Biology Honors Thesis Biology 402 (3 credits) New Mexico State University, Fall 2009

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1 Biology Honors Thesis Biology 402 (3 credits) New Mexico State University, Fall 2009 Instructor: Dr. Timothy Wright Office: Foster 375 Phone: (but prefer that you me through Blackboard) Office Hours: Tuesday 1:00-2:15 in Foster 375 or by appointment. Intern: Lisa Ramirez Office: Milton D22 Phone: Office hours by appointment Class Meetings: Tuesdays and Thursdays, 2:35-3:50 in O Donnell Hall 242 Course Webpage: The course web page is available in Blackboard, the new system that replaces WebCT at NMSU. This will be the main point of contact outside of class and you should make a point of checking it on a regular basis. General course information, announcements, and class readings will be posted on this site. It is also the preferred route for ing me. Log in to Blackboard at <learn.nmsu.edu> and locate page for 'BIOL-402-M01'. Please note that other official communication from the university will often come through your NMSU box. Please access it regularly, or forward it to your currently used address, as your success in college may ride on your ability to respond quickly to these messages. Texts: The required textbook is How to Write and Publish a Scientific Paper, 6th ed by Day and Gastel, Greenwood Press. It is available in the bookstore, new and used. Course Overview: The purpose of this course is twofold: to teach you how to write a scientific paper, and to produce a thesis based on your Hughes research. Dissemination of scientific results through peer-reviewed journals is fundamental to the scientific process and is the culmination of months, and sometimes years, of intensive research effort. This is true whether one is an established scientist or an undergraduate research scholar. Although you will be producing an undergraduate honors thesis, the writing principles and strategies you will learn in this class apply equally well towards preparing a manuscript suitable for submission to a scientific journal. The strategy we will follow is to break a paper down into its component parts (introduction, methods, tables and figures, results, discussion, literature cited and abstract) each of which you will write, critique and revise several times. You will also learn to become a better writer by analyzing published papers and by reviewing and critiquing the paper sections written by your classmates. Peer reviews will be conducted in small (3 person) groups composed of students working in related areas of biology to enhance the quality of the reviews. Class Format: There will be two class meetings each week, on Tuesdays and Thursdays. Class activities come in several different flavors. As detailed in the class schedule at the end of the syllabus, the three class sessions following the introductory class will consist of individual Page 1 of 7

2 meetings between students and the instructor and intern in my office. These meetings will be scheduled during the first class and will be held in my office, 375 Foster Hall. During these meetings I will expect to hear from each student an overview of your project, a summary of project to date, and your research plans for the fall semester. After these individual meetings, class meetings will cycle among several types: Lectures: Lectures by the instructor will introduce each section of the paper, discuss its purpose and give tips for effective writing. Peer review: In peer review sessions students will work in small groups to constructively critique the draft sections of their group members. Paper analyses: Paper analysis sessions will be conducted within peer review groups and will focus on papers of interest to that group. Analyses will focus on dissecting how papers are constructed on a section-by-section basis and how the authors build their presentation. The groups will then summarize their analyses to the entire class and look for common threads in how papers are constructed. Students must read the assigned paper sections before class. Writing time: During some sessions class will not meet to allow you more time for writing. Note that there is no chance you can complete all writing assignments only during this time! You will do best if you put time for reading and writing into your daily schedule and then do your best to ensure that this time does not get squeezed out by other activities. There is a detailed schedule at the end of the syllabus describing the focus of each class meeting. Assignments: There will be 6 types of class assignments. All assignments are due in class at the beginning of the period; they will lose 25% of their point value for each day they are late. Points for each assignment are given below in the Grading section. A detailed schedule describing when each assignment is due is at the end of the syllabus. 1) Annotated bibliography: Your annotated bibliography must include at minimum 20 references from peer-reviewed journals relevant to your work. Annotated bibliographies should consist of a list of formatted references each followed by a brief discussion of its relevance to your thesis. Papers may be relevant for their theoretical approach, experimental methodology, study system, analysis, the discussion points, or all of the above. Your paragraphs should focus on those aspects of the paper that are directly relevant to your project; they should not be general summaries of the paper. References should be formatted in the style of a target journal that would be appropriate for your paper/thesis; this target journal should be selected in consultation with your mentor. I strongly encourage you to use a citation manager, such as Endnote, to catalog your citations and quickly format citations in a variety of styles. Endnote is available as a stand-alone program (encourage your mentors to invest in it if they haven't already) and is also available on the literature search engine BIOSIS available through the NMSU library. Tutorials on its use are available through the library. This bibliography will be graded on the extent of its completeness and thoughtfulness in its paper reviews. 2) Outline: Your detailed outline of your paper will describe the material that will be in each section of your paper (Introduction, Methods, Results, Discussion and a list of Tables & Figures) on a paragraph-by-paragraph basis. When you turn in your outline you should also provide a printed copy of the Instructions to Authors section for your target journal. You are expected to follow the format of this journal when producing subsequent sections. You will turn four double-spaced copies of the outline, one for the instructor, one for the intern, and two for your Page 2 of 7

