We recognize and acknowledge that McMaster University meets and learns on the traditional territories of the Mississauga and

Haudenosaunee nations, and

within the lands protected by the “Dish With One Spoon” wampum, an agreement amongst all allied Nations to peaceably share and care for the resources
around the Great Lakes.

MOLBIOL 3I03 – Independent Research Project

2023 - 2024 Multi - Term
Instructor: Dr. Ian Dworkin | E-mail: Dworkin@mcmaster.ca | Office: LSB 428

Course Administrator: Tyler Charlebois| E-mail: biology@mcmaster.ca | Office: LSB 218

Course Description
The objective of this course is to give students the opportunity to gain experience in a research
environment. Research is integral to the Biology Program. It supports the development of a number of
relevant and highly transferable skills. Students enrolled in Mol Biol 3I03 gain valuable experience in
preparation for a career in the private sector, professional schools or for advanced studies at the
graduate level. Therefore, completion of a research project is a major contributor of a successful
undergraduate education. An independent research project offers a great opportunity to experience a
potential work place, network with Professors and peers and engage in hands on learning.
The course consists of a twelve-week research project conducted during one term under the supervision
of a full time or associate faculty member from the Department of Biology or any other department at
McMaster University. While the workload is comparable to that of a 3-unit course, this course differs
from other courses by the independent nature of the work and the degree of initiative required to
complete a research project. Students should consider the time commitment to be around 8-10 hours per
week (scheduling arranged by supervisor). If you are working with a supervisor outside the Department of
Biology, you will require a co- supervisor within the Biology Department. Your co-supervisor will
communicate with the supervisor in determining a final mark for the course. The Course Coordinator is
available throughout the term for consultation and guidance as needed. The Course Administrator is
responsible for entering the permission and final marks. Students may receive credit in only one of Bio
3IR3 or MolBiol 3I03.

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Prerequisite(s): Registration in level III or IV of any Honours Biology program. Biology 2L03 is
recommended preparation. Permission of the department is required. Students are expected to have a
C.A. of at least 9.0 for Mol Biol 3I03.

Finding A Suitable Research Supervisor and Project

It is the responsibility of the student to make arrangements with a supervisor (and co-supervisor in case
the supervisor is not associated with the Department of Biology). A research project is agreed upon
following discussion by the supervisor and the student. It must be focused and suitable for the twelve-
week period of the term. The supervisor is responsible for providing the information and guidance on the
research project, explaining the assessment scheme and submitting the evaluation at the end of the term.
The student must obtain permission to enroll in the course by completing and submitting the permission
form (attached) and a one-page research proposal to the Course Administrator in LSB 118. After review
and approval by the Course Coordinator, the permission will be entered on-line.

Acknowledgement of Previous Work Related to the Project

Any work completed prior to the student’s registration in MolBiol 3I03 should not be included as part of
the student’s evaluation or final report without clearly identifying and acknowledging it. Students who
may have previously worked in the same laboratory in which they are completing a research project in
MolBiol 3I03 are asked to provide a one-page summary of any work that is related to the project being
undertaken in the course. This summary should be submitted with the research proposal.

Materials & Fees

• Note - Splash resistant goggles meeting the ANSI Z87.1 D3 classification and a lab coat are
required for all in person labs.

Course Overview and Assessment

Guideline on course evaluation, written submissions and deadlines

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A) Mid-term Progress Report (20%)
• Term 1: submitted to supervisor third Friday of October
• Term 2: submitted to supervisor third Friday of February
The mid-term progress report must be submitted directly to the supervisor. The report should represent
the beginning outline of the final report. It is suggested you follow the format of a standard journal in
Biology (discuss with your Supervisor which journal) and include the following sections:

1. Title Page:
- Title of project
- Student name and number
- Supervisor name
- Course name
- Date submitted

2. Table of Contents (with page numbers)

3. Abstract: Provide a one page concise summary of the question(s) being addressed, results and
significance of the project.

4. Introduction: Briefly summarize the state of knowledge in the area of study, provide a rationale for the
project, a statement of the question addressed in the project and the approach(es) used in your studies.

5. Materials and methods: This section should contain sufficient details of the experimental protocols for
someone else to repeat the experiment. If the procedure has already been published in a journal article in
detail, a reference will suffice. However, if a published procedure was modified, the alterations to the
original protocol should be clearly outlined. Describe in detail any new techniques developed during the
project.

