Bio 185: Diversity of Organisms Supplemental Laboratory Syllabus Orange Coast College Course Syllabus Spring Semester 2009 (Jan.

Transcription

1 Bio 185: Diversity of Organisms Supplemental Laboratory Syllabus Orange Coast College Course Syllabus Spring Semester 2009 (Jan. 31 May 31) Lab times: M&W 2:20 5:30; T&Th 2:20 5:30 pm; T&Th 6:30 9:40 pm Lab locations: Science 142 Instructor: Marc Perkins Web page: Phone: Office Location: Science Hall 133 Office hours: Mon. and Wed. 11:30 am 12:30 pm, Tues. 12:00 noon 2:00 pm, and by appointment. IM contact info: Google Talk occmperkins; AOL - marcperkins53; MSN - mperkins@occ.cccd.edu IM contact times: I will be available via IM during my office hours and at many other times. Required texts: See the lecture syllabus for full details. To summarize, you will need a lab notebook, the 3 rd edition of Freeman s Biological Science, and the 4 th, 5 th, or 6 th edition of Pechenik s A Short Guide to Writing About Biology. Supplies needed: Access to a computer with word processing software, Adobe Acrobat Reader, a printer, and internet access is required (and supplied by the college). Students will be required to print copies of lab handouts before coming to lab each day. Prerequisites: Biology 181 or 181H with a grade of C or better. Field trip: There will be one required weekend field trip to a rocky intertidal area at Crystal Cove State Park. There are two possible days to attend the field trip, either Friday May 1 or Saturday May 2, though there will be a limit to the number of students that can attend each day. The trip will start at 9:00 am each day and continue until approximately 2:00pm. Students will meet at Orange Coast College and will be transported to the field site in OCC transportation. Students may be required to pay an entry or parking fee at the park. The trip will include walking up and down stairs, hiking along sandy beaches, and extended periods working in a wet rocky area far from amenities. Students who are not able to attend the field trip will get no attendance credit for that day, and will be required to do a makeup assignment. Please see me as soon as possible if you have any questions or concerns regarding this trip. Use of organisms: Because the topic of this class is biology, we will use either live or dead organisms in the vast majority of labs. We will not dissect any vertebrate animals, though we may dissect invertebrate animals, plants, and fungi. Some labs will entail working with a range of live organisms, including mice, insects, snails, plants, fungi, protists, bacteria, archaeans, and other organisms. If you have any questions about or anticipate having problems working with these organisms, please see me as soon as possible. Safe environment: Free and open discussions in this class will be critical. However, as some of the topics we will be discussing may be controversial and highly charged, please keep discussions on a professional level at all times. 1

2 Grading and assignments: 1. Laboratory examinations There will be two laboratory exams, each covering material presented up to that point in the semester. Exams will be completed in class and may have a mix of fill in the blank, multiple choice, drawing, and short answer questions. Exams will focus primarily on the anatomical, life history, and taxonomic traits of the lineages introduced in lab; spelling will be graded. The laboratory exams will each be worth 65 points. 2. Laboratory notebooks Most organismal biology experiments last weeks, if not months or years, and thus any organismal biologist conducting an experiment must keep good records of their work. These records are typically kept in a lab notebook, and are essential when writing papers and sharing data (it's surprisingly easy to forget what you did yesterday, not to mention last year!). Your notebooks will be a record of your experimental work in the lab (including each experimental lab's question, hypotheses, methods, data, and conclusions), and will be kept in the lab room except before paper due dates. The lab notebooks will be graded sporadically throughout the semester (possibly without notice), and will be worth 50 points over the course of the semester. Guidelines for maintaining the notebooks will be available elsewhere; see the schedule for an indication of which labs will use the lab notebook. 3. Laboratory exercises Each lab that doesn't involve recording information in your lab notebook or an exam will have an assignment due at the end of the period; the assignment will be completed in lab and is due at the end of lab, unless otherwise specified on the day of lab. Each lab exercise will be worth 5 points. The total number of laboratory exercises completed will depend on the number of labs offered during the course and the number of labs which use the laboratory notebook. 4. Journal articles Two of the experimental labs will have a journal article (laboratory report) written for the lab in addition to the laboratory exercise / laboratory notebook. This journal article will be written in the style of a published scientific paper, and is designed to give you experience writing in a scientific style and analyzing experimental results. These journal articles may be written individually or in groups of two (or three if the laboratory group is composed of only three people), but never in groups larger than three; the instructor may require all students to write an individual report for one or both papers. If a journal article is written by a group, each individual must write a separate portion of the paper and the primary author of each section should be clearly identified; failure to do so will result in lost points. Individuals (or groups) writing separate papers that are based on the same experiment must work entirely separately on their papers; any shared content (excluding raw data and statistical output) will be considered plagiarism. Each journal article will be worth 30 points and must be typed; the first journal article will have a draft version due prior to the final version, which will be worth 10 points. 5. Scientific Poster One of the primary methods of presenting research at scientific meetings is to create posters that summarize the experiments researchers have performed on a topic. To help expose you to this style of presentation, one of the experimental labs will have a scientific poster created for it. Specific guidelines for the poster will be provided in class and are available in Pechenik s book. Grading will be based on a number of components, including the quality of the experiment the poster is based on, thoroughness of data analysis, clarity of the written work in the poster, and visual presentation. The poster will be worth 30 points and must be typed. 2

