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NTRODUCTION TO

CIENTIFIC

ESEARCH

YORK COLLEGE
Fall 2012

INSTRUCTOR: Dr. Brad Rehnberg OFFICE: LS 122 OFFICE HOURS: Tuesday & Thursday 11:00-12:00, Monday, Wednesday & Friday 10:00-11:00 OFFICE PHONE: 815-1262 E-MAIL: brehnber@ycp.edu WEB PAGE: http://faculty.ycp.edu/~brehnber BIO200.101 MEETING TIME: Tuesday and Thursday from 9:30-10:45 LOCATION: LS 125 BIO200.102 MEETING TIME: Tuesday and Thursday from 2:00 to 3:15 pm LOCATION: GH 101

TEXT: none

For many people, science stands as the noblest and most profound of all human endeavors. It is a complex activity in which scientists explore and learn about our earth and the great beyond. By majoring in biology, you have begun the process that may lead to a life-long commitment to some aspect of science or science teaching. But Who are scientists and what do they really do? What is research and how is it done? Does science require experiments? Why is scientific knowledge tentative and is that a good thing? To tackle some of these questions, we will consider profoundly philosophical ideas while attempting to keep our feet on the ground. To acquire necessary career skills, we must deal with the concrete details of research design, data analysis, software, and communication while realizing that many of these details have grand philosophical implications. The goals of this course are wonderfully ambitious: (1) convey realistic perspectives on science, scientists, and research, (2) promote understanding of how the primary literature is created and used, (3) enhance the communication and analytical skills needed for a career in biology, (4) prepare students for rigorous upper division science courses, and (5) stimulate sophomores to begin work on their senior thesis research.

*Attendance - Come to class. Regular attendance is expected and is an easy way of enhancing
your performance level. There will be no makeups for class meetings that are missed. See the list of class meetings when attendance is mandatoryunexcused absence from those meetings will result in point deductions. Chronic tardiness is inconsiderate of peers. Class is disrupted every time someone makes a late entry. Be on time.

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To be eligible to make up a missed exam or an assigned speaking performance, you must notify the instructor of your absence BEFORE it happens. Without evidence of an attempt at notification, a missed exam or presentation will be recorded as a zero. Do not make plans (e.g., buy plane tickets) to begin vacations early if those plans will conflict with the final exam period for ISR.

*e-Reserve Readings for ISR are found on the Schmidt Library website under Reserves. Select
e-reserves and then log in. Under Instructor, look for Rehnberg and then use the password brown.

*Computers - All written assignments must be done using a computer and printer. Save all of your
written work in more than one location (network drive, jump drive, etc.). Do not erase any of your files until after the semester ends. Also, an important part of this course is becoming proficient with some of the scientific software found on the network. Course Expectation: routine checking of your YCP email. Not knowing course information distributed via YCP email is to be avoided.

*Printing - Students need to be able to fund the printing of assignments on an ongoing basis. An
assignment submitted late due to lack of printing funds will be graded as a late assignment. Do not email assignments to your instructor as a substitute for a printed version. * Disability Support - If you are a student with a disability in need of classroom accommodations and have not already registered with Linda Miller, Disability Support Services Coordinator, please contact her at 815-1785 or lmille18@ycp.edu. She can address policies and procedures related to disability services and establish the accommodations for which you are eligible.

Class Meetings and Topics


** Dates with double asterisks indicate mandatory attendance.

8/28 COURSE INTRODUCTION. Review the syllabus and discuss our expectations. e-reserve: chapter 1 in Lee.

8/30 EXPECTATIONS FOR SENIOR THESIS. What is a thesis? What happens in BIO200 and BIO400? In answering these questions, well talk about two general options for your thesis. Dr. Rehnberg will suggest some strategies for getting the thesis process underway. He will also present the thesis timeline and the necessity of establishing early contact with a faculty mentor regarding your research. Assignments --(a) Topic for your thesis proposal and supporting literature. A thesis topic and a LIST of at least 3 primary literature citations are due in 62 days on Wednesday, Oct 31. (b) Thesis proposal progress report is due in 81 days on Monday, Nov 19. (c) Written thesis proposal due in 98 days on Thursday, Dec 6.

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9/4 NATURE OF SCIENCE. What is science? Types of science. Is there "a" scientific method? ereserve: chapters 2, 3, & 4 in Lee

9/6 NATURE OF SCIENCE CONTINUED. Research and the publication of primary literature. The role of colleagues and the power of peer review. e-reserve: Horrobin, Akst, Working Double Blind Assignment --- paraphrase writing from a primary journal article.

