Literature in Biology (BIOL-30100)

Fall 2008. Tuesdays 4-5pm CNS 119
Topic: The Honey Bee Genome

Instructor:

Marina Caillaud

Office:

165 Center for Natural Sciences

Office hours:

Tuesday 3-4 pm

or by appointment (e-mail me!)

E-mail: 

mcaillaud@ithaca.edu



Course Description and learning Objectives


The topic of this course is the scientific literature. You will learn how to find and read scientific papers, how to write them, and how to deliver research reports (orally) as you would at a scientific meeting.  The major goal is to teach you the logical structure of papers and presentations, and to provide guidelines for conveying information effectively.  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.

 

Text:

 

Writing Papers in the Biological Sciences, Victoria E. McMillan, St. Martin Press


Assessment

 

You have 6 major assignments including two oral Powerpoint presentations of 12-15 minutes each.  These assignments mirrors the forms of presentations currently given at scientific meetings in Biology.  You are also expected to read the textbook and participate in class - including participation in the question and answer / discussion period after each talk. Details for each Assignment can be found below.

 

-Oral presentations (2): 25% each
-Written assignments (4): 10% each
-Participation and attendance: 10%

 

Policy for Attendance and Conduct

 

Attendance is mandatory!  Even if you are not making a presentation that day, you are expected to listen to your classmates’ talks, to participate in discussion, 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.  Coming to class late will be considered equivalent to not attending. Because of scheduling, presentations cannot be postponed except for valid excuses - not being prepared is not a valid excuse. Also note that 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 or phone my number (277 1181) to leave a message.  Such notification does not guarantee my accepting your reason for absence, but failing to notify me guarantees that you will not be excused. 

 

Accommodation Policy

 

I will make reasonable accommodations for any students with disabilities.  The student must inform me of their need for accommodation, and be registered with the Office of Academic Support Services for Students with Disabilities.

 

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 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. .....”

 

Using figures and tables in presentations is acceptable as long as you cite your sources.

 

Class Schedule:


9/02/08: Organizational meeting.

 

Presentation of Library Search Techniques

Overview of the research theme: The Honey Bee Genome.

Assignment #1:  Literature search – due September 9.

Reading assignment:  Chapters 1 and 4 .

Sign up for the 1st round of oral presentations.

 

9/9/08: General organization of research papers and Oral Presentations.

 

Overall Structure of a Research Article.

How to organize an oral presentation.

Presentation of a Research paper by the Instructor.

Assignment #1 is due.

 

9/16/08: Oral presentations by Students (max of n=5)

9/23/08: Oral Presentations by Student (max of n=5)

9/30/08: Data presentation: Figures and Tables.

 

Assignment #2:  Creating Figures and Graphs – due October 21
Reading assignment:  Chapters 2 – 3, and 10 (pg 170-174)


10/7/08  Oral presentations by Students (max of n=5)

10/14/08: Oral presentations by Students (max of n=5)

 

10/21/08: Last meeting

 

Course Evaluation:  MANDATORY

Assignment #3:  Critical evaluation of a paper – due November 11

Assignment #4:  Critical evaluation of 302 presentations – due Dec. 16th


Description of the Assignments

Assignment #1:  Literature Search

*Part 1. Using the computerized search engines available on the library home page, use one or more the databases listed on the course handout, or browse the databases yourself.  You will find that if your use more than one database, you will find more papers, although many of the same papers will appear with different databases.  In general, it’s a good idea to use more than one database, since each has their own specific limitations.

  • Find ten research papers on the Honeybee (Apis mellifera). While you may include some review articles on this list, at least 7 of the papers must be primary research articles.
  • Hand in: a typed list of ten articles using correct citations: authors, year of publication, title, journal  name, volume, and  pages <>       


*Part 2. Go to the NCBI home page, the public access point to many resources (http://www.ncbi.nlm.nih.gov/). A quick glance at this page shows that NCBI contains far more than just the sequence repository. It is a rich source of information on all aspects of genetics and genomics. All of the divisions are searchable and information ranging from gene sequences, to the position of a locus on a human chromosome, to direct access to the scientific literature dealing with a particular gene, is immediately accessible. Click on ‘PubMed’. PubMed is the NCBI gateway to the biomedical research literature. It is a searchable  database and information can be retrieved based on combinations of parameters such as author, subject key words, or organism. A complex query can be entered and a list of  publications matching it will be returned. For instance, we could enter a simple search by author. If we entered Hartwell LH (one of the winners of the 2001 Nobel Prize in Medicine) and pressed ‘Go’, PubMed would return a list of his current publications. Give it a try. The list of Hartwell's publications is 5 pages long. Only the top and therefore most recent papers are displayed on the first page. Each paper is linked to its abstract and sometimes the full text of the articles.

