Bio 240L:Ecology, Evolution and Biodiversity Lab
TentativeSyllabus
Fall 2008
CRN: 40636 (section1) and 40637 (section 2)
Dr.
SuzyWorcester
Office: Bldg. 53/Room E212 (E212 is throughE210)
Phone: 582-3840
e-mail: suzanne_worcester@csumb.edu
Office hours: M 11:30-12:30 or Th 11-12 or byappointment
Course web site: http://blackboard.csumb.edu (withhandouts, lectures, etc.) and http://masteringbio.com(for GraphIt!, BioSkills, etc. associated with Freeman text)
Labs meets Thursdays 2-4:50 (section
1) and Fridays 9-11:50AM (section 2) in
Inthe lab portion of ÒBiology I: Ecology, Evolution and BiodiversityÓ the focuswill be on learning biodiversity, performing and writing about experiments inecology, and learning evolutionary biology principles through computer-guidedactivities. There will be onemulti-week lab where you will be work on a current restoration site andconducting research. In additionbeing able to write like a scientist is an important skill that will beactively taught in this lab using your experimental results.
Chem110L or equivalents plus CST 101 (basic computing skills) is recommended
The purpose of the labs is to learnhow to design and conduct experiments in biology, to write about yourexperiments in the biological version of the scientific style, and to learnabout the diversity of life. To beable to truly accomplish this goal, it is necessary to take more lab time perexperiment than is typical in introductory biology. Therefore it will take about three weeks to accomplish eachexperimental lab. There will betwo experimental labs where you will conduct an experiment and write up theresults as a formal scientific paper (the ciliate and dune restoration labs).Because of this format, the labs are partially de-coupled from the lecturematerial. We will also review thediversity of life covered in lecture to help solidify your knowledge aboutorganismal diversity. We will alsohave a few labs oriented toward reinforcing the concepts learned in lecturethrough computer simulations or other activities. Finally the last lab will be a field trip to sum up thecontent of the whole course during the last week of classes.
Students with disabilities who mayneed accommodations please see me as soon as possible during office hours ormake an appointment by calling 582-3840 or e-mailingsuzanne_worcester@csumb.edu AND bring your Course Accommodation Form from theCSUMB office for Student Disability Resources (SDR) in Bldg. 47. You can contact SDR through thefollowing channels: Student_Disability_Resources@csumb.edu,Building 47, Student Services, First Floor; Phone: 831/582-3672 voice, or582-4024 fax/TTY, http://sdr.csumb.edu/
Lab Reports (2) 40%
Ciliate lab Ð100 pts (15%)
Dune lab Ñ 100pts (25%)
Peer Review 10%
Participation andAttendance 10%
Data turned in ontime/in correct form 5%
Biodiversityquizzes 5%
Two complete draftsof each report submitted for review 10%
Lab Practical 15%
Computer Modules(Evolution/Ecology) 5%
To get extra copies of coursematerials for lecture or lab go to the blackboard websites for this course (http://blackboard.csumb.edu).
One goal of the biology labs is tohelp you to learn about how to write a good scientific paper in ecology andevolutionary biology style. Youwill learn, over the course of your time at CSUMB, that the differentbiological sciences (ie. molecular biology vs. ecology) have slight variationswith regard to the way papers are written and formatted. Differences are larger for differentscientific disciplines (such as biology vs. physical sciences). For this class, you never want toinclude raw data (but you will be asked or have been asked to include raw datain your Chemistry labs). Inbiology, instead you synthesize your results into means, percentages, etc intables and figures. As with anyformal writing assignment, you should write in complete sentences using correctgrammar, punctuation, etc. and without using slang.
There will be two experimental labs where you will work witha partner to either design an experiment or collect data as part of largerresearch effort. In both cases you will have the opportunity to come upwith your own questions to test. The focus of these labs will be on doingscience, and learning how to write like a scientist. For the latter taskwe will draw heavily on the McMillan text "Writing papers in thebiological sciences". I'll expect you to read the assigned sections before lab on the days they are assigned and I will referto pages of the text in your drafts. Indeed you should read the sectionsbefore you write your rough drafts to understand the style of biologicalwriting. This will lead to less revision for your final papers. Ifyou need assistance with general English issues (composition, grammar,punctuation, style), I recommend purchasing a writing handbook such as theRaimes ÒKeys for WritersÓ (see texts for ESSP 300 in the campusbookstore). (I can give you suggestions of writing handbooks if you needthem.) In addition, if you need additional work on your English skills Imay ask you to attend sessions with an ASAP writing tutor.