9/11 LITERATURE LAB. We will work in groups to handle, examine, and describe different types of scientific literature. We will consider examples of primary, review, and popular science publications. Does the Internet count as "literature"? e-reserve: Descriptive Science, What is Research? Assignment --- view pop and primary periodicals via Schmidt Library.

9/13 NATURE OF SCIENCE COMPLETED. Diversity of research. Pseudoscience. Funding of science.


--- optional bonus --- Write an essay on an assigned topic dealing with the nature of science & the role of literature. This option can be done at any point during the semester see Dr. Rehnberg for a prompt.

9/18 EXAM on all previous topics.

9/20 RESEARCH DESIGN. What is a research question? How does one creatively and aggressively attack a research question? Are research questions answered? Descriptive vs Experimental designs. Random sampling and n. e-reserve: How Cats Survive Falls Assignment --- Each student will be assigned an imaginary but realistic research question/scenario. The goal will be to come up with a sensible research design to answer specific questions. The oral presentations of designs will be given on 9/27, 10/2, 10/4, 10/9. Strong recommendation: Visit early with Dr. Rehnberg about your design strategy.

9/25 PUBLIC SPEAKING. Matthew Randall, Director of the Center for Professional Excellence

9/27** STUDENT REPORTS OF RESEARCH DESIGNS. 10/2** STUDENT REPORTS OF RESEARCH DESIGNS. 10/4** STUDENT REPORTS OF RESEARCH DESIGNS. 10/9** STUDENT REPORTS OF RESEARCH DESIGNS.

10/11 DATA AND THEIR MANIPULATION. What are data? Basic types of data. Types of variability,

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sample size, replication and pseudoreplication. Data notebooks.

10/16 VACATION

10/18 STATISTICS. Learning about nature from numerical data. Descriptive and inferential statistics. Linear regression & prediction. Hypothesis testing with parametric & nonparametric tests.

10/23 INSTAT SOFTWARE. An introduction to friendly software that can be used for descriptive and inferential statistics. Meet in the computer lab where well work through some examples. Assignment --- Each student will statistically analyze an assigned data set using INSTAT.

10/25 SCIENCE GRAPHICS. Discussion and illustration of the importance of clear graphical presentation of data. Review basic guidelines and critically examine good and bad examples from the literature. Assignment --- Take-home Final. This project will require students to bring many recently acquired skills to bear on an assigned research scenario that contains hypothetical raw data. One goal is to analyze data and make appropriate statistical tests, figures, and tables. Results and Discussion sections will also be written to promote data interpretation as well as writing skills. The end result will be the submission of a polished IMRAD manuscript. Due Tuesday, 11/20 in class.

10/30 PRISM SOFTWARE. An introduction to scientific graphics software. Meet in the computer lab where well work through some examples. Assignment --- Each student will graphically display an assigned data set using PRISM.

10/30 11/1 Brief office visit to (1) TELL Dr. Rehnberg about your topic for the thesis proposal and (2) SHOW a written list of supporting literature citations that relate to your topic and that might prove useful for your proposal. This list should minimally include 3 primary journal articles and written in the YCP literature citation format. You will earn 0 to 10 points for this office visit.

11/1 OPEN SOFTWARE LAB

11/6 SCIENCE WRITING: The IMRAD STRUCTURE A look at the organization of research papers: Introduction, Methods, Results, And Discussion. Introduce the standard IMRAD-based format for lab reports used in the YCP Department of Biology.

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11/8** SOFTWARE EXAM. Meet in the computer lab for an in-class exam on data analyses. You must have money in your account to print your exam.

11/13** SOFTWARE EXAM CONTINUED.

11/15 SCIENCE WRITING: AN UNNATURAL ACT. A look at some of the major distinctions between "normal" writing and science writing. Topics include passive and active voice, verb tense, paraphrasing and plagiarism, citation style, and the pitfalls of jargon and other horrors.

11/20 SCIENCE WRITING: COMMON CONVENTIONS. A review of expressions peculiar to science writing.

11/19 - 11/20 THESIS PROPOSAL PROGRESS REPORT. Sign up for an office visit to orally present a progress report (0 10 pts) on the thesis proposal process. See the course web page for meeting expectations.

11/22 VACATION 11/26


BONUS OFFER: SUBMIT A DRAFT OF YOUR WRITTEN THESIS PROPOSAL. Benefits = bonus points and early feedback.

