Biology 121 - Plant Diversity
Fall 2004


Professor Robert Thomas
Office: 423 Carnegie (X6105)

Kathy Claerr, Assistant in Instruction
Office: 512A Carnegie (X6389)
Hours: by appointment

Meeting times Lecture Tues./Thurs. 1:10- 2:30 113 Carnegie
Lab Mondays 1:05- 4:00 430/431 Carnegie

Text: Raven, Evert & Eichhorn. Biology of Plants - Diversity. Freeman Press


Two exams and a final (20% each)
Critique (5%) and research paper (15%; 10 page maximum)
Lab project (10%)
Lab hand-ins and attendance (10%)

Plants Database: red line, brown line, green line

Biology 121 Fall 2004 Schedule

 Week  Thursday  Monday  Tuesday  Assignment Due
 1  Sept. 9
Intro & Euglena
 Sept. 13
Thorncrag Field Trip
 Sept. 14
Green algae
 2  Sept. 16
 Sept. 20 Euglena
Green algae, Bryophytes
 Sept. 21
Ferns & Allies
 3  Sept 23
 Sept. 27 Ferns & Allies, Gymnosperms  Sept. 28 Angiosperms  
 4  Sept. 30
Angiosperms (continued)
 Oct. 4 Angiosperms
Library Workshop*,
 Oct. 5
Exam I
 5  Oct. 7
Blue-green Algae
 Oct. 11 Blue -green Algae, Lab Projects  Oct. 12
Red Algae
 6  Oct. 14 Zygomycetes  Oct. 18 Red Algae,
Writing Workshop*, Zygomycetes
 Oct. 19 Ascomycetes  Oct. 19
Primary lit. article copy due at beginning of lecture
    Monday   Tuesday  Thursday  
 7  Oct. 25
Rocky Intertidal Field Trip
dress appropriately!
 Oct. 26
 Oct. 28
AR paper and Hands-on Lab Project Topics due at beginning of lecture
 8  Nov. 1 Ascomycetes, Basidiomycetes, Lichens, Review  Nov. 2
Exam II
 Nov. 4 Dinoflagellates, Diatoms  Nov. 1
Experimental lab project procedure and materials lists in lab.
Nov. 5 (Fri.)
Primary lit. article Critique due at 3 PM
 9  Nov. 8 Dinoflagellates, Diatoms, lab projects  Nov. 9
Phytoplankton ecology
 Nov. 11
Brown Algae
 10  Nov. 15
Bigelow Labs Field Trip
 Nov. 16
 Nov. 18
Slime molds
 Nov. 15
Analytical Review Paper due at beginning of lab
 11  Nov. 29 Brown Algae, Slime molds, Flagellated Fungi  Nov. 30
 Dec. 2
Lecture catch up if needed
 12  Dec. 6
Project Reports*
 Dec. 7
Project work
 Dec. 9
Exam review
 Dec. 10 (Fri) Hands-on lab projects due by
3 PM.

Exam III Friday, December 17 3:45 PM

* Attendance is required at activities in bold.

Reading Assignments

Plants Database: red line, brown line, green line

 Week Topic Readings
 1  Introduction, Euglena, Green Seaweeds Chapter 13 Chapter 16 (350-352) Chapter 17 (382-398)
 2  Bryophytes, Ferns, Fern Allies Chapter 18 Chapter 19
 3  Gymnosperms, Angiosperms Chapter 20 Chapter 21 & 22
 4  Angiosperms continued  
 5  Cyanobacteria, Red Seaweeds Chapter 14 (281-292) Chapter 16 (357-362)
 6  Zygomycetes, Acomycetes Chapter 15 (306-317; not 312-314, chytrids Chapter 15 (317-320)
 7  Basidiomycetes, Lichens Chapter 15 (320-330, 334-344)
 8  Fire plants, Chrysophytes Chapter 16 (361-366 Chapter 17 (375-379) Chapter 16 (366-367)
 9  Pytoplankton ecology, Brown Seaweeds Chapter 16 (348-350) Chapter 17 (379-385)
 10  Oomycetes, Slime molds Chapter 17 (371-375) Chapter 16 (352-356)
 11  Chytrids Chapter 15 (312-314)

Laboratory sessions

Laboratory is scheduled for Mondays from 1:10 to 4:00 PM. Plan on being present for the entire period each week. Absences from lab require a Dean's excuse, otherwise points assigned for attendance and lab reports are forfeited. With a Dean's excuse, labs usually cannot be made up due to lab scheduling conflicts, the nature of group work in lab or the availability of live specimens. For labs that cannot be made up, the substitute activity will be a two page paper with 5 references (two from websites are accepted) on a prearranged topic.