After completing the two experiments (Ciliate and DuneRestoration), you will write a scientific paper about your experiment. For each paper you will turn in three versions: first a draft to be peerreviewed in class, a second draft where I will review one or more suggestionsyou feel still need work after a self-evaluation, and then a final draft onwhich youÕll be graded. (Note: even the best papers will be givenfeedback on their rough drafts for further revision, because everyone canimprove -- including myself.)
Drafts are due at the beginning of lab on the day listed on the lab schedule. To receive fullcredit you need to have submitted to Blackboard a complete draft on the day ofpeer review. Partial drafts willreceive half credit, but if you donÕt submit any draft you will receive zeropoints. We will have an in-classpeer review of the first draft (version 1). I will assess the quality anddepth of each peerÕs comments in class and add my own comments to each paperwhile you are peer reviewing each others. Over the next week, I expectyou to incorporate both of your peerÕs comments and submit a second draft(version 2) to the same Blackboard thread as your first draft. (This must be submitted before labstarts the next week.) Beforeyou come to class, cross check your 2nd draft with a peer reviewsheet, and let me know which specific areas of your paper you would likeadditional feedback on prior to finishing your final draft. I willuse your self-assessment to give you feedback to further improve your paperwhile in class. I will not givefeedback on any papers that: (1) have not been revised through the first weekÕspeer review process, and (2) are not submitted on time.
Your final paper will be due two weeks after your first
roughdraft. Please make sure that all drafts and peer reviews have
beensubmitted to the Blackboard thread. I will check to see if all
papers have been submitted at the end of the weekthey are due. If you do not turnin a lab on the day it
is due, you have until the Monday following to turn itin. You will then get 10 percentoff the
final grade. I will acceptthe final
lab up until one week after it was due.
Any labs submitted between Monday and the next lab periodwill be docked
20%. Anyfinal labs submitted
more than one week after their due date will get zerocredit.
The two lab papers are each worth increasingly more towardyour grade as you write longer and more complicated papers. The pointsgiven for each section of each paper are on the peer review sheets. Thisis important because you should focus your writing attention where most of thepoints will be assigned. These sheets will be available on Blackboard andI will hand them out in class.
I encourage everyone to work in groups to design
yourexperiments, collect and analyze your data, and to discuss the implications
ofyour results in a broader context. However, each student
mustturn in a separate lab paper that is written in her/his own words.
Before turning in each paper (both drafts and finalversions),
I recommend filling out a Peer Review Guideline sheet to self-assesshow well
you have met the expectations for the paper. If you aren't surehow to
fill out the self-assessment, consult the pages listed in the McMillantext on
the peer review guide sheet for that section as well as the samplepapers I've
handed out (including my feedback on those sample papers). Inaddition,
there are other parts of McMillan that may be helpful that are notdirectly
referred to in each section. For instance, chapter 1 on locatingand
reading scientific literature may be especially useful, as well as chapters7
& 8 on revising and preparing the final draft. I expect the finalpapers
to be polished, final products and will grade them accordingly. However, I
do want to conserve trees Ð so I would like all finalpapers submitted
electronically. Allpapers must be typed with 12 point font,
single-spaced.
Remember to bring the McMillan text to lab with youon the days we will be discussing how to write a scientific paper (see labschedule).
