BIO 447 - Cell and Molecular Biology Research Methods

Fall 2007

Instructor: Jeff Newman

Room: Heim 107

Phone: 570-321-4386

email: newman@lycoming.edu

office hours: Tu 9-10, W 2-3, F 11-12

Lecture: MW 11:30am-12:20pm Heim 113

Lab: to be arranged individually;

Tuesdays encouraged

Course web site: http://moodle.lycoming.edu

Catalog description of course:

This course focuses on the culture and methods of biology research. Students will meet twice per week to learn experimental design, good record keeping, ordering/preparation of materials, equipment maintenance, and analyses of primary biology literature. Each student will design and conduct a lab project that can be supervised by any member of the biology faculty. Each student will prepare an oral presentation, poster presentation, and a research journal-style paper. Two one-hour seminars and six to eight hours of laboratory work per week. Prerequisites: Bio 110, 111, at least two other biology courses and consent of instructor.

Learning Goals:

Content Knowledge: Students should understand:

The steps in the Scientific Method
The different levels of reliability of scientific information from different sources
How to analyze—not regurgitate!--a research article
The current standards for ethical scientific experimentation and communication
The current US graduate and professional school admissions process
The current US system for funding graduate and professional studies

Skills: Students should be able to:

Generate questions/hypotheses and design appropriate experiments to answer/test them
Work in groups to solve scientific questions or problems
Access the scientific literature and evaluate its reliability and usefulness in their projects
Use instruments including pipettors, centrifuges, chromatography columns, tissue culture apparatus, microscopes, and immunological assay plate readers as appropriate during the course of experiments
Use computers and mathematics to analyze experimental data
Report experimental results as a scientific poster presentation
Report experimental results as a research journal-style paper
Give constructive criticism about a research paper or proposal
Discuss current topics in biology with one another and with their Professors as fellow scholars
Use Powerpoint to present their ideas to a larger group

Overview: During this course, you will develop your own laboratory experiment. You will make a proposal, survey the literature to help refine your hypothesis, work with the Professor to design an experiment suited to the available reagents and time, keep proper notebook entries, and write up your lab experiments clearly and succinctly so that your fellow students can attempt to replicate your work. You will serve as a peer reviewer, offering constructive criticism of your fellow students’ research proposals and presentations—and receiving constructive criticism of your own work.

Lectures: Monday and Wednesday 11:30am-12:20pm Heim 113

This course takes a constructivist view of the learning process: it will make you think and talk and learn in new ways! A few lecture periods will consist of traditional lectures, but most will evolve into highly interactive discussion sessions. This means you must come to class prepared, having done the assigned reading ahead of time, so that you can take part in group discussions. Some weeks you will be working in groups to analyze research papers or to discuss specific scenarios. You may need to meet with your group outside of scheduled class time to do some of this work. Be prepared to be flexible in this scheduling, and know that I will change the groups several times throughout the course.

Laboratory (6-8 hrs/week): TBA (Monday afternoon or Tuesday is recommended). All lab time must be supervised by a Professor who is in the building at the time you are working, and documented with signed lab notebook pages. Students who do not document the appropriate amount and intensity of lab time will be penalized in grading and may fail the course if the situation does not improve after one warning. This is a serious research project that requires a serious time commitment.

You will prepare weekly Project Status Reports that describe what you set out to do each week, how much time you spent in the lab, what you learned and achieved, any problems you encountered, and what you plan to do during the upcoming week. These are due each Monday from weeks 3-12. Project Status Reports should be 1-2 pages and emailed to your instructor and research supervisor (if different).