Students with anticipated, excused absences (such as for team sports) are expected to make arrangements for make-ups well in advance of their absences. Team members are expected to provide to Kathy via email ( with a list of the dates of their absences from lab.

Field Trips

Three major field trips are scheduled for this semester, and cannot be made up. The substitute activity will be a two page paper with 5 references (two from websites are accepted) on a prearranged topic along with a Dean's excuse.

Students will meet vans for transportation at the Carnegie loading dock facing the Hathorn Quad. If you are a certified student driver and are willing to drive a van, please contact Kathy (x6389), who will arrange for your hire for this paid position.

Dress appropriately for the field trips. Wear the proper clothing and footwear depending upon the terrain and weather conditions. Sandals are not suitable. Bailey's Island, where the Rocky Intertidal lab takes place, is a coastal setting that is often windy and chilly. We suggest wearing a sweater, jacket, warm socks, waterproof boots, gloves and a hat. These articles of clothing can be left in the van if the weather is warmer than expected. If rain is forecast, a rain-repellent outer garment will be necessary.

Required Assignments Information

All assignments are due on the date specified by 4PM.
 Primary literature article copy  Tues Oct 19  in lecture
 Hands-on/Lab project topic selection  Thurs Oct 28  in lecture
 Analytical Review paper topic selection  Thurs Oct 28  in lecture
 Experimental Lab project proposal and materials list  Monday Nov 1  in lab
 Critique of primary literature article  Fri Nov 5  at 3 PM
 Analytical review paper  Mon Nov 15  in lab
 Hands-on/Lab project oral report  Mon Dec 6  
 Hands-on/Lab project "report" Fri Dec 10 at 3 PM

The Writing Component

The writing component for this course consists of a series of three assignments (Primary Literature Article, Critique of Primary Literature Article, and the Analytical Review Paper) meant to build critical thinking and writing skills over the semester.

Credit for the Analytical Review (AR) Paper is awarded only when the student has submitted both a copy of a Primary Literature Article, and the Critique of Primary Literature Article by the specified due dates and time.

Plagiarism on any assignments or lab exercise will not be tolerated. It is the responsibility of the student to read and understand the Bates College Code of Student Conduct ( If you do not understand what constitutes plagiarism, read the Bates website on plagiarism (, contact the Writing Workshop, or see your instructor. Students or groups who plagiarize will be referred to the appropriate dean for disciplinary action by the College, will receive no credit for the work in question, and may fail the course.

Primary Literature Article
A primary literature article is one that reports for the first time the results from an experiment or survey performed by the author. These articles are published in professional, peer-reviewed journals. Often primary literature articles are written in a format specific to science consisting of Introduction, Materials and Methods, Results, Discussion, and Literature Cited sections. Primary literature articles are NOT reviews of several articles; primary literature articles do not report the current state of understanding among scientists on a particular topic. Many of these articles are clearly titled or labeled "review." More will be said about primary literature during the Library Workshop lab session. Review articles are helpful, however, in orienting you to a particular topic.

Your assignment is to submit a copy of an article from the primary literature that you intend to cite in your AR paper. (This copy will not be returned.) You will base your Critique on the primary literature article you submit. Do not select an article that is so sophisticated in its scope or terminology that you cannot understand its implications. For example, primary literature articles dealing with esoteric methods, obtuse terminology, or high level mathematics or statistics is most likely unsuitable. Find another article! Most articles require reading thoroughly three times before its content can be fully grasped.

The topic of this article must directly deal with one (or more) of the plant groups discussed during this semester. This assignment assures that students can correctly identify appropriate articles and topics for their term paper. If the article submitted is not a primary literature article, Kathy will notify you by email. You are then required to submit another article within two days.