Asalready mentioned, the first draft of each lab report will be peer reviewed inclass by two peers. For each labthere is a different set of peer review guidelines that focus on differentareas of a scientific paper. Youcan download the peer review guidelines for each lab from the blackboardwebsite: under Òcourse documentsÓ and the name of lab (ciliate or dune). I have also posted sample paper that Ihave assessed with a peer review sheet. The idea is to give you a model of how to do a good peer review. We will also do one or more public peerreviews in class of past papers to teach you how to do quality peerreviews. I will assume youÕve readthe pages assigned in McMillan before class as well so that you have an ideaabout the form of a scientific paper. Finally, we will read together several papers from the primaryscientific literature. We are doingthis to give you a sense of what published literature is like in the biologicalsciences. After all of these stepseach of you will peer review two papersfor each experimental lab. I want you to take this very seriouslyand really work on helping your peer. For this reason, you will be graded on the quality of your peer reviews. (These are worth 10% of your grade.) I expect you to make comments both onthe text of each paper and to fill out and comment with the peer reviewsheet. I recognize that for someof you this will be the first time youÕve had to read a paper with a criticaleye and give substantive feedback. I will be looking for improvement on your peer reviews from the ciliatelab to the dune lab as well.
Whopeer reviews whose papers? Ihave two rules I want you to follow. Review a peerÕs paper who put approximately the same level of effortinto their draft as you did. First, one peer reviewer (and preferably both) needs to be outside yourlab group so they are unfamiliar with the details of your experiment. This is to see if you were able tocommunicate successfully to a new audience. I will try to help facilitate thison each day of peer review.
Whatdo you do if you canÕt come to class on a day when peer review is happening? First, I expect you to come to mostclasses and thus this should happen infrequently, if ever. If you must be absent, you could showup in the other class section instead, if that helps.
Howdo I grade the peer reviews? Iam looking for your ability to learn about the form and style of these papersand apply that to your peers. I amalso looking for the application of critical thinking skills Ð did theauthor make a cogent argument that is internally consistent and plausible giventhe evidence available? Is thewriting clear and understandable? Could this be said more concisely? Did the author plagiarize the available sources? These are the more difficult parts oflearning how to peer review well, and I will be looking for improvement as thesemester progresses. I acknowledgethat you are all at different levels coming into this class and that is why Iwill be factoring in improvement. I will also grade your peer review on completeness. If you check the boxe ÒexcellentÓ forreferring to figures in the text and the author didnÕt do that, IÕll know youwere not being particularly thorough or careful.
I will be giving 10 points for eachpeer review for a total of 20 points for each lab experiment. I am also looking for people toactively learn from their peers to improve their writing. If I or your peer gave you good,substantive feedback on your paper and you choose to ignore it then the totalnumber of points youÕll receive on your final paper will almost certainly belower. On the other hand, if youand your peer forgot to do the peer review ahead of time and you decide to peerreview each otherÕs final papers a few minutes before class and turn them inwith your final papers, then the peer review will receive no credit. How will I know this? First I can see if the peerÕs commentswere actively considered in the final paper. Second, I know who turned in their peer reviews the weekbefore (on time). The reason I amdoing this is to encourage you to actively use the peer review as a learningtool.
Pleasesubmit your first draft to Blackboard under Communications>DiscussionBoard. We will be doing peerreviews in class of each of your papers. Each peer reviewer will download your first draft from this site onBlackboard and peer review it. S/he will then submit his/her peer review and any revisions typeddirectly into the draft as a thread under the authorÕs initial submission of apaper.
IÕdlike you to submit your final draft of each paper on Blackboard underAssignments. Notice that youusually need to type something in to the text box to have Blackboard acceptyour paper.
Inorder for me to decipher and process all of the files the class will besubmitting, I have created some strict naming conventions and formats. This helps you peer review othersdocuments as well. Here is thenaming format you must follow for yourciliate and dune lab reports.
Inappropriately named files like"doc~1.doc" or "Dune.final.doc" will be ignored and treatedas if they were never turned in.
You will also be submitting data to me electronicallyfor the dune lab. All data needsto be entered into an Excel spreadsheet and saved as ".xls" (Excel) or".txt" (text). Pleaselimit the extra formatting that you add to these files. Remember that many people will besharing these files so that uniformity is more important than splash. For both labs include either the firstnames or the first and last initials of everyone in your group. In the file name include either thename or location of your plant transect. For instance, a dune lab data file might be: "R5_6.Alex.Joel.trxt4.xls"(which means Range 5 & 6, transect 4 done by Joel and Alex) or "R3_Jill.Sharon.NW.transect.xls"(which means Range 3, NW transect, done by Jill and Sharon).
