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Biology 406 – Symbiosis

Spring 2014

Lectures: 9:05-9:55 a.m., M,W,F

106 Wartik


Dr. Chuck Fisher


Office:  219 Mueller Lab

Office phone: 865-3365

Office Hours: M, W 11:00 – 12:00, and by appt. (Room 219 Mueller)


Dr. Erin Becker


Office:  217 Mueller Lab

Office phone: 863-8360

Office Hours: T 11:30 – 12:30, and by appt. (Room 217 Mueller)


TA: Arunima Sen


Office:  217 Mueller Lab

Office phone: 863-8360

Office Hours: M, W, 10:00 – 11:00, F 8:00 – 9:00, and by appt. (Room 217 Mueller)


Course Description:

This course covers a variety of different types of symbiotic relationships between unicellular symbionts and plants, fungi, or animals.  Among the associations that are addressed in some detail are: rhizobium/legume symbioses (bacterial/plant), mycorrhizal associations (fungal/plant), lichens (algal/fungal), algal/invertebrate symbiosis (including corals and giant clams), symbioses between chemoautotrophic or methanotrophic bacteria and marine invertebrates, bioluminescent symbioses, a variety of digestive/nutritional symbioses (including ruminants, termites, aphids and shipworms), and ant/plant/fungi symbioses.  Other symbioses may be covered at the request of students. The subject is multi-disciplinary both in regard to the variety of associations studied and the types of phenomena addressed.  Lectures will cover topics ranging from molecular interactions, through physiological adaptations and interactions between partners, to the ecology of the intact symbioses and the surrounding communities.  In addition to some review papers, current primary literature is examined and you will be required to critically evaluate data and reach your own conclusions.


Course Objectives:

1. To introduce symbiosis as a re-occurring theme in biology.

2. To familiarize students with a diverse sample of mutualistic symbiotic associations.

3. To apply basic concepts learned in other biology courses to complex systems, and gain an in-depth understanding of some symbiotic systems.

4. To introduce a variety of the techniques used in experimental biology, and gain an understanding of experimental design and the limitations inherent in different techniques.

5. To learn to locate, read, and critically examine primary scientific literature.


Course Materials:

Review papers:  We will provide you with 4-5 review papers or book chapters over the course of this semester to provide background information for the lecture material.  These will be posted on the course web site.

Additional reading materials: There will also be primary literature papers that you will need to read in preparation for presentations/discussions each Friday. You will be able to download these papers from the course web site.  You will need a .pdf viewer such as Acrobat Reader to view and print these papers (Acrobat Reader is available for free on the Web, there is a link on the Library’s web-site).

Course on Angel.  Using your student access account you can log onto the course web site and will find the syllabus, lecture and presentation schedules, assigned readings, assorted extra material, and announcements.  You will also find portions of the lectures in powerpoint format. These will provide a framework for taking notes, and you will need to fill in details in class. We do not make the final powerpoint files or our own notes available to students who miss class, so please make arrangements with other students if you should have to miss a class.  The webpage will also provide all papers used for Friday discussions in pdf format a week before they are to be presented in class. All material is in folders under “Lessons”.

This web page is intended for you and we are open to any suggestions that you might have for improving the site. Please contact Arunima Sen if you have any difficulties with the website or available files.



Class will begin at 9:05 a.m.  We will lecture on Mondays and Wednesdays.  On Fridays, students (you) will give short presentations on primary literature papers that are relevant to what’s going on in lecture or on other topics in the broad field of symbiosis that you find interesting (more details on these presentations are given below).  You will not be expected to remember the finer details of all of these primary literature papers;, however, there will be one general question about each “Friday paper” on either a midterm or the final.  The assigned readings from the review articles will help you to more fully understand the concepts we cover in class, and reading this material in advance will greatly enhance your ability to follow and comprehend lectures.  At least 90% of the material on the exams will have been discussed in class, and much of this material will not be in any of the assigned readings.  This means that ATTENDANCE IN CLASS IS HIGHLY CORRELATED WITH FINAL GRADES.  At the beginning of each lecture period, there will be five minutes of questions that will review recent lecture material (you can ask me questions, or I will ask you). 


Lecture exams:

There will be two midterm exams and one final exam.  The midterms will not be cumulative.  Approximately one half of the final will be cumulative.  The other half will cover the material from the last third of the class. The exams will include short answer, fill in the blank, true or false, multiple-choice, and short essay questions. 


Grading and Grade Assignment:

Each mid-term exam will be worth 100 points (25% of the 400 point total for the course) and the final exam is worth 200 points (50%).  Your preliminary course grade will be calculated from your point total, however class participation and Friday paper presentation can raise (or lower) your grade by up to 2/3 of a grade. Although the final grade cutoffs may be slightly higher or lower then indicated below (if there are natural break points in the class point distribution), the following chart based on previous years can serve as a general guide of your standing in the course.


93 - 100%

372 - 400 points


90 - 92.9%

360 - 371 points


87 - 89.9%

348 - 359 points


83 - 86.9%

332 - 347 points


80 - 82.9%

320 - 331 points


77 - 79.9%

308 - 319 points


70 - 76.9%

280 - 307 points


60 - 69.9%

240 - 279 points


Less than 60%

239 or fewer points

 Remember, class participation is important and can have a positive influence your final course grade.