3 6. Experimental proposal Before scientists conduct experiments, they must first get funding to carry out their experiment. To do this they submit grant proposals, documents that contain a summary of the research the scientist hopes to complete, along with background information that shows why the proposed research is important and should be funded. To give you a glimpse of what this type of proposal is like, you'll write an experimental proposal before conducting one of the experimental labs this semester. The experimental proposal will be worth 15 points, and must be typed. 7. Fast feedback assignments Fast feedback assignments are designed to give you non-graded (and non-stressful) feedback about your progress in the course. Fast feedback assignments are short assignments at the end of or during a class period, usually consisting of one or two short questions, which should take only a minute or two to answer. These assignments are NOT graded, but will help me understand how you are progressing with the course material. 8. Re-grading I, like most other humans, have been known to make mistakes. Because of this I am more than happy to go over returned assignments with you to attempt to clarify any questions and/or fix any grading mistakes. However, I ask that all regrading requests be made within two weeks of the assignment s return. 9. Grading summary Journal article rough draft 10 points 1 experimental proposal 15 1 poster presentation 30 1 lab notebook (on ~10 labs) 50 2 journal articles * lab exercises 90 * 2 lab exams 130 Total 385 * * - The total number of lab exercises may vary; thus the number of points possible in the lab may vary as well. Grading policy: Lab points are combined with lecture points into a single grade; see the lecture syllabus for more information. If the total number of points for lab is different on the lab and lecture syllabuses, the lab points will be scaled to the total number of points specified on the lecture syllabus. For example, if a student got 150 out of 200 possible points in lab, but the lecture syllabus specified that lab was only worth 100 points, then the student would get 75 points for lab in the context of lecture. Assignments for which the majority of the class received extremely low grades may be adjusted to account for the difficulty of the assignment. The instructor may deduct points from students assignments if they do not come to lab prepared to carry out the assignments (e.g., they arrive at lab without the day s lab manual or worksheet printed). Important dates: Last day for withdrawal with nothing on transcript Feb. 27 Last day for withdrawal May 2 Final lab exam date May 4/5 3

4 Attendance policy: Attendance is mandatory for this course. You may miss up to three days of lab with no penalty; however, additional unexcused absences may result in your being withdrawn from the class without notice. If you are absent for a lab that has a journal article or other written assignment due based on it for an excused reason, you may turn in the journal article, acquiring data as decided by the instructor. If you are absent for an unexcused reason you may not turn in the journal article or other written assignment for the lab you missed. To encourage good attendance, anyone who has missed no days of lab at the end of the semester will get an additional 5 points of extra credit. Excused absences count against this perfect attendance, the sole exceptions being official absences for school functions and religious holidays. Missing a significant portion of a lab (e.g., being 20 minutes late) will be counted as an absence with regard to this perfect attendance extra credit. Absence policy: An absence will be excused if it is a documented instance of one of the following: an official absence (for a school function, verified with an official absence memo) a religious holiday (provided that I am notified in writing at least 2 working days in advance) a serious personal injury or illness a serious family illness, injury, or death a major emergency or other severely time-sensitive matter beyond your control Any other absence, or any absence without written notification within 5 working days, is unexcused. Late/missed work policy: There will be no make up laboratory exams for unexcused absences; excused absences can make up the lab exams, but may only do so the week of the exam (unless prior written arrangements have been made). Except in the case of genuine emergencies I must be notified (by phone or ) before the exam takes place to arrange a makeup exam for an excused absence. Posters, journal article drafts, and any assignment required for in-class work may not be turned in late, though journal articles may be turned in late. Late assignments will be reduced in points by 15% of the total points available for the assignment per day the assignment is late. Weekends and holidays count towards the number of days an assignment is late. If you want to turn in a late assignment over a weekend or holiday, please it to me or contact me to arrange a drop off. Assignments that were missed due to an excused absence may be turned in late without penalty (subject to the exceptions listed in this section); contact your instructor as soon as possible to arrange a makeup deadline. In general, makeup assignments must be turned in within a timeperiod no longer than twice the amount of time that was missed due to the excused absence. For instance, if you have an excused absence for one week, any work you missed in that one week must be turned in during the two weeks following your return to class. However, all missed assignments must be turned in within four calendar weeks of the original assignment's due date (or by the end of the semester, if that is within four weeks of the missed deadline) for them to count towards the course grade, even if the work was missed due to an excused absence. Academic honesty: To put this simply, all work that you present as your own must be your own. If you do any work with another person you must indicate who you worked with. If you take any ideas from another source (e.g., another person, a website, a published work) you must cite that source. If you take direct wording from a source you must put those words in quotes and cite them. See the lab manual s section on how to cite references and Pechenik s writing guide if you need help citing references. I fully expect you to talk to other people about your assignments (other than exams), and this policy is not designed to prevent that. If you do work with another student or another person simply say, somewhere in your assignment, that you worked with that person no points will be taken off if you do this, assuming you haven't plagiarized or otherwise been academically dishonest. If a project or other assignment is worked on by a group and turned in for a group grade, each individual must indicate their contributions to the final version; failure to do so will result in lost points. Individuals (or groups) writing separate papers that are based on the same experiment/data/research must work entirely separately on their final papers; any shared content (excluding raw data and statistical output) will be considered plagiarism. Any student suspected beyond a reasonable doubt of plagiarism or academic dishonesty (e.g., cheating on an exam, turning in a paper with a few sentences directly copied from a source without quoting and citing them) will at the minimum receive no credit for the assignment in question, will be unable to receive a grade of A in the class, and may receive punishment as severe as expulsion from the college. All incidences of academic dishonesty will be reported to the Dean of Students. 4

