Bruce Smith:  smithb@ithaca.edu,  CNS 166 / 171, 274-3971
Office Hours:  Tuesday 1-3:00 p.m. or by appointment
Class meeting time:  CNS 118, 4:00-5:50 pm

• Writing Papers in the Biological Sciences (4th edition), Victoria E. McMillan (2006), Bedford/St. Martin Press
• Victoria E. McMillan (2006), Bedford/St. Martin Press (required)

One primary goal of our department, stated in our mission statement, is to foster the writing and communication of biology.  This course is designed to teach you about the scientific literature - how to find and read scientific papers, how to write them, and how to deliver research reports (orally and as posters) as you would at a scientific meeting.  Skills that you develop in this course will also help you in other courses, including Junior Research, and in future life.  In any career,  an ability to deliver professional reports clearly, concisely, and logically will markedly affect people’s perception of you.

Each section in Literature in Biology is theme based: the secondary goal is for you delve deeper into one specific topic, developing a deeper understanding in one field of biology.  This is an opportunity to develop critical thinking skills: questioning whether the authors have used appropriate methods, correctly interpreted their results, and presented a logical argument that leads to their conclusions.  In this section of Literature in Biology, we have 3 major assignments: two oral powerpoint presentations of 12-15 minutes each, and one powerpoint poster presentation.  You are also expected to read the textbook and participate in class - including participation in the question and answer / discussion period after each talk and during the poster session.

Learning Objectives: The Biology Department identifies seven student learning objectives for our majors, six of which are addressed in this class:

1)    demonstrate an understanding of the fundamental concepts and principles in biology encompassing cell biology, molecular biology and genetics, organismal biology, population and evolutionary biology, ecology, and global biology.

2)   demonstrate an understanding of the application of biological concepts to everyday life.

3)   articulate connections among biological concepts at various levels (e.g. molecular, cellular, organismal, ecological) as well as between biology and other natural sciences.

4)   critically analyze biological information, including analysis of the effectiveness of methods, the meaning of observational and experimental data, and the appropriateness of conclusions.

6)   effectively communicate scientific works in both oral and written form.

7)   carry out work in a way that demonstrates a professional standard of ethics, collaboration, and respect for nature.

Expected Learning Outcomes:

1. conduct scientific literature searches 
2. understand major components of science papers and how to write them
3. interpret figures and tables within scientific papers 
4. present scientific papers in oral and poster presentations
5. critique oral presentations
6. learn key biological concepts related to the course topic

Grading:         

• Attendance and class participation will be noted by the instructor (see attendance section, below)
• Random quizzes may be given to test your comprehension of course material
• In class student presentations will be evaluated on clarity, organization, and the depth at which you understood the research paper on which you based your presentation
• Your poster presentation will be graded based on clarity, organization, and your ability to extract and present in your own words the major concepts and findings of the original research paper on which you based your presentation.  Also, your ability to follow instructions of using a good poster style versus bad poster styles from the examples presented in lecture and posted on Blackboard.

Oral presentations (2 per student):       60% (30% each)

                                    Poster presentation (1 per student):      30%

                                    Participation, Attendance, Quizzes:     10%

                                    ---------------------------------------------------------                                    

                                    Total:                                                   100%

Blank grading sheets are provided on Blackboard, which indicate specific areas in which oral presentations and the poster presentation are evaluated.  I am looking for clear and concise organization, evidence of understanding the content of the paper, and that you correctly assess the significance of this research within the context of the general discipline of biology.  Through your presentations, you should be able to demonstrate that you have the ability to critically analyse the biological literature.  As well, I will be assessing your technical skill in making a clear and coherent presentation, with appropriate use of graphics and powerpoint.  Everyone gets nervous during a talk: I’ll be offering constructive comments on how to control and nerves and avoid distracting habits, and the impact of this on your grade is minimal.

In summary, grading is as follows:

A =      exceptional work, extremely impressive, near flawless in terms of content and presentation, clear and well organized, made complicated concepts easy to understand; effective use of time (in talks) and space (on posters).

B =       above the expectations of the assignment, but has some room for improvement in terms of content, organization, and presentation.

C =       meeting the minimal obligations of the assignment, significant room for improvement in terms of content, organization, and presentation.