B) Laboratory Performance (30%)

This component of the evaluation will take into consideration the daily work of the student in the
laboratory. The supervisor will evaluate, the work habits (10%), ability at research (10%) and initiative of
the students in the laboratory (10%). Learning in a research environment requires students to interact
and communicate adequately with their laboratory colleagues. Problem solving is an acquired skill that is
essential for all students who want to become independent investigators. Moreover, good work habits

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(approximately 8-10 hours per week), ability in research and a good degree of initiative are all required to
be a successful scientist as well as any other professional. Students are encouraged to explore alternative
interpretations of data and to suggest lines of investigation to be undertaken.

Safety in any laboratory setting is first and foremost. Before performing any protocol, students should
be familiar with the materials, reagents and possible hazards involved in the experiment. Students are
reminded to consult the Material Safety Data Sheets (MSDS) for each reagent that they use. Don’t
hesitate to ask questions in case you are not comfortable with any aspect of the experimental
procedures.
C) Laboratory Notebook – preliminary review
• Term 1: submitted to supervisor third Friday of October
• Term 2: submitted to supervisor third Friday of February

Maintaining a good laboratory notebook or any other kind of record of activities is essential in
government, industrial and academic laboratories for many reasons. In government health laboratories,
detailed records of procedures must be kept for later scrutiny. In the biomedical industry (e.g.
pharmaceutical manufacturing), properly recorded laboratory notebooks must be supplied for patent
applications. In academic laboratories and other research environments, the laboratory notebook also
provides the “memory” or archives of the research project, containing detailed information on past
procedures, results/data and pitfalls/problems encountered in the research project. Since research
projects often span a period of several years, the amount of accumulated documentation can be
considerable. It is therefore important to learn to keep good, complete and accurate notes in the
laboratory notebook.

For this course, you are requested to purchase the Student Laboratory Notebook in the bookstore. The
laboratory notebook should be thought of as a diary of activities that are described in sufficient detail to
allow another scientist to follow your steps. The notebook section will be worth 20% of your final grade.

Important overall criteria for the evaluation of your laboratory notebook will be its accuracy and
organization. As much as possible, you should write legibly all information and procedures required to
understand the experiments and, if necessary, to repeat them even by an outside investigator who is not
familiar with the project. Draw tables with rulers (you may also create tables and graphs on the
computer, print and paste them in) and clearly label the different subsections and figures of your writing

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so that others can easily comprehend what you did. We do not recommend first writing the information
on a loose piece of paper and then transcribing the information in your laboratory notebook. This practice
creates errors or omissions that are not compatible with proper research practices. We understand that
errors may occur when notes are taken at the bench and do expect that laboratory notebooks may not
always be “neat”. It must however be complete and accurate.

For each experiment or study, the following format is recommended:

1. Date at the beginning of each section/experiment.
2. Title: e.g. Microscopy and Examination of Living and Stained Cultures
3. Objective: Briefly state what you are attempting to do/determine (measure, weight, stain, identify,
infect…)
4. Materials and Methods: If the same as an established procedure (routinely used in the lab), used in
previous studies described in your laboratory notebook or drawn integrally from a published source
(ex.Textbook), provide the relevant reference. If different, state the modifications. For your own
understanding, use flow charts to illustrate procedures.
5. Results: If possible, use table(s) and/or figure(s) to present raw data. Provide brief descriptions of
what the data mean.
6. Discussion: Briefly discuss what you can conclude from your results. Sometimes experiments fail
either because of an unanticipated variable or because of experimental error. If your results
deviate from expectations, identify possible sources of error, provide alternative hypotheses, and
suggest improvements for future experiments.
7. Sign each single page. This is an essential practice in government and industry labs.

The laboratory notebook should be submitted to the supervisor with the final report (see below) at the
end of the term.

D) The final report (30%) and the laboratory notebook (20%) should be submitted to the supervisor
(and co-supervisor if applicable) by the last official day of classes. The Course Administrator will require
a copy of the final report for archiving.