The participation portion of yourlab grade will include attending lab regularly and being an active participantin lab activities. This includesdoing your fair share of group work. During the labs you will be working in pairs to design experiments, collect the data, and discussand interpret the results. Howeveryou will work as individuals towrite up your draft and final lab reports. Your participation grade will reflect how well you pull yourweight when working in groups.
To facilitate your group work inlab you will be grading your peer's efforts during group work (anonymously ifyou prefer). In terms of scoring,you will be working in groups of two in most cases and each person in a teamwill get 10 points for a total of 20 points available for the team (if thereare 3 team members then each will get 10 points for a total of 30 points; ifthere are 4 team members, then they will get 40 points total, etc.). At the end of each lab section you willbe given an evaluation sheet where you each get to divvy up the points betweeneach group members. (I may alsohand out a similar sheet for lecture groups during the semester.) For example, if you feel everyonecontributed equally, then give every one 10 points each (includingyourself). If you feel thatPrudence pulled her weight more than the others on the team, give her 12 pointsand the other team member and yourself 8 points each. Remember you must give yourself a score as well as your teammembers. I will be averagingeveryone's contributions to determine the majority of your participationgrade. There are a few rules forthese peer grading sheets: (1) you can't give any team member more than 15points, you can not assign more than the total available points, (2) you canassign less than the total available points, (3) anyone who averages less than7 points for the entire semester will fail the course, and (4) be fair. I will incorporate your pointvalues, your peerÕs point values and my own observations of your level ofeffort in determining your final participation grade.
Inorder to get the most out of lab, you need to come to lab. For example, youÕll be able to givemuch more substantive feedback to your peers if youÕve gone through through thein-class exercise of reading scientific literature to learn the style ofscientific writing. Similarly theonly way to learn about the diversity of life is to come to class and really commityourself to learning about all of the taxa that are presented.
Forthe Dune restoration lab you will be collecting data sets that will need to beentered into Excel in specified formats and then sent to Blackboard under theappropriate assignment name (i.e. ÒR5.planted.T1.dune.xlsÓ). Each team will be given credit forcorrectly entering their data and sending it to me in a timely fashion (i.e. bythe deadlines posted on the schedule). The correct form for the data is available on Blackboard>CourseDocuments>Dune lab (dune data template.xls). The entire team will be graded equally on completing thedata management portion of each lab. This will be the ÒWork turned in on time/correct formÓportion of your grade which is worth 5% of the total. I will post collated datasets on Blackboard from each labsection for each of you to use to write your papers. In order for me to provide these datasets to you in a timelyfashion, each team has to send their data, and any revisions I request, in aprompt fashion. Often I requirestudents to edit their datasets 2-3 times before the final one is ready. Please be prepared to turn your firstdataset in on time, and then to respond within 24 hours with any reviseddatasets (or answered questions) that I e-mail you about. You may want to decide ahead of timewhich team member will be responsible for communicating with me.
Duringthe labs where you will be reviewing your knowledge of biodiversity conceptsfor lecture, I will be giving brief quizzes during every lab period about theorganisms in the lab, or from previous labs (they will be cumulative). Usually there will be 2 oral questionseach lab period to each person. Imay do these informally going around the room, or I may set up a station withthe questions that you need to answer before you leave. Questions may include:the scientific name, the common name, give three characteristics, or name anecological or economic function of a particular taxon. These quizzes are intended to helpprepare you for both the lab practical and the second midterm in lecture. They are worth 5% of your grade. If you have to miss a lab during this session,you can take the quiz during the other lab section that week if need be.
Duringthe lab practical I will have ~24 stations of live or dead specimensrepresenting most of the diversity that you studied over the previous fourweeks in lab and lecture. At eachstation there will be 2-6 questions about the creature that is on display. These can include its taxonomic name(anything from Class to Domain, depending on the group), the keycharacteristics of that taxonomic level, and other questions related to thestudy guide IÕll hand out. Thelab practical is hard. If you donÕt spend time during each labsection looking at all of the specimens, taking notes and quizzing yourselveson the names, characteristics and features you are using to identify eachcreatures youÕll likely do poorly on this exam.