D=       does not meet obligations of assignment, lacking sufficient attention to content and presentation.

F =       unacceptable level of effort for the assignment, or failure to complete the assignment.

Participation/attendance/quizzes:

Your participation will be determined by observing whether you were engaged in the material being presented to you, and actively participating in class.  You are expected to ask questions during discussion periods that follow each peer’s oral presentation. You must attend every lecture, unexcused lectures will result in a lower grade (see policy, below).  Several short quizzes may be given at random to assess your preparedness and the depth of what you learned materials from both the reading assignments and lecture content.  It is your responsibility to do the readings and take notes during lecture so that you are prepared for a possible quiz.

Policy:

Attendance is mandatory!  Even if you are not making a presentation that day, you are expected to listen to your peers, participate in the discussions, and offer constructive criticism. Failure to attend class without a valid excuse will result in a 10% penalty in your final grade, two unexcused absences will result in failure.  Arriving more than 10 min. late to class without a valid excuse may result in a 5% deduction in grade. Because of scheduling, presentations cannot be postponed except for valid excuses - not being prepared is not a valid excuse. Also note that all electronic devices such as cell phones, pagers, etc. are to be kept turned off during classes.

The college’s policy is that acceptable reasons for absence include 1) student illness, requiring the student to be bed-ridden; 2) death or serious illness in the immediate family; 3) appearance in court; 4) religious holidays.  If you have to miss a class, you MUST inform me before the class if at all possible, but if not physically capable, then notify me as soon as possible afterwards.  You can send me e-mail, phone my number (above) or the Biology Department (607-274-3161) to leave a message.  If you do not have the number with you, phone directory assistance and get the number for the main switchboard of the College (they will either transfer your call, or provide the correct number).  Such notification does not guarantee my accepting your reason for absence, but failing to notify me guarantees that you will not be excused. 

1)      Academic Honesty:

All the work in this class must be your own, unless stated otherwise.  Please note college policy that material submitted for grades in one course cannot be submitted for credit in another course (currently, previously, or in the future) - your presentation cannot be based on an article used in another class.  Confirmed instances of academic misconduct will result in a zero for that test or assignment and referral to the school judiciary system.  Please refer to the Student Handbook for a detailed description of the policies regarding student academic conduct.

2)      Accommodations:

In compliance with Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act, reasonable accommodations will be provided to students with documented disabilities on a a case by case basis.  Students  must register with the Office of Academic Support Services and provide appropriate documentation to the college before any academic adjustment will be provided.

3)      Plagiarism:

Please be aware of plagiarism: if you take a sentence from someone else's work and only change one or a couple of words, it is still plagiarism even if you cite the source.  You must rewrite the information or ideas in your own words.  Plagiarism is a serious offense of academic misconduct: check the student handbook and library website  (http://www.ithaca.edu/library/research/plagiarism.php) for details, but it can lead to judicial proceedings and even expulsion from the college.  Each idea has to be referenced (and in the sentence where the idea appears), you cannot simply cite the reference once at the end of a paragraph containing many ideas from the same source.  In such cases, you can avoid referencing each idea yet still indicate your source through careful writing,

e.g.:      “Roberts and Janovy (1985) were the first to study this phenomenon.  They found that ..., further, when the ... .  Roberts and Janovy go on to state that ... and their conclusion was... .”

Or,       “Roberts and Janovy (1985) were the first to study this phenomenon.  In the following paragraph, I will review their work. .....”

1)      Course Evaluations:

Student input is highly valued and is important to maintain high quality instruction. Course evaluations are mandatory and must be completed online by the last day of class.  An incomplete may appear on your transcript  if it is not submitted by that time.  The evaluation will be submitted to the Department Assistant. She will verify that you have submitted the form.  Once that has been checked, your identification will be removed and will not be printed with the comments. Further instructions will be given at the end of the semester.