11/27 TBA 11/29 TBA

12/4 SCIENCE, RESEARCH, & ETHICS. Ethical situations, personal ambition, data and truth, you and your thesis mentor.

12/6** THESIS PROPOSALS. Everyone submits their final written proposal for the senior thesis. Oral presentations of proposals will begin today and end during the final exam period. This is an opportunity to use your knowledge of experimental design, statistics, software, speaking, and writing. All of your learning in ISR leads to this moment.

12/11 ORAL PRESENTATIONS OF PROPOSALS CONTINUED.

ORAL PRESENTATIONS OF PROPOSALS COMPLETED 9:30 section: Saturday, December 15, 8:00-10:00 am 2:00 section: Thursday, December 13, 12:45-2:45 p

Assignment Information
Activity Paraphrasing literature Pop vs Primary literature Exam Research design report INSTAT assignment PRISM assignment Software exam Points 10 10 50 50 50 50 100 Assigned Date 9/6 9/11 9/18 9/20 10/23 10/30 11/8 11/13 10/25 Due Date 9/13 9/18 9/18 9/27, 10/2, 10/4, 10/9 11/1 5 pm 11/1 5 pm 11/8 11/13 11/20

Take-home final

100

Thesis-related assignments: Selecting topic for thesis proposal Thesis progress report Thesis proposal (written) Thesis proposal (oral) 10 10 50 50 8/30 8/30 8/30 8/30 10/31 (Weds.) 5 pm 11/19-11/20 12/6 12/6, 12/11, final exam period

540 total course points

Final Exam Periods: 9:30 section Dec. 15 @ 8-10 am, 2:00 pm section Dec. 13 @ 12:45-2:45 pm
0-5 bonus points for consistent in-class participation 0-10 bonus points for optional nature of science essay 2 points for attending each Clark Lecture Final course grades: 4.0 = EXCELLENT (90-100) accomplishment that is truly distinctive and decidedly outstanding 3.5 = VERY GOOD (85-89.99) denotes mastery of the subject matter 3.0 = GOOD (80-84.99) considerable understanding of the subject matter 2.5 = ABOVE AVERAGE (75-79.99) above average understanding of the subject matter 2.0 = AVERAGE (70-74.99) average understanding of the subject matter 1.0 = BELOW AVERAGE (60-69.99) 0.0 = FAILURE (below 60)

Final withdrawal date: Friday, October 26, 2012

ACADEMIC INTEGRITY IN THE DEPARTMENT OF BIOLOGICAL SCIENCES YORK COLLEGE Science and the teaching of science represent a search for truth and they rest on ethical behavior and intellectual honesty. As such, both the Department of Biological Sciences and York College of Pennsylvania unequivocally condemn academic dishonesty. Academic dishonesty is defined in the York College Student Handbook as cheating, plagiarism, fabricating research, falsifying academic documents, etc. and includes all situations where students make use of the work of others and claim such work as their own. Because the Department of Biological Sciences maintains high expectations for all students and is committed to stringent standards of academic integrity, we contend that all published information, in any form, must not be used unless rigorously paraphrased and properly cited. Moreover, all tests, projects, assignments, and lab reports require a solo effort unless specifically noted otherwise by the instructor. This means that the sharing of text, images, tables, figures, or data analyses with classmates is a breach of academic integrity. Furthermore, providing such information to others will be considered as dishonest as accepting or taking the information. Work done in lab may involve partners, but the formal partnerships end when the laboratory period ends. At the end of a lab, each partner should leave with his or her groups protocols, hypotheses, data, and any information about procedural problems. Once the in-lab work is completed, the work shifts from a group effort to a solo effort. This does not mean that students shouldnt discuss lab concepts, problems, and general strategies and broad interpretations. Talking about science is healthy and is encouraged. And, it is understood that lab groups may obtain similar or identical quantitative data for a given project. In the end, however, data analyses and report writing as well as the overall presentation and interpretation of these data are to be done independently by the individual and not by the group. If work submitted by two or more students appears unexplainably and unreasonably similar, or if credit for previously published information or ideas is not given through literature citation, academic dishonesty will be assumed. In this event, the instructor will provide written notification to the student, the Department Chair, and the Dean of Academic Affairs of the charge and the sanction. Documentation related to instances of academic dishonesty will be kept on file in the students permanent record. If the academic dishonesty is the students first offense, the instructor will have the discretion to decide on a suitable sanction up to a grade of 0 for the course. The faculty member may request that the Student Welfare Committee conduct a hearing and decide on the sanction, which can involve academic suspension or dismissal from the College, if the faculty member believes the offense to be of an extremely egregious nature. If the Dean of Academic Affairs determines that the breach of academic integrity is the students second offense, the Dean will provide written notification to the student, the instructor, and the Department Chair. The Student Welfare Committee will automatically conduct a hearing to review the charge and decide on an appropriate sanction, which will involve academic suspension or dismissal from the College. Students are not permitted to withdraw from a course in which they have been accused of academic dishonesty. If questions about academic integrity arise, see the course instructor before completing and submitting your work. In addition, specific information about the York College of Pennsylvania Academic Integrity Policy can be found in the most recent edition of the Student Handbook. Sign below: Students Name: (Please Print) _________________________________________