5 Incomplete policy: A grade of I may be awarded at the end of the semester to a student who has completed the vast majority of the coursework, is passing, and is unable to complete the remaining coursework due to illness or other circumstances beyond the student s control. If approved, the student and I will fill out an incomplete contract before the end of the semester that will specify the work that needs to be done and the deadline for completion (not to exceed 12 months). Audio/video recording: You may make audio recordings of the class periods, but they may only be used as personal study aids. Video recordings may only be made with prior written approval, and may only be used as personal study aids. Disability accommodations: If you need disability accommodations in the class, please see me or contact either the Disabled Students Center or the Learning Center as soon as possible; reasonable accommodations will be made. Information regarding disability will be held in strict confidence. Sexual harassment and discrimination: Sexual harassment and discrimination are not tolerated at Orange Coast College and will not be tolerated in my classroom. See the college policy on sexual harassment and discrimination if you have any questions. If you feel that you may have been sexually harassed or discriminated against, contact either the Orange Coast College Vice President of Student Services or the College Grievance Officer. Student Learning Outcomes: Student Learning Outcomes related to both lecture and lab: 1. Compare and contrast major anatomical, physiological, and ecological characteristics of the currently recognized high-level taxonomic groups (e.g., domains, kingdoms, phyla), relating structure to function where appropriate. 2. Identify major groups of organisms and viruses, organize them within currently recognized taxa, and justify their placement of the organisms within those taxa. Students will also be able to create, compare, and critique phylogenies. 3. Create diagrams displaying the major life history characteristics of selected organisms for each kingdom of life, highlighting major differences between the lineages introduced. 4. Discuss the basic tenets of evolution and apply evolutionary theory to real-life scenarios, including contrasting the mechanisms by which evolution can occur and analyzing a variety of selective forces organisms from various kingdoms might experience. 5. Compare and contrast the major habitat types found on the planet, including terrestrial, freshwater, and marine. Students will also be able to analyze the interactions (both between organisms and between organisms and the environment) that might occur in these habitat types. Lab-specific Student Learning Outcomes: 1. Explain the major steps in the scientific method and apply them to experimental questions. 2. Design and conduct a controlled, replicated experiment using modern laboratory equipment, the results of which differentiate between student-created hypotheses. 3. Write and present technically accurate summaries of their experiments in the style of a professional scientific work (e.g., scientific journal article, scientific poster). 4. Evaluate experimental designs to determine whether they test the hypotheses they were intended to test, as well as analyze data collected within experiments to determine which (if any) hypotheses are supported by the data. 5. Cooperate with other students while carrying out laboratory activities. 5

6 !!!!Special, super-duper Bio 185 coupon!!!! Turn in any one laboratory exercise one lab day late without penalty. This coupon valid only for one lab exercise only. Coupon must be attached to the front of the laboratory exercise when it is turned in; multiple coupons may be attached to the same assignment. This coupon may be copied and/or reproduced, but each person may only use a maximum of one coupon of this type per semester. Attempts to use additional coupons will result in an automatic grade of no credit on the assignment in question. Expires May 31, 2009.!!!!Special, super-duper Bio 185 coupon!!!! Free pass: arrive to lab one day without the lab manual or worksheet. This coupon valid only for one lab day only. Upon presentation of coupon student will not lose points for failing to print out the lab manual or worksheet ahead of time for any one day of lab. This coupon may be copied and/or reproduced, but each person may only use a maximum of one coupon of this type per semester. Attempts to use additional coupons will result in an automatic loss of all points on the assignment in question. Expires May 31, 2009.!!!!Special, super-duper Bio 185 coupon!!!! Turn in any one journal article one day (24 hrs.) late without penalty. This coupon valid only for one journal article only. The journal article must be submitted within 24 hours of its original deadline for this coupon to apply, and this coupon must be attached to the front of the journal article when turning in the paper copy. This coupon may be copied and/or reproduced, but each person may only use a maximum of one coupon of this type per semester. Attempts to use additional coupons will result in an automatic 20% point loss on the assignment in question. Expires May 31,