The final report should follow the format of a standard journal in Biology (see the general guidelines
provided below) and include the following sections:

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1. Title Page:
− Title of project
− Student name and number
− Supervisor name
− Course name
− Date submitted
2. Table of Contents (with page numbers)
3. List of Abbreviations:
Only describe abbreviations that are not commonly used; for instance, do not describe acronyms such
as “DNA”, “RNA”, etc… or units of time and mass
4. Abstract:
Provide a one-page concise summary of the question(s) asked, results and significance of the project.
5. Introduction:
Review the state of knowledge in the area of study as published in the current scientific literature,
provide a rationale for the project, state the question(s) and hypothesis addressed in the project and
brief outline of approach (as) used in your studies
6. Materials and Methods:
This section should contain sufficient details of the experimental protocols for someone else to repeat
the experiment. If the procedure has already been published in a journal article in detail, a reference
will suffice. However, if a published procedure was modified, the alterations to the original protocol
should be clearly outlined. Describe in detail any new techniques developed during the project.
7. Results:
Summarize the data obtained from your experiments in figures and/or tables, as appropriate and
including a proper heading (for tables) and figure legend. Figures and tables should be clearly labeled
and easy to interpret. Proper statistical analysis is required in most cases or at least some statement
about reproducibility. Include both positive and negative results, making mention of failed
experiments.

8. Discussion:

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 Provide the interpretations of your results in this section. Do not simply restate the conclusions but
analyze the meaning of these results in the context of the question addressed in your project and
stated at the end of your Introduction. If appropriate, use models to illustrate your point. Discuss the
potential carats and pitfalls of the experiments. Discuss the reason(s) why an experiment may have
failed and, if possible, provide an alternative experimental approach to alleviate the problem. Also
include suggestions for future work.
9. References:
All statements of facts that appear anywhere in your research proposal must be substantiated with a
citation of a peer reviewed publication. Include the most relevant and current papers on the subject.
In the case that the observation or conclusion described has not yet been published but has been
directly communicated to you by members of your laboratory or colleagues in another Institution a
statement to this effect must be included (e.g. S. Harper and J. Chretien data not published or E.
Snowden and J. Assange, personal communication). Accuracy is important. The use of a referencing
program is strongly recommended. Any standard style of referencing used in scientific journals is
acceptable. We request that the format chosen include the complete title of the article.
10. General Guidelines:
− 10-20 pages in length
− double-spaced throughout (but excluding the reference list)
− 11-12 point font
− 2.5 cm side margins
− 3 cm top and bottom margins
− all pages numbered consecutively, including title page, references, tables and figures
− the report may be bound in any manner the student desires

Grading
• 50-59: Did not meet standards expected of third year student (D)
• 60-69: Met minimum standards expected of third year student (C)
• 70-76: Met average standards expected of third year student (B to B-)
• 77-79: Met above average standards expected of third year student (B+)
• 80-84: Readily exceeded expectations of third year student; shows promise in placement work (A-)

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• 85-89: Greatly exceeds expectations of a third year student; demonstrated placement work
competence (A)
• 90+: Greatly exceeded expectations of third year student; highly accomplished placement worker (A+)
Evaluation
The assessment in the course is based on the laboratory performance (approximately 8-10 hrs per week
in one term), on keeping a proper laboratory notebook or equivalent record of research activity and data
gathering, a mid term progress report and a final written report.

Assessment Weight
1. Mid-term progress report 20%

2. Laboratory performance 30%

3. Laboratory notebook 20%

4. Final report 30%

Safety Training and Liability Issues

Appropriate safety training (i.e. WHMIS, Radiosafety, Biosafety, Fire Safety) must be completed prior to
beginning laboratory work. It is the responsibility of the supervisor to ensure that students have received
the required safety training. The information regarding safety training can be found on the Biology web
site. The student is responsible for bringing written confirmation of training dates and location of training
to the Course Administrator in LSB 118.

Application Deadlines
Fall, Term 1: first week of July
Winter, Term 2: third week of November
Fall/Winter, Term 3: first week of July
Spring/Summer, Term 1, 2 or 3: mid-March

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 Molecular Biology - 3I03 Independent Research: Project Permission Form

STEP 1. Student to complete the following:

Student Name ______________________________________________ Student No. _____________________

Surname, Given Name

MACID ________________________________ Preferred E-mail ______________________________________

Current Program: ____________________________________________________________________________

I wish to be considered for enrolment in: BIO 3I03 ____ (Please select the desired option with a checkmark.)

Fall Term 1 ____ Winter Term 2 ____ Spring/Summer ______

STEP 2. Obtain the permission of a Supervisor:

Supervisor ________________________________ Signature ___________________________________

Department ____________________ E-mail Address _________________ Telephone Ext. _________

Office Address ______________________________ Mailing Address _________________________

Student will be working in Room ___________________ Ext. _______________________________

Project Title /Description

If you are working with a supervisor outside the Department of Biology, you will require a co- supervisor within the
Biology Department. Your co-supervisor should be provided with a copy of the mid-term progress report and the
final report and will communicate with the supervisor in determining a final mark for the course.