Critique of Primary Literature Article
Base your one to two-page Critique on the primary literature article you submit. More will be said about critically reading scientific articles during the Writing Workshop lab session. Your Critique is not graded, however, it will be read and assessed by the teaching staff. In this way, you are given an opportunity to "practice" your critical evaluation skills and receive feedback before writing the Analytical Review (AR) Paper.

Analytical Review Paper
Your Analytical Review Paper must be submitted by the due date and time both in word-processed hard copy, and in an MS Word document emailed as an attachment to

The AR paper should critically evaluate the information in the literature you cite. You should look for articles that allow you to make comparisons and contrasts, and/or evaluate conclusions or results. Be sure that articles you select allow you to connect your AR paper topic to a group of plants, with a smooth, logical transition from idea to idea. (Hint: the more time you spend in the library homing in on a topic, the better off you will be when it comes to writing.)

In this critical review of information, you will need to provide some background (i.e., briefly summarize the issue) and critique the information contained in the literature. A simple summary of information is not sufficient. Most likely writing from your lecture notes is not appropriate. Be sure to read and refer often to the handout from the Seri Rudolf/Writing Workshop entitled, "Evaluating an Article from a Scientific Journal."

A minimum of 3 articles from the primary literature is required. Literature referenced in the Analytical Review paper must have been published within the last 5 years. (Older papers, however, may provide useful background information.) Internet sources may be cited in your paper, but will not be accepted as primary literature. No more than 1 internet source will be counted in the final number of references. The following rubric will be used to grade your papers.

Grading Rubric Analytical Review Paper
Within each grade level, importance of each requirement is weighed in order from top to bottom of list. Assistance in organizing and writing your paper is available from Seri Rudolph in the Writing Workshop (X6159). The earlier in the semester you start writing, the better the assistance Seri can give you!

A = More than 3 references treated in detail (i.e., significantly more than simply mentioning content: adequate background information, but does not rely on background)
3 primary literature articles used
thoughtful, original commentary present, good connections among references
excellent spelling and grammar
excellent organization progressing to summary position

B = More than 3 references used and treated adequately (i.e., more than simply mentioning content: adequate background information, and does not overly rely on background)
3 primary literature articles used
original commentary present, limited connections among references
good spelling and grammar
good organization progression to summary position

C = 3 primary literature articles used
original commentary is limited; relies largely on reporting background information
few or no connections among references
organization is unclear or does not progress to summary position

D = fewer than 3 primary literature articles used
no original commentary, i.e., consists solely of report of background information
organization is unclear or does not progress to summary position

F = some or all of the paper has been plagiarized
fewer than 3 references used, or no primary literature articles used
no original commentary, i.e., consists solely of report of background information
organization is unclear or does not progress to summary position

Hands-on Lab Project

Students may work alone or in groups of 2 or 3 to perform their projects. This project is to consist of some kind of treatment of botanical specimens or products, a vehicle for presentation of your project work for 1) handing in and grading, and for 2) displaying in class during your 5 minute oral report.

Topics must to pertain in some way to the groups of organisms studied during the semester. These hands-on-type projects may consist, for example, of experimental or observational lab work, field observations, field collections, photographic collections, or making useful products. Other kinds of projects may also be undertaken with the approval of the teaching staff.

Many projects require a number of days or weeks to complete. You should be well on your way to identifying an appropriate activity by the 5th week of classes.

Oral reports
Oral reports will be given in class on the last day of lab. Your group should prepare a 5 minute (no more!) presentation on your project, the importance or relevance of this topic, and your findings, along with some sort of summary of your work. This presentation can be a poster, Powerpoint presentation, illustration, demonstration, dramatization, original musical piece, or other appropriate, original creation. We love creativity and humor, and so will your audience! Visual aids, such as posters, should be neat, preferably word processed, with titles in a font large enough to be read easily at the back of the classroom, and the rest readable from 5 feet away. The department has a large-format printer that can make a color poster from a Powerpoint slide. See Kathy for details.

Lab project
The graded lab project consists of the final product or visual presentation of your project. The project may take the form of a paper for library-based research topics, a scientific article-style paper for experimental work, or posters, photographs, collections, recordings, CD files, dramatic scripts, etc., depending upon the nature of the project. This final project should be prepared in such a way that it can be understood on its own by someone who did not attend your oral presentation. The Biology Department may reimburse students whose projects require the purchase of materials and supplies beyond office supplies. However, first check with Kathy, as the department my have the materials or equipment you need. Needless or excessive purchases will not be reimbursed.