Course grading:

Grades will be determined based on the following assessments:

Weekly Project Status reports 10 x 10 pts = 100 pts

Class Discussion Participation 100 pts

Research Proposal 100 pts

Lab Notebook Checks 4 x 25 pts = 100 pts

Journal Club Presentation 50 pts

Research PowerPoint Presentation 50 pts

Research Poster 100 pts

Research journal-style article 200 pts

Total possible 800 pts

Grading Scale

	B+ = 86.7 - 89.9%	C+ = 76.7 – 79.9%	D+ = 66.7 - 69.9%
A = 93.3 – 100%	B = 83.3 – 86.6%	C = 73.3 – 76.6%	D = 63.3 – 66.6%	F= below 60%
A- = 90.0 – 93.2%	B- = 80.0 – 83.2%	C- = 70.0 – 73.2%	D- = 60.0 – 63.2%

How to succeed in this class:

Do the assigned readings before class, so you can focus on the fine points in discussion.
Come to class on time and attentive, ready with questions.
Take good notes of your own to fill in the details.
Ask questions during and at the end of each lecture--don’t let any confusion or misunderstanding or brilliant insight go until another day.
Arrive in lab prepared with questions. Better yet, stop by after lecture to ask questions about the next lab day, or email me your questions ahead of time. There is no such thing as a silly question or a dumb question, especially when dealing with lab work—it’s always better to ask first!
Keep up with your lab work throughout the semester: don’t assume you can always make up a missed lab period “later.”
Pay special attention to the intermediate lab event deadlines—they are designed to keep you on track and to help you avoid last-minute panic.
If you feel you are falling behind the class or have hit a wall in your experiment preparation—come talk with me for help right away.
Come see me during office hours--I like to talk with you, and I do think about other subjects beyond the biology lab! If you are interested in going into more detail on a subject, jot it down and come talk to me. Your ideas and curiosity could evolve into a laboratory exercise later in the course, or into an Independent Study or Honors Project.
Have fun—and remember, your experiences in this course will likely form the basis for a graduate school admissions essay and/or letter of recommendation in the future!

Course Schedule:

	Monday	Lab (Tuesday)	Wednesday
Week 1 8/27-31	Course introduction; set up student lab schedule, being a good lab colleague	First oral discussions of projects.	Review of the Scientific Method; Maintaining a Lab Notebook
Week 2 9/3-7	One-page proposals due Suppliers of research materials	Order required materials	Accessing the Scientific Literature; Research Lab Topic
Week 3 9/10-14	Wet Lab Math – dilutions, molarity How to prepare and use stock solutions. How to label stocks and stored materials	Prepare solutions, gather all required materials	Annotated Bibliography drafts due How to Analyze the Scientific Literature Critically
Week 4 9/17-21	Lab Meeting: 8 minute progress reports Lab Notebook Review # 1	Lab Experiments	First draft of Research Proposals due Being a Good Peer Reviewer
Week 5 9/24-28	Peer Reviews of Research Proposal drafts (small groups)	Lab Experiments	Peer Reviews of Research Proposal drafts (small groups)
Week 6 10/1-5	Final Research Proposals due Oral presentations of proposals (5-8 min)	Lab Experiments	Preparing formal protocols for bench use.
Week 7 10/8-12	Lab Meeting: 8 minute progress reports Lab Notebook Review # 2	Lab Experiments	The Culture of Science: Conferences
Week 8 10/15-19	UMBC Conference Review - What makes a good Research Poster?	Lab Experiments	Annotated Bibliography Updates due Research Ethics: class discussion of specific scenarios
Week 9 10/22-26	How to give a research presentation.	Lab Experiments	Research Paper Introduction* draft due* Literature Analysis – “Journal Club”
Week 10 10/29-11/2	Lab Meeting: 8 minute progress reports Lab Notebook Review # 3	Lab Experiments	Research Paper Methods* draft due* Literature Analysis – “Journal Club”
Week 11 11/5-9	Literature Analysis – “Journal Club”	Lab Experiments	Research Paper Results* draft due* Literature Analysis – “Journal Club”
Week 12 11/12-16	Lab Meeting: 8 minute progress reports Lab Notebook Review # 4	Lab Experiments	*Complete* Research Paper draft due Graduate and Professional School Applications, Admissions, Funding, and Survival Skills
Week 13 11/19-23	Peer reviews of research paper drafts	Lab Experiments	Thanksgiving Holiday !!!
Week 14 11/26-30	Final Powerpoint Presentations	Finish Posters	Final Powerpoint Presentations Research Posters due
Week 15 12/3-7	Final Powerpoint Presentations	Clean-up, material storage	Research Papers due Public Poster Session