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STEP 3. Obtain the permission of a Co-supervisor:

Co-supervisor __________________________ Signature _____________________________ (Please Print)

Department ____________________ E-mail Address _________________ Telephone Ext. _________

Office Address ______________________________ Mailing Address _________________________

STEP 4. Student and supervisor to review course evaluation rubric and deadlines and agree upon
format of the final report and the laboratory notebook (please consult “Guidelines on course
evaluation written submissions and deadlines” below).

Final grades must be submitted to Nicole Smith, the Course Administrator before the end of exam period
of the academic term in which the research project occurred (biology@mcmaster.ca ). Please consult the
McMaster calendar for precise dates (https://registrar.mcmaster.ca/category/dates/ ).

• Midterm progress report 20%

• Laboratory performance 30%
• Laboratory Notebook 20%
• Final report 30%

STEP 5. Attach a ONE-PAGE summary of the research proposal

Students who may have previously worked in the same laboratory in which they are completing a
research project are asked to provide an additional one-page summary of any work that is related to the
project being undertaken in the course. Any work completed prior to the student’s registration in
MOLBIO 3I03 cannot be included as part of the student’s final report without clearly identifying and
acknowledging it.

STEP 6. The Communication Agreement must be reviewed and signed by the student and both
supervisors.

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 Molecular Biology 3I03 Communication Agreement
1. Should the Supervisor be unavailable for more than 2 weeks, adequate supervision by a colleague,
postdoctoral fellow or senior graduate student must be arranged and communicated in advance
to both the Student, the Course Coordinator and contact information forwarded to the Course
Administrator.

2. The Supervisor will ensure that the Student has completed the required Health and Safety Training
prior to beginning work in the laboratory.

3. The Student is responsible for ensuring the entire Supervisory Committee [Supervisor, Co-
Supervisor(s) or other Supervisory individuals if any] are kept up-to-date on progress and change
in research topic or experimental procedure throughout the course.

4. Supervisors are expected to communicate grades for each component in a timely manner. The
Student should consult with the Course Coordinator if a mark for the first two course components
has not been received within one week of the due date (see List of Important Dates).

5. Any modifications of the mark breakdown for the course must be discussed and approved by the
Supervisor, Student and the Course Coordinator.

6. Any change in submission deadline for the final thesis or project report must be justified at least 5
days in advance, and in writing to the Course Coordinator. The Course Coordinator reserves the
right to penalize late submissions by up to 5% per day.

I acknowledge that I have read, understood and accept the above course requirement

________________________________________________________________________________________________
Signature of Student Date
_______________________________________________________________________________________________
Signature of Supervisor Date
_______________________________________________________________________________________________
Signature of Co-Supervisor Date

STEP 7. Return this form and a ONE-PAGE summary of the research proposal to Nicole Smith
(biology@mcmaster.ca) for final approval by the Course Coordinator. The Course Coordinator will
consider the application only after submission of the ONE-PAGE summary and all forms completed and
signed.

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For Department Use:
Course Coordinator Approval: ______________________ Date: ____________________

Retain a copy for your records and make sure that both supervisors have a complete copy of the signed forms.

The information gathered on this form is collected under the authority of The McMaster University Act, 1976. The
information is used for the academic, administrative, and statistical purposes of the Department of Biology
including, but not limited to, maintaining records; academic counseling and the administration of examinations.
Personal student information provided on this form will not be used for any unrelated purpose without the consent
of the student. This information is protected and is being collected pursuant to section 39(2) and section 42 of the
Freedom of Information and Protection of Privacy Act of Ontario (RSO 1990). Questions regarding the collection or
use of this personal information should be directed to the Manager of Instructional Programs, Department of
Biology, McMaster University.

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 Policies and Procedures
Requests for Relief for Missed Academic Term Work
McMaster Student Absence Form (MSAF): In the event of an absence for medical or other reasons,
students should review and follow the Academic Regulation in the Undergraduate Calendar “Requests for
Relief for Missed Academic Term Work”.

Academic Accommodation of Students with Disabilities

Students with disabilities who require academic accommodation must contact Student Accessibility
Services (SAS) at 905-525-9140 ext. 28652 or sas@mcmaster.ca to make arrangements with a Program
Coordinator. For further information, consult McMaster University’s Academic Accommodation of
Students with Disabilities policy.