For your lab grade, each paper will each be worth 20-30% ofyour grade. Each paper will be graded on a straight scale like thelectures exams. Only the final version will be graded; however you areunlikely to do well on the labs unless you turn in rough drafts and getfeedback from your peers. Both labreports together will be worth 50% of your grade. The number of pointsassigned to each section of a given paper will vary depending on the sectionswe are working on at that time. Review the ÒPeer Review GuidelinesÓ foreach lab to see the point break down. In terms of the peer reviews, youwill get full credit (10%) if you do a thorough job of peer reviewing two different papers at each of the peer reviewsessions. You will be considered to have done a thorough peer review ifyou have critically read each paper using the peer review guidelines and givenconstructive feedback. You will receive full credit for each complete draft.You will only receive half credit for incomplete drafts and no draft willreceive zero credit. You will receive full credit for the first rough drafteven if you end up revising the entire paper for the final version. The point is that you must come toclass with a full working draft during peer review. Bringing complete draftsfor both peer reviews (see table) comprises 5% of your grade.
If you do not turn in a lab report on the day it is due,
youhave until the Monday following to turn it in. You will then get 10 percent off the
final grade. After theMonday following the lab due date no lab reports will be
accepted.
Participation will be worth 15% ofyour lab grade. It will includehow much you participate with your peers and me in daily discussions,activities and laboratory exercises. It may seem obvious but it will be impossible to get full credit forparticipation if you routinely miss labs. Part of the participation will be my perspective on your activeinvolvement in trying to learn biology. If you sit on the sidelines during labs and let your peers do all of thework, your participation grade will be low. In addition, over half of your participation grade will bedetermined by your peers in lab. Iwill hand out a Team Evaluation form that describes the scoring process (andthe form is on Blackboard).
The entire course will be graded ona straight scale . This means thateveryone could get AÕs (in theory) and everyone could get FÕs (in theory). In practice, there will most likely be amixture of grades for the course. To get a C in the course you will need to meet minimum expectations in all of the categories listed under ÒGrade BreakdownÓ.You need to receive a C or better in the lab to fulfill this part of the MLO inESSP or BIO.
Plan to complete this course beforethe end of the semester. Incompletes will only be given for emergencies. In addition, the new university policyis that students will only be able to withdraw after the 3rd week of classesfor a medical or other very substantive reason (with a doctorÕs note). (For instance, getting behind in yourclasses is no longer a viable reason to withdraw from a class.)
LABS: There willbe no make-up labs. If you need to miss a lab, contact yourlab instructor in advance to see what we can do about making up the material. If you do miss a lab, you are responsible for the material covered that daywhether you attend or not. In some cases, it may be possible to visit theother lab section Ð please talk with me in advance. (Some days it is easy to have extrapeople in a lab, other days it is difficult.)
Papers: There are no late lab reports accepted after the
Mondayfollowing the lab due date. If you do not turn in a lab on the day it is
due,you have until the Monday following to turn it
in. You will then get 10 percent
off the final grade. After theMonday following the lab due date no lab reports
will be accepted. When you graduate from CSUMB, in any job that you have,late work will not be accepted. This policy will help gear
you toward how to deal with work outside ofschool and the jobs or graduate
schools that you attend after yougraduate. Given that the labs together
are worth 50% of your grade, youcannot pass the class if you do not turn them
in. If you have a problemthat comes that will not allow you to complete a
lab on time, please talk withme on or before the day the lab is due.
Peer Reviews: You need to submit 2 peer reviews of each rough draft (2 for the ciliate labdraft 1 and 2 for the dune lab draft 1) to Blackboard at least one day beforethe second draft of the paper is due on the schedule. That is total 4 peer reviews for the entire semester topotentially get full credit. You also need to put effort into each peerreview to get full credit (see grading above).
Although you will be working together to collect and analyzethe data for your labs, each lab paper should be written in your ownwords. Nearly identical lab papers will receive zero points.