We may ask you to fill out a release form if you are willing to let us display your final product on the Biology Department bulletin boards, or use your final product, for example, as a demonstration in classes or labs.

A Collection as a Hands-on Lab Project
Collections of green plants and algae must be started early in the semester, not only because frost does away with deciduous and herbaceous specimens, but the specimens must be pressed or prepared for your project presentation and/or report. (Plant presses are available for loan from the Biology Department.)

A minimum of 10 species, generally, must be identified in and presented with your project report to achieve a B- or above grade. Speak with Dr. Thomas or Kathy Claerr to ascertain the taxonomic level to which your collection must be identified. For example, the lichen growth habits (folios, fruticose, and crustose) are not taxonomic categories. Identification to the genus level is required at minimum for lichens. For tree and herbaceous green plants, identification to the genus level is required. Correct identification, and in fact simply the use of identification keys, requires learning terminology and location of morphological structures on the plants. Some of these structures may be microscopic; hand lens loans and the use of department microscopes can be arranged with Kathy.

DO NOT collect your specimens from horticultural or landscaped places, especially on campus. These plantings often are non-native species or varieties not covered adequately by keys. Keys for identifying your specimens are readily available on the internet or in library collections. However, you should be certain you are using a key appropriate to the flora you have sampled. (For example, a key to Western US conifers wouldn't work at all on the evergreens you collected over break in Florida.)

Fungi can only be adequately identified with fresh, in-hand specimens; you may NOT rely on photographs for fungi identification purposes. Lichens must be identified by chemical means.

Preserved specimens where practical are required to be handed in with your final lab product. Please mount your specimens flat and protected in such a way that, when everyone's posters are stacked, your specimens will not be crushed or broken off of your poster.

A hint for your project presentation: Please take time to consider the interest of your audience in your in-class presentation. Most of us would rather not sit through a mere litany of the list of species you identified. Think of some clever spin you can put on your presentation. Perhaps your collection represents a particular habitat type(s) (e.g., beach, south vs. north slope, marsh) or geographical area (e.g., coastal Maine, Virginia). What special techniques or features did you have to learn to identify your specimens? Use these parameters to create an interesting format for describing your collection or work. This extra effort will win you accolades from your audience (and teaching staff).

Experimental Hands-on Lab Projects
If you choose to perform a simple lab project that is experimental in nature, you may select a topic from the following list. No more than three groups may select the same topic.

Your proposal for the lab project due on Monday, November 1st must include the hypothesis that you will test, the procedure you will follow as well as a list of the materials and equipment you require. You are responsible for coming up with the complete list, which means you have to plan your procedure well ahead of time. Searches through Google, lab manuals in the library and the scientific literature are helpful for finding procedures and materials lists. Appropriate controls for the experiment are expected.

The lab project report handed in at the end of the semester should be a paper in scientific literature format, with a descriptive title, and introduction, material and methods, results, discussion, and literature cited sections. See the Biology Department website for additional information about how to write a scientific paper. An abstract is not necessary for this assignment. Your data should be presented in figures and/or graphs. The length of this paper should be sufficient to give some pertinent background on your research topic, and discuss what your results mean. We do not expect that these papers would be less than four double-spaced pages in length without figures and graphs. The figures and graphs could provide part of an appropriate visual display for your oral report.

Experimental Lab Projects List
Effect of sulfur dioxide on three lichen species
Plant growth and development, a continuation of the tropism experiments performed in lab with corn seeds
Assay of toxicity in herbal tea extracts using Brine shrimp
Effects of various solutions on the germination, growth and development of plants (e.g., salt, fertilizer, or acid solutions on radish, bean or Arabidopsis)
Rate of photosynthesis in Elodea under different light conditions
Effect of colored light on spore ejection in Pilobolus

Other Interesting non-experimental projects
These projects could be accompanied with an informative poster with photographs to demonstrate your work.

Mitosis in onion root demonstration
Growth of monocot and dicot seedlings and fern gametophytes from forest soil
Growth and development of a cellular slime mold
Isolation of algae from various sources and identification to genus