A Bit about the Primary Literature Presentations:

Each Friday, three or four students will give presentations on primary research papers that they have discovered.  Students will have the opportunity to sign up for paper presentation topics during the first week of class.  Primary research papers must be relevant to the material being taught in class, and should be approved by one of the instructors at least two weeks prior to the date of the presentation.  A .pdf file of the paper must be emailed to Arunima Sen for posting to the course website no later than one week prior to the date of the presentation.  Students can either present alone, or choose to work in pairs. The presentations should be 15- 20 minutes in length for pairs working together, and 10-15 minutes in length for people presenting alone (this includes time for a short question/answer period after each presentation).  Student presenters should provide some background information and discuss the hypotheses, research methods, and findings of the paper they have chosen.  Tables and figures should be summarized and displayed within the presentation.  Presenters should indicate whether they feel the conclusions are justified by the data and what take-home message they got from the paper.  The use of PowerPoint is suggested, but not required. Do not procrastinate! If you wait until the last minute to work on these, you are on your own.  If you start in a timely manor, we are happy to help you in any way we can.  All students are required to read at least two of the assigned papers before they are presented each week and should be prepared to answer questions about these papers during class.  Lecture exams will include questions about the primary research papers presented each Friday. We suggest you print at least the abstract of each paper before you come to class.

These presentations and participation in class will be considered when calculating your final grade. We will grade these presentation as ++,  +, 0, or -.  As a general guideline, a “++”  with average class participation will raise your grade, a “+” along with above average class participation will raise your grade, a ” 0” will not affect your grade and a “–“ will contribute to at least a 1/3 grade reduction from the grade originally calculated from your point total.


Exam attendance 

Attendance at exams is mandatory, and absence during the scheduled exam time will result in a grade of zero unless prior arrangements have been made or a legitimate and verifiable excuse is provided within 48 hours of the exam. The following are the only legitimate excuses accepted:


A) An illness that is documented by a doctor's letter or note and receipt (an appointment card from Student Health Services is not acceptable). In addition, the student must provide her/his doctor with written authorization to disclose information to the Instructor should the Instructor require additional information in order to verify that the illness was significant enough to miss the exam.

B) A religious holiday, that is celebrated by the student AND that is officially recognized by the University. 

C) A University-sponsored event (which must be documented by a letter from the sponsor or coach and given to the Instructor prior to the date of the exam that will be missed). 

D) A death in the immediate family (which must be documented according to the Instructor's request). 

Oversleeping is not an acceptable excuse for missing an exam.

Documentation of a legitimate excuse for missing an exam is required before the make-up exam will be administered. The Instructor may seek to verify the submitted documentation by talking to the person who signed or wrote the documentation. All requests for make-up exams must be submitted to the Instructor within 48 hours after the exam, written on paper (not sent via e-mail), and signed and dated by you.


Academic Integrity/Academic Dishonesty  

Each student in this course is expected to work entirely on her/his own while taking any exam, completing any assignments, and completing any work for any points in this course, unless directed otherwise by the instructor.  Students are also expected to abide by all University, Eberly College of Science, and Department of Biology policies about academic integrity and academic dishonesty.  Academic dishonesty in this course can result in either assignment of “F” by the course Instructor or "XF" by Judicial Affairs as the final grade for the student.  Academic dishonesty is not limited to simply cheating on an exam or assignment.  The following is quoted directly from the "PSU Faculty Senate Policies for Students" ( regarding academic integrity and academic dishonesty: “Academic integrity is the pursuit of scholarly activity in an open, honest and responsible manner. Academic integrity is a basic guiding principle for all academic activity at The Pennsylvania State University, and all members of the University community are expected to act in accordance with this principle. Consistent with this expectation, the University's Code of Conduct states that all students should act with personal integrity, respect other students' dignity, rights and property, and help create and maintain an environment in which all can succeed through the fruits of their efforts.”

All University and Departmental policies regarding academic integrity / academic dishonesty apply to this course and the students enrolled in this course.  To ensure you understand the academic policies at Penn State, refer to the following for further details:

Faculty Senate Policy G-9: Academic Integrity (  

Eberly College of Science's Web pages on academic integrity (

Academic Integrity Policy of the Eberly College of Science ( 




Qualified students with disabilities are encouraged by Penn State University (PSU) to participate in the University’s programs and activities.  Should you need any type of accommodation in this course because of a disability or have questions or concerns about the physical access, please contact the Instructor or the PSU Office for Disability Services.


Miscellaneous Information:


Use of e-mail: 

E-mail is an effective way to handle brief communications, but is not effective to communicate concepts, major ideas, or to discuss a student's performance in the course.  Thus:

E-mail should be used to:

Point out any errors or oversights made by the instructor during lectures.

Set up an appointment to talk with the instructor if you cannot meet during regularly scheduled office hours.

Ask questions about lecture material that can be answered in a brief sentence.

E-mail should NOT be used to:

Ask for explanations about concepts, ideas, theories, processes, or any other information that requires more than a very short answer.  We will explain things and answer major questions much better by talking with you in person than via e-mail.

Ask about your points or grade -- if you feel that a grading mistake has been made we can discuss your concerns in person.

Provide final documentation for a missed exam or assignment.


Preparation and Participation are very important to your success in this course!:  

Your participation during lecture is vitally important to your understanding the lecture material.  If you have a question or comment, please feel free to stop me during or after lecture.  

The best thing that can be done to ensure success in this course is to be prepared when you come into lecture.  So again, we strongly recommend reading the relevant material and reviewing the notes from previous lectures before lecture begins.