Academic Accommodation for Religious, Indigenous Or Spiritual Observances (RISO)

Students requiring academic accommodation based on religious, indigenous or spiritual observances
should follow the procedures set out in the RISO policy. Students should submit their request to their
Faculty Office normally within 10 working days of the beginning of term in which they anticipate a need
for accommodation or to the Registrar's Office prior to their examinations. Students should also contact
their instructors as soon as possible to make alternative arrangements for classes, assignments, and tests.

Courses with An On-Line Element

Some courses may use on-line elements (e.g. e-mail, Avenue to Learn (A2L), LearnLink, web pages, capa,
Moodle, ThinkingCap, etc.). Students should be aware that, when they access the electronic components
of a course using these elements, private information such as first and last names, user names for the
McMaster e-mail accounts, and program affiliation may become apparent to all other students in the
same course. The available information is dependent on the technology used. Continuation in a course
that uses on-line elements will be deemed consent to this disclosure. If you have any questions or
concerns about such disclosure, please discuss this with the course instructor.

Online Proctoring
This course may use online proctoring software for tests and exams. This software may require students
to turn on their video camera, present identification, monitor and record their computer activities, and/or
lock/restrict their browser or other applications/software during tests or exams. This software may be
required to be installed before the test/exam begins.

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Academic Integrity
You are expected to exhibit honesty and use ethical behaviour in all aspects of the learning process.
Academic credentials you earn are rooted in principles of honesty and academic integrity.
It is your responsibility to understand what constitutes academic dishonesty.
Academic dishonesty is to knowingly act or fail to act in a way that results or could result in unearned
academic credit or advantage. This behaviour can result in serious consequences, e.g. the grade of zero
on an assignment, loss of credit with a notation on the transcript (notation reads: “Grade of F assigned for
academic dishonesty”), and/or suspension or expulsion from the university. For information on the
various types of academic dishonesty please refer to the Academic Integrity Policy.

The following illustrates only three forms of academic dishonesty:

• plagiarism, e.g. the submission of work that is not one’s own or for which other credit has been
obtained.
• improper collaboration in group work.
• copying or using unauthorized aids in tests and examinations.

Authenticity / Plagiarism Detection

Some courses may use a web-based service (Turnitin.com) to reveal authenticity and ownership of
student submitted work. For courses using such software, students will be expected to submit their work
electronically either directly to Turnitin.com or via an online learning platform (e.g. A2L, etc.) using
plagiarism detection (a service supported by Turnitin.com) so it can be checked for academic dishonesty.

Students who do not wish their work to be submitted through the plagiarism detection software must
inform the Instructor before the assignment is due. No penalty will be assigned to a student who does not
submit work to the plagiarism detection software. All submitted work is subject to normal verification
that standards of academic integrity have been upheld (e.g., on-line search, other software, etc.). For
more details about McMaster’s use of Turnitin.com please go to the McMaster Office of Academic
Integrity’s webpage.

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Conduct Expectations
As a McMaster student, you have the right to experience, and the responsibility to demonstrate,
respectful and dignified interactions within all our living, learning and working communities. These
expectations are described in the Code of Student Rights & Responsibilities (the “Code”). All students
share the responsibility of maintaining a positive environment for the academic and personal growth of
all McMaster community members, whether in person or online.

It is essential that students be mindful of their interactions online, as the Code remains in effect in virtual
learning environments. The Code applies to any interactions that adversely affect, disrupt, or interfere
with reasonable participation in University activities. Student disruptions or behaviours that interfere with
university functions on online platforms (e.g. use of Avenue 2 Learn, WebEx or Zoom for delivery), will be
taken very seriously and will be investigated. Outcomes may include restriction or removal of the involved
students’ access to these platforms.

Copyright and Recording

Students are advised that lectures, demonstrations, performances, and any other course material
provided by an instructor include copyright protected works. The Copyright Act and copyright law protect
every original literary, dramatic, musical and artistic work, including lectures by University instructors.

The recording of lectures, tutorials, or other methods of instruction may occur during a course. Recording
may be done by either the instructor for the purpose of authorized distribution, or by a student for the
purpose of personal study. Students should be aware that their voice and/or image may be recorded by
others during the class. Please speak with the instructor if this is a concern for you.

Research Ethics
The following information on ethical issues related to the course and labs in particular is available to be
reviewed.

Extreme Circumstances
The University reserves the right to change the dates and deadlines for any or all courses in extreme
circumstances (e.g., severe weather, labour disruptions, etc.). Changes will be communicated through
regular McMaster communication channels, such as McMaster Daily News, A2L and/or McMaster email.

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