Assignment #2:  Creating Figures and Graphs

An essential component of any research paper is the presentation of the data collected in the Results section.  For this assignment, you will be given some “raw data” from a hypothetical study.  You need to organize the data into a logical format for presentation in a paper.  This includes a labeled figure, graph, or table.  It also includes a title for the figure and a figure legend.  You should examine the general experimental questions and results and determine, in your own mind, the best way to present this data.   

 

Assignment #3: Critical Evaluation of a Student research paper

You will be provided with a research paper, written by an anonymous, former (already graduated) undergraduate, to read and critique.  Although the topic of the paper will probably be unfamiliar, the expectation is that there will be enough information in the Introduction to allow you to understand the rest of the paper.  Assume, for this assignment, that you are a faculty member who has been asked to review this paper.  Grade the paper with a justification for your grade.  Provide comments on the paper.  Some points to consider when evaluating the paper are: 

 

Assignment #4:  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, you need to think about:

 

Assignments # 5 and 6. Oral 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 the honeybee genome.  Papers for oral 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.  Please note college policy that material submitted for grades in one course cannot be submitted for credit in another course - your presentation cannot be based on an article used in another class.  I need to receive a copy of the paper at least one week before your presentation so that I can approve it - either a photocopy or a .pdf copy of the paper sent by email, whichever you prefer. 

 

Each student will give two oral presentations, using Powerpoint, on a primary research paper.  The presentation should last approximately 15 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 readable by people in the back of the room. If it's a table, maybe you should underline the important data points in red so the audience knows where to look, or if necessary, rewrite the table including only the important information. 

 

Each presentation should include:

• an introduction that describes the background information that is necessary to understand the research. Specifically, what is the general topic (i.e. the alterations in DNA repair proteins which result in phenotypes associated with cancer), and what was known of this problem when the paper was written? Please start simply. While you 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? For example: "this paper concerns effects of mutations in genes for nucleotide excision repair upon development of cancer in mice." To introduce the audience to the topic, please use a figure from a course text (or another simple diagram that is likely to be familiar to students) in your introduction. This will encourage you to (a) think about the general area of the research, and how these experiments fit into the material that students in this course have learned; and (b) to begin your talk as simply as possible.

• an explanation of the hypothesis, or question being addressed?

• a description of the experiments performed. 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 (for example, if the hypothesis is correct that a DNA repair protein binds to a specific DNA sequence, then when the fragment of DNA is incubated with the protein, a shift in the mobility of the fragment should be seen upon electrophoresis.). Were appropriate controls used? Be sure to explain them.

• 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 gel, explain what is loaded in each lane. If you are explaining a graph, be sure to explain what on is on the x‑axis, y‑axis, etc. If explaining a photograph, give some context (i.e. "this is a photograph of a cell, stained with antibodies that recognize...").

• what are the interpretations or conclusions of the work? Again, place the paper in context: what is the significance to the overall area of research, to our understanding of general biological or biomedical problems? This is perhaps the most important part of the talk from the perspective of the listener; after hearing complex experiments, what is the bottom line? It is important for you as a speaker/teacher to step back from the specifics of the experiment 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.)


• 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 (or on an overhead or slide).


• Use the board, to write new terms, or to make simple drawings.

• If you find outlines useful in helping you to follow lectures, consider using an outline to help students follow your talk.

• Tables help to summarize data. For example, imagine cells treated with drug A for 2 hours, 6 hours, and 24 hours, and drug B for 2 firs, 6 firs and 24 firs. Keeping all the results straight would be greatly helped by presenting it as a table.


• You may wish to make a figure(s) of your own. Sometimes those in books will simply not be quite right for the point you are trying to make. In addition, sometimes the easiest way to explain results is to show a figure of your own


• Summarize what you've said. To just go through a list of experiments, then end, is not acceptable.

 

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Last updated August 27, 2008