3 group members who will review this outline in the following class. You will then turn in a single final version to me that will be graded on the basis of its completeness, clarity, logic and the level of detail. You are strongly encouraged to discuss this outline with your research mentor to get their input on the overall direction of the thesis. To encourage this interaction, you are required to have your research mentor initial your final outline before turning it in to me. 3) Draft sections: You will turn in four double-spaced copies of section drafts for the following sections: i) Introduction, ii) Methods, iii) Results, Tables & Figures, iv) Discussion (see schedule for dates). One copy goes to the instructor one to the intern, and the other two will be distributed to your group members for peer review. Each section should include a citation section at the end with citations to appropriate references formatted in your target journal's style. These draft sections will be graded on the basis of their completeness and adherence to the expectations for content within that section as discussed in class. 4) Peer reviews: Each person will be responsible for carefully and constructively critiquing the section drafts of all their group members. We will discuss effective peer reviewing in class to aid you in targeting your critiques. Comments should be written directly (and legibly!) onto the drafts copies provided by your group members. During review sessions you will go through your comments one by one with your group members to make sure they are clear and to allow for discussion of your points. The marked draft copies will then be returned to the authors so they can use them to revise their sections. Note that these peer reviews are a critical part of the writing process; the reviews you are given will improve your writing directly while those that you produce will improve it indirectly by forcing you to think about how to improve the writing of others. I will be grading peer reviews on their thoroughness and the utility of the comments. 4) Paper analysis: Papers for analysis will be selected by peer review groups based on their interests and in consultation with the instructor. PDF files of the assigned papers will be distributed through Blackboard; students should print out copies of these papers and bring them to the discussion. Students will be responsible for reading the assigned papers before coming to class, with a particular focus on the designated sections. Discussions will occur in two stages during the class period. In the first stage peer review groups will dissect their papers to uncover how the authors structured that particular section and what aspects of their writing either contribute to or detract from effective communication. In the second stage groups will present the results of their discussion to the entire group to search for common themes among different papers. Students will be graded on their participation in the discussions. No written assignment is due for paper analyses. 5) Final sections: Based on the peer reviews you are given and your own judgments, you will revise each of your section drafts to produce a final draft of each section. These final drafts are due the same day as the draft version of the next section. You must turn in both the final version of the section and the drafts with your peers' comments to me in one stapled package. I will review each of these sections and provide comments that you can use to improve your complete thesis. Final sections will be graded on completeness, adherence to the format of the target journal, specific expectations for that particular section, and clarity and effectiveness of writing. Page 3 of 7

4 Note that these final sections are typically due the same day as the drafts of the next section. Writing on a consistent, daily basis (rather than the night before the deadline) will help you avoid overload at these deadlines and greatly improve your writing. 6) Complete thesis: A draft of your complete thesis will be due on 12/1 and will undergo peer review on 12/3. A draft must also be given to your thesis mentor at that date for their review. This draft should represent a thorough revision of the component sections based on any comments provided by me, your peer reviewers, your research mentor and any other reviewers. It will also include a newly-written abstract summarizing your research. Your final complete thesis is due at 3:30 on 12/10 in class during the final exam period. The final thesis will be graded on completeness, adherence to the format of the target journal, clarity and effectiveness of writing. Note that final acceptance of your thesis as a Hughes Thesis may require an additional round of revision if the thesis does not meet the formatting guidelines or does not adequately reflect the input of your reviewers. Final acceptance of your Hughes Thesis is a requirement for completing the HHMI Research Scholars Program. Attendance: Class attendance is required and part of your grade will come from class participation. Students who must miss a class on documented university business must provide the written documentation to Dr. Wright at least two weeks in advance and must make arrangements with him to turn in any assignments before leaving on university business. Failure to follow this procedure will result in the student obtaining a zero for that assignment. Cell phones and pagers must be turned off or silenced during class. Withdrawals: It is the responsibility of the student to complete the necessary paperwork to withdraw from the class should they decide to do so. The deadline to drop with W is October 14. Note that this class is required of all Hughes Research Scholars. Academic Honor: Intellectual honesty is a fundamental expectation of all students in this course and is taken very seriously by the instructors. Work on all assignments must be your own unless explicitly stated in this syllabus or other written instructions for the assignments. Cheating, plagiarism (both intentional and unintentional), and other academic misconduct will not be tolerated. Students judged to be guilty of academic dishonesty on a particular assignment will receive no points for that assignment and the instructors reserves the right to consider more severe penalties such as failure of the course and referral to the Dean and Student Judicial Affairs. Note that failure to put quotation marks around direct quotations constitutes plagiarism, even if the source is cited, because the lack of quotation marks implies that the writing is your own. Material should either be paraphrased or clearly designated as a quotation. Note that replacing words with synonyms, changing verb tense or other minor alterations do not qualify as paraphrasing and would be considered evidence of plagiarism. A limited definition of plagiarism is available in the NMSU Student Code of Conduct at A more complete definition of what constitutes plagiarism and why it must be avoided are available at the NMSU Library ( ). A useful tutorial and self-test on plagiarism is available at the Page 4 of 7