I, _________________________, have read this statement and the syllabus for this course and I understand

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and accept departmental and college expectations of academic integrity and ethical conduct. ACADEMIC INTEGRITY IN THE DEPARTMENT OF BIOLOGICAL SCIENCES YORK COLLEGE Science and the teaching of science represent a search for truth and they rest on ethical behavior and intellectual honesty. As such, both the Department of Biological Sciences and York College of Pennsylvania unequivocally condemn academic dishonesty. Academic dishonesty is defined in the York College Student Handbook as cheating, plagiarism, fabricating research, falsifying academic documents, etc. and includes all situations where students make use of the work of others and claim such work as their own. Because the Department of Biological Sciences maintains high expectations for all students and is committed to stringent standards of academic integrity, we contend that all published information, in any form, must not be used unless rigorously paraphrased and properly cited. Moreover, all tests, projects, assignments, and lab reports require a solo effort unless specifically noted otherwise by the instructor. This means that the sharing of text, images, tables, figures, or data analyses with classmates is a breach of academic integrity. Furthermore, providing such information to others will be considered as dishonest as accepting or taking the information. Work done in lab may involve partners, but the formal partnerships end when the laboratory period ends. At the end of a lab, each partner should leave with his or her groups protocols, hypotheses, data, and any information about procedural problems. Once the in-lab work is completed, the work shifts from a group effort to a solo effort. This does not mean that students shouldnt discuss lab concepts, problems, and general strategies and broad interpretations. Talking about science is healthy and is encouraged. And, it is understood that lab groups may obtain similar or identical quantitative data for a given project. In the end, however, data analyses and report writing as well as the overall presentation and interpretation of these data are to be done independently by the individual and not by the group. If work submitted by two or more students appears unexplainably and unreasonably similar, or if credit for previously published information or ideas is not given through literature citation, academic dishonesty will be assumed. In this event, the instructor will provide written notification to the student, the Department Chair, and the Dean of Academic Affairs of the charge and the sanction. Documentation related to instances of academic dishonesty will be kept on file in the students permanent record. If the academic dishonesty is the students first offense, the instructor will have the discretion to decide on a suitable sanction up to a grade of 0 for the course. The faculty member may request that the Student Welfare Committee conduct a hearing and decide on the sanction, which can involve academic suspension or dismissal from the College, if the faculty member believes the offense to be of an extremely egregious nature. If the Dean of Academic Affairs determines that the breach of academic integrity is the students second offense, the Dean will provide written notification to the student, the instructor, and the Department Chair. The Student Welfare Committee will automatically conduct a hearing to review the charge and decide on an appropriate sanction, which will involve academic suspension or dismissal from the College. Students are not permitted to withdraw from a course in which they have been accused of academic dishonesty. If questions about academic integrity arise, see the course instructor before completing and submitting your work. In addition, specific information about the York College of Pennsylvania Academic Integrity Policy can be found in the most recent edition of the Student Handbook. Sign below: Students Name: (Please Print) _________________________________________

I, _________________________, have read this statement and the syllabus for this course and I understand

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and accept departmental and college expectations of academic integrity and ethical conduct.

PERSONAL DATA SHEET


INTRODUCTION TO SCIENTIFIC RESEARCH Fall 2012 Preferred 1st name _________________

NAME ________________________________

YCP email address ______________ Other Email ________________ Phone _______________

Working outside job? Hrs/week = ______

YCP Athlete? _________________

List all your courses and their meeting times on Tuesdays & Thursdays this semester:

Circle one:

sophomore

junior

other = ________

Name of your academic advisor ____________________________________

YCP biostatistics course? BIO I BIO II Genetics

yes yes yes yes

no no no no

What are your short-term plans after graduation?

What are your long-term life/career plans? Option 1: Option 2: What do you expect to learn from this course?

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Do you have a possible topic for your senior thesis? If yes, what is it?