, ideally using a flow diagram. Do not recite detailed
methods unless they are absolutely essential to the interpretation of your results. Be prepared to
describe details of methods if questions arise in the question and answer period after your talk.
Expected Results and Interpretation section of the oral presentation
1. Use future tense.
2. Verbally summarize each of the important expected pattern(s) and indicate how these patterns
will be statistically analyzed.
Questions following the oral presentation
1. During the 3 minute question period after your oral presentation you should be prepared to deal
with questions about any aspect of your proposed research project and its implications.
2. Be sure that you understand the question before attempting to answer.
3. Clearly distinguish between the parts of your answer that you are reasonably certain are accurate
and the parts of which are less certain. If you are unsure of the answer to a question, be honest
about your uncertainty. Honest uncertainty is generally viewed much more charitably that an
answer stated with great certainty which turns out to be incorrect.

Paper Format Evaluation Form (This copy is for student's reference)
Student Name _________________________________________
Course ______________
Proper sections present in paper ?
All sections of paper properly formatted ?
Proper reference style in text of paper ?
Proper reference style in Literature Cited ?
Literature Cited references all used in the text ?
Citations in the text all included in Literature Cited ?
Figures and tables properly done ?
Figure and table legends properly done ?
Other problems ?
Total Paper Grade Reduction
(1 letter grade maximum)
_______________________

Evaluation of Biol 299 Oral Presentation(This copy is for student's reference)
Student ______________________________________
____ / 2 Effective communication of background information
____ / 2 Effective statement of the question
____ / 2 Effective communication of the proposed methods
____ / 1 Effective communication of the analysis to be applied to the results
____ / 1 Effective delivery (clarity of speaking, physical presence)
____ / 2 Effective organization of the talk
_____ / 10 Total score

RESEARCH ADVISOR'S EVALUATION (Student's reference copy)
This form must be given to the Research Advisor as soon as the student selects the Research
Advisor. The Research Advisor will give the form to the Biology 299 Instructor at the end of the
semester. The form will be graded by the Instructor and will constitute a potential 40 points in the
Weekly Seminar Grade in Biology 299.
STUDENT'S NAME
_________________________________________________________
The student gave me this form
The student
during during during during during failed
the the the the the to give
first second third fourth last this form
3 weeks 3 weeks 3 weeks 3 weeks week to me.
of the semester.
(10 pts) (8 pts) (6 pts) (4 pts) (2 pts) (0 pts)
(Please mark one space)
The student made and kept
10-13 7 - 9 5 - 6 3 - 4 1 - 2 0
appointments with me during the semester.
(10 pts) (8 pts) (6 pts) (4 pts) (2 pts) (0 pts)
(Please mark one space)
The student's library research was
complete minimal not
and and done.
timely.
late.
(10 pts) (8 pts) (6 pts) (4 pts) (2 pts) (0 pts)
(Please mark one space)
The student submitted
numerous one no
high
poor
quality
quality
rough drafts of the proposal for my comments.
(10 pts) (8 pts) (6 pts) (4 pts) (2 pts) (0 pts)
(Please mark one space)
_______________________________________________
Research Advisor's Signature

APPLICATION FOR ADMISSION TO A BIOLOGY RESEARCH COURSE
This form must be the front page of all proposals when they are turned in to Dr. Martin.
NAME
_________________________________________________________
TITLE OF PROJECT
_____________________________________________________________
_____________________________________________________________
_____________________________________________________________
TYPE OF PROJECT
LIBRARY PROJECT____
FIELD or LABORATORY PROJECT____
OFF-CAMPUS PROJECT ____
COURSE WHICH WILL BE TAKEN
Biology 300 ____ (Topics in Biology)
Biology 487-488 ____ (Departmental Honors in Biology)
[Open only to Honors Program students]
Biology 497-498 ____ (Senior Project)
SEMESTER(S) IN WHICH PROJECT WILL BE DONE
Fall____ Spring____
YEAR(S) IN WHICH PROJECT WILL BE DONE
20____
PROJECT ADVISOR'S SIGNATURE _________________________________

APPLICATION TO DO AN OFF-CAMPUS BIOLOGY RESEARCH PROJECT
This form must be submitted to the Chairperson of the Biology Department no later than the ninth
week of the semester prior to the semester in which the project will be done.
NAME
_________________________________________________________
TITLE OF PROJECT
_____________________________________________________________
_____________________________________________________________
_____________________________________________________________
LOCATION OF PROJECT
______________________________________________________________
______________________________________________________________
______________________________________________________________
COURSE(S) WHICH WILL BE TAKEN
Biology 300
____ (Topics in Biology)
Biology 487-488 ____ (Departmental Honors in Biology)
[Open only to Honors Program students]
Biology 497-498 ____ (Senior Project)
SEMESTER(S) AND YEAR(S) IN WHICH YOU WILL REGISTER FOR THIS(THESE) COURSE(S)
Summer____ Fall____ Jan____ Spring____
20____
SEMESTER(S) AND YEAR(S) IN WHICH THE PROJECT WORK WILL BE DONE
Summer____ Fall____ Jan____ Spring____
20____
PROJECT ADVISORS' SIGNATURES
On-campus _________________________________
Off-campus _________________________________
REASONS FOR DOING AN OFF-CAMPUS PROJECT
Attach a typed justification which explains
1. Why you want to do the project off-campus
2. What resources will be provided by the host location
3. What resources must be provided by Randolph-Macon

RESEARCH ADVISOR'S EVALUATION
This form must be given to the Research Advisor as soon as the student selects the Research
Advisor. The Research Advisor will give the form to the Biology 299 Instructor at the end of the
semester. The form will be graded by the Instructor and will constitute a potential 40 points in the
Weekly Seminar Grade in Biology 299.
STUDENT'S NAME
_________________________________________________________
The student gave me this form
The student
during during during during during failed
the the the the the to give
first second third fourth last this form
3 weeks 3 weeks 3 weeks 3 weeks week to me.
of the semester.
(10 pts) (8 pts) (6 pts) (4 pts) (2 pts) (0 pts)
(Please mark one space)
The student made and kept
10-13 7 - 9 5 - 6 3 - 4 1 - 2 0
appointments with me during the semester.
(10 pts) (8 pts) (6 pts) (4 pts) (2 pts) (0 pts)
(Please mark one space)
The student's library research was
complete minimal not
and and done.
timely.
late.
(10 pts) (8 pts) (6 pts) (4 pts) (2 pts) (0 pts)
(Please mark one space)
The student submitted
numerous one no
high
poor
quality
quality
rough drafts of the proposal for my comments.
(10 pts) (8 pts) (6 pts) (4 pts) (2 pts) (0 pts)
(Please mark one space)
_______________________________________________
Research Advisor's Signature