5 Duke University website You are expected to have read at least one of these websites by the second meeting and have a clear idea of what constitutes plagiarism. Please consult the instructor if you have any questions or concerns regarding academic honesty. Disabilities and Accommodations: Please call Jerry Nevarez, Director of Institutional Equity, at with any questions you may have about NMSU's Non-Discrimination Policy and complaints of discrimination, including sexual harassment. Please call Michael Armendariz, Coordinator of Services for Students with Disabilities, at with any questions you may have on student issues related to the Americans with Disabilities Act (ADA) and/or Section 504 of the Rehabilitation Act of All medical information will be treated confidentially. Grading: Your final course grade will be determined by the points you accumulate on each part of the course. The different parts are valued as follows: Annotated bibliography 100 Outline draft 10 Outline peer reviews 25 Outline final 50 Intro draft 10 Intro peer reviews 25 Intro final 50 Methods draft 10 Methods peer review 25 Methods final 50 Results, Tables & Figures draft 10 Results, Tables & Figures peer review 25 Results, Tables & Figures final 50 Discussion draft 10 Discussion peer reviews 25 Discussion final 50 Class participation 100 Complete thesis draft 25 Complete thesis peer reviews 50 Complete thesis final version 300 Total Points 1000 You can use the following points scale as a guide to your overall grade in the course; I reserve the right to adjust the scale in assigning final grades. A B C D F 900 and above points, points points 599 and below Page 5 of 7

6 Tips for success in class: Here are several tips to improve your success as a writer. 1) Find a quiet place to write and use it regularly. 2) Set aside time in your daily schedule for writing and reading and treat that time as sacred. Do not allow other demands to impinge on your writing time. You will get much more done, and the writing will be much less painful, if you try to write a little bit every day instead of saving it all for the night before assignments are due. 3) Treat peer review very seriously. Work hard on your constructive criticisms of your group members. Treat your reviewers' comments with respect and make their recommended changes unless you strongly disagree. 4) Make use of your Hughes mentor. Mentors may differ in the degree to which they can help review your thesis as it is being written, but all are experts in your study area and should be your first resource for research related questions. 5) Visit me in office hours. I am happy to answer questions and help your write the best possible thesis. Page 6 of 7

7 Class Schedule (Note: Instructor reserves the right to revise the schedule.) Date Class Activity Thesis Section Due Reading 8/20 Introduction to class 8/25 Special class: Endnote and Web of Science Demos by T. Westbrock, Branson Library 8/27 No class: reading time 9/1 Individual meetings with instructor 9/3 Lec 1: What are scientific papers? Annotated bibliography 1-5, 15, 35 9/8 Lec 2: Principles of effective writing Guest lecture by L. Ramirez 9/10 No class: writing time 30-34, 40 9/15 Lec 3: What is an introduction? Outline draft, target journal 6-8, 10 9/17 Peer review: Outline Outline peer reviews 9/22 Paper analysis: focus on introduction selected papers 9/24 No class: writing time 9/29 Lec 4: What is a methods section? Outline final, Intro draft 11 10/1 Peer review: Introduction Intro peer reviews 10/6 Paper analysis: methods, tables, figs selected papers 10/8 No class: writing time 10/13 Lec 5: How are results presented? Intro final, Methods draft 12, /15 Peer review: Methods Methods peer reviews 10/20 Paper analysis: results, tables, figs selected papers 10/22 No class: writing time 10/27 Lec 6: What is a discussion section? Methods final, Results draft 13 10/29 Peer review: Results Results peer reviews 11/3 Paper analysis: focus on discussions selected papers 11/5 No class: writing time 11/10 Lec 7: What is an abstract? Results final, Disc. draft 9, 14 11/12 Peer review: Discussion Discussion peer reviews 11/17 No class: writing time 11/19 Lec 8: How to submit a paper Discussion final /24, 26 Thanksgiving Holiday 12/1 Lec 9: Giving a scientific presentation Guest lecture by Dr. K. Hanley Complete thesis draft /3 Peer review: Complete thesis Thesis peer reviews 12/10 Final Class Meeting, 3:30 in ODH 242 Final Thesis due Page 7 of 7