Everystudent is expected to write their own papers in their own words. Students who directly copy orsignificantly paraphrase either a peer's paper, a sample student paper, orother reference I hand out will failthat paper. I will also bechecking for plagiarism of outside sources as well. All sources used in a paper are to be cited. If you are unclear about how much youmight be able to paraphrase another's work, see the plagiarism discussion onpp. 16-17 of the McMillan writing text. With that said, I encourage you to work together. I just want each of you to write your own papers. I have posted the CSUMB Academic Honesty policy on Blackboard underCourse Documents.
Ialso recommend that you use my office hours. I have the best idea of anyone in the class what materialyou will need to know to succeed in the class (since I write and grade thequizzes and lab practicals, and grade your final papers). I am available at my posted times andalso by appointment. If my posted timesconflict with your class or work schedules, please talk with me after class orsend me an e-mail to find additional times that I can meet with you.
Whenwe
visit the
|
Date |
Lab Topic |
|
Due Dates |
|
Aug 28, 29 |
Intro to Bio240L labs Review: DNA, protein, & the central dogma Discussion: Is there proof in science? |
Freeman: pp. 43-53, ch. 4, pp. 320-322 Also skim the rest of ch. 3 |
|
|
Sep 4,5 |
Ciliates: Begin Experiment How to use stereomicroscopes |
Ciliate handout (before class) |
|
|
Sep 11, 12 |
Monitor Ciliates Learning Evolution: Darwinian Snails & Sickle Cell Anemia Scientific Writing: Figures & Tables |
M: ch. 3 MasteringBio: GraphIt! ch. 1 |
|
|
Sep 18, 19 |
Monitor Ciliates Scientific Writing: Methods, Results & Discussion sections Learning Evolution: Flowers & Trees |
M: ch.4 (pp. 78-96) |
|
|
Sep 25, 26 |
Monitor ciliates on Mon & Tues of this week Peer Review ciliate drafts Begin Biodiversity section: Viruses & Prokaryotes |
F: ch. 35 & 28 |
*Due: Ciliate Draft |
|
Oct 2, 3 |
ÒProtistsÓ (bring your medical insurance info to fill out travel forms) |
F: ch. 29 M: ch. 7 & 8 |
* Due: Revised Ciliate Draft Biodiversity Quiz |
|
Oct 9, 10 |
Green Plants and Fungi |
F: ch. 30-31 |
*Due: Ciliate Final Paper Biodiversity Quiz |
|
Oct 16, 17 |
Animals |
F: ch. 32-34 |
Biodiversity Quiz |
|
Oct 23, 24 |
Lab practical |
F: all of Unit 6 |
|
|
Oct 30, 31 |
Dune ecology & restoration - learning local dune plants |
|
|
|
Nov 6, 7 |
Dune ecology & restoration Ð survey dune plant communities |
|
*Due: dune data in correct form due Nov. 9 |
|
Nov 13, 14 |
Dune restoration - data analysis Scientific Writing: Abstract, Introduction & Literature Cited sections Library Research: finding peer reviewed literature |
M: pp. 68-77, ch. 1 & ch. 6 |
Any revisions to your dune dataset due by Wed. Nov. 11 |
|
Nov 20, 21 |
Dune Lab Ð Peer Review |
|
*Due: 1st draft dune lab (complete draft due in class for peer review) |
|
Nov 27, 28 |
Thanksgiving |
|
|
|
Dec 4, 5 |
Ecology Modules In class review of 2nd draft of dune lab |
M: pp. 68-76, & review ch. 7 |
* Due: 2nd draft dune lab |
|
Dec 11, 12 |
Final field trip for Ecology Modules |
|
Due: Final Dune |
|
Dec 18, 19 |
Assessment Week - no labs |
|
|
M = McMillan text, F = Freeman text
á Skimchapters 7 and 8 each time your write up a lab report for great tips.
á Referto the checklists in McMillan on pp. 66-7 and 94-6 before submitting yourciliate and dune labs
¤ Field Days: wear layers, bring warm clothes, and wearappropriate shoes. I'll givedetails about each field trip the week before in class.
¥ The lab technician for our course is Wendi Newman. You can reach her on First Class under wendi_newman@csumb.edu or at582-4431.