Oral Presentations:

Each student will give two oral presentations, using PowerPoint, on primary research papers. The presentation should last no more than 12 min. Within this time period, you need to give a general introduction (so that people understand the topic, the question being asked, and the relevance), enough methods to understand what they did, an overview of the important results, and a discussion of what these results mean and how the study adds to our overall understanding of the topic. Most research papers will contain more information than you need to present. In many cases, the types of information that you can exclude are minute details of the methods and occasionally, some of the results (control experiments to show that their technique works, for example). The first task for you as the presenter – and in many cases the harder task – is to determine what information you need to discuss and what you can leave out. Each student in the class will evaluate the presentations of their peers (see attached sheet). These evaluations will be summarized and given to the presenter, along with my evaluation and a grade. Peer evaluations are NOT used in determining the grade.

Make sure your visual aids are legible in the back of the room. If it's a table, maybe you should highlight the important data points in color so the audience knows where to look, or if necessary, rewrite the table including only the important information, or make a figure based upon it.

Choice of Papers for Oral and Poster Presentations:

This course is theme based: the article on which you base your presentation must clearly fit the topic chosen for this section of the course.  In this case, papers must relate to communication, specifically in non-human species.  Communication can be accomplished through acoustic, visual, chemical, or electrical signals, and the message may serve to maintain group contact, attract mates, warn about predators, or to repell others in order to defend resources.   Signals can be honest or deceptive, and may benefit the emitter and/or the receiver.  The topic includes how signals evolve as well as how illicit receivers may exploit the signals.  In one of the first classes I will provide an overview of the topic and some guidance as to how to find articles.  Papers for oral and poster presentations must be from primary research articles that have been published in peer-reviewed journals. You cannot use review papers, perspectives, notes, briefs, short communications, etc.  Look for papers that are of reasonable length and complexity - if the paper is too short and simple or too long and complex, then it could adversely affect your presentation.  Students cannot choose a paper already selected by another student.  I need to receive a .pdf copy of the paper at least one week before your presentation so that I can approve it.   Please send the electronic copy as an email attachment, with the subject heading being Literature in Biology and your last name.  Posters must be submitted at least 24 hrs before class, as I need to post them on a website for viewing the day of the presentation.  The penalty for missing deadlines is 5% per day, however not having your poster ready 24 hours in advance is a 50% penalty, and 100% if the poster cannot be posted by presentation time.

Class Schedule (Spring 2011):

 Week 1 ( Jan. 25)        Introduction to course and overview of course content on Blackboard; background on course topic. [For next week: Read pgs 5-32]

 Week 2 (Feb. 1)          Introduction to literature searching and types of scientific papers; nuts and bolts of a research article; understanding figures and tables; practice with library search  techniques. [For next week: Read pgs 39-44; 44-67; resources on Blackboard regarding Statistics; Read pgs 215-226; paper for example talk (posted on Blackboard).]

 Week 3 (Feb. 8)          The basics of statistics; how to prepare for your oral presentation, including example talk.

 Week 4 (Feb. 15)        Student Presentations (first presentation)

 Week 5 (Feb. 22)        Student Presentations (first presentation)          

Week 6 (March 1)       Student Presentations (first presentation)

Week 7 (March 8)       Student Presentations (first presentation) [For next class: Read Chapter 4; pgs 226-233; resources on Blackboard regarding posters.]                    

Week 8 (March 15)     SPRING BREAK (no class)                     

Week 9 (March 22)     Discuss how peer-reviewed papers are written learn how to make and present a poster                                                           

Week 10 (March 29)   Student Presentations (second presentation)

Week 11 (April 5)       Student Presentations (second presentation)

Week 12 (April 12)     Student Presentations (second presentation)

Week 13 (April 19)     Student Presentations (second presentation)

Week 14 (April 26)     Poster Presentations; Course Evaluation

Week 15 (May 4 & 5)  Attend at least one day of Junior Research presentations (hand in a summary paragraph of two student 302 research presentations,  Due on May 6^th  at 4:00 pm)

Guidelines for Presentations:

Oral Presentations:

     each talk should include:

• an introduction that describes the background information necessary to understand the research. Specifically, what is the general topic and what was known of this idea/organism when the paper was written? Please start simply. While you may have struggled through this paper several times, remember that no one else in the room has ever seen it. What general topic does the paper deal with? To introduce the audience to the topic, use a figure or photo to connect your audience with the idea or the organism you are talking about.
• an explanation of the hypothesis, or question being addressed.
• a description of the experiments or observations conducted. What methods were used? This is likely to require some explanation of specific experimental details. For unfamiliar techniques, it may be helpful to explain the possible outcomes of the experiment. If relevant, were the appropriate controls used? Were the appropriate analyses conducted? Were the appropriate species included for analysis?
• an explanation of the observed results. Do not confuse results with interpretation. Results are what is clearly observed or measured. Interpretation is the explanation, or what the authors believe is happening. Take time to explain the results clearly; remember no one else in the room has ever seen this paper before. If you are explaining a figure, be sure to explain what on is on the x‑axis, y‑axis, etc. If explaining a photograph, give some context.
• what are the interpretations or conclusions of the work? Again, place the paper in context: What was the original question? What is the broader significance of the work? This is perhaps the most important part of the talk from the perspective of the listener; after hearing complex analyses, what is the bottom line? It is important for you as a speaker/teacher to step back from the specifics of the research to explain the conclusion in understandable, simple terms. I strongly recommend using a simple figure with which students are likely to be familiar. This will help to put things in context, and to relate it back to the course material. Were the authors able to answer the questions originally posed? Are there problems in the logic or interpretation? (some authors will try to gloss over these). What new questions have been raised by the results and/or interpretation? 
•  any general conclusions or comments? non‑scientific comments are ok [but not required] here; for example, ethical or economic concerns; what this might mean for society, etc.)

Additional Tips:

• You may use notes, but please do not read your notes.
• You may not be able to cover all the experiments that were performed in the paper. For longer papers, you will have to limit your talk to only some of the experiments.
• Use straightforward language that is understandable. If you need to use new terms, explain them. The whole talk should be in English that will be understood by a tired, restless audience. There is no point in preparing and delivering a talk that your audience will not understand.
• Explain new terms. If you use a term that no one has heard before, explain what it means, and write it on the board.
• You may wish to make a figure(s) of your own. Sometimes those in books will be too complex, and need to be simplified so that they can be easily interpreted by your audience.
• Summarize what you've said. To just go through a list of experiments, then end, is not acceptable.

Poster Presentation:

Using one of the papers you found through your literature search, produce a poster that describes the research with a little bit of background and introduction (context). Although you will NOT print your poster, the final size of the poster should be 36 inches by 48 inches (in PowerPoint, go to Page Setup and select custom size and type in the dimensions in inches).

Title & Authors: A brief, descriptive title (under 80 characters), with authors of the study listed below and presented by you

Statement of Purpose: Clearly and concisely state what scientific question is being asked.

Background: Provide a brief background of the question: why the subject is interesting, and what is already known about it.

Hypotheses: What are possible answers to the question? (may not be applicable to all studies)

Methods: Briefly explain the methods used to answer the question. What data were used? How were data collected? Make a drawing of the experimental setup, provide a picture of the organism, anatomical part, molecule, etc. as appropriate.

Results: Present results as figures, tables, and illustrations with informative captions. You may be able to summarize your results with just figure captions and some concise text between the figures. Limit the results section to a presentation of facts; all interpretations and conclusions belong in the discussion/conclusion.

Discussion/Conclusion: Present interpretations of the results in light of the question that was addressed. Relate the findings back to the prior work presented in the introduction, and place them in a broader context. Perhaps some earlier work can be reinterpreted in light of these discoveries! What do you see as the directions for future research?

Literature Cited: References should be cited in the body of the poster (methods, results, etc.). If short on space, use a smaller font for citations. At the bottom of your poster, provide the complete citations for these references. Use the standard scientific format for citations – in the text of the poster, refer to the author and year, and in literature cited, give the complete citation.

Hand in: (1) the original paper, (2) a PowerPoint file of your poster. E-mail submission is expected. You will present your poster to the class using powerpoint so there is no need to print your poster.

Critical Evaluation of 302 Presentations:

During the last week of classes, students doing 302 research this semester will present their talks to the department. You are required to attend one of these sessions. As your assignment, you  need to write up a critique on two of the talks presented. For this critique explain what the authors did especially well in their presentation and how would you improve on their talk.

Hand in: Two critiques, typewritten, that address the above criteria. For each critique, provide the title of the talk, and the student presenter. E-mail submission is accepted.