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SYSTEMATIC BIOLOGY |
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| HOME | WEEKLY ASSIGNMENTS | J. SYSTEMATIC BIOLOGY | TAXA OF LIFE | |
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COURSE ASSIGNMENTS |
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The following may seem somewhat daunting in its expectations, but DON'T PANIC. This is an opportunity for almost complete autonomy, an experience not to be found so easily elsewhere. Within the given structure there is the freedom to pursue your own theories and at the same time compare them with the theories of others. Have fun with this freedom. Genina Troutman, student editor, 1993.Your success in this course requires that you understand and internalize the following statements:
Verba volant, scripta manent.
A fool's mouth is his destruction. Proverbs 18:7
I. THE STRUCTURE AND ORGANIZATION OF THE PAPERS:
A. JOURNAL ARTICLES (RESEARCH ARTICLES AND RESEARCH NOTES):
RESEARCH ARTICLES (PROJECT 1)
We expect the student teams to produce a journal-style article that will have the following general outline. In all parts of the paper we expect good grammar (e.g. limit the use of the passive voice, and consistent tenses through the paragraph), spelling, and appropriate use of technical terms.
1. TITLE: The title is a one phrase (usually not a sentence) synopsis of the paper. Choose your title carefully. Authorship and order of authorship also is part of the title. The team leader should be the first author.
2. ABSTRACT: The abstract is a one paragraph synopsis of your paper and its findings. It must include a hypothesis (i.e. statement of purpose), a sentence about methodology, results and conclusions as well. The abstract never employs citations, and it can be no longer than 150 words.
3. INTRODUCTION: This section is an introduction to the systematic history of the larger taxon in question. Also, the introduction prefaces the cladistic analysis and subsequent phylogenies and taxonomies. In short, this section introduces the hypothesis (purpose) and convinces the reader that this hypothesis is appropriate.
Sources used in the introduction and throughout the paper should be primary (presentation of original research from a peer reviewed source) or secondary (a review paper from a peer reviewed source). In rare cases formal papers cite tertiary sources (usually text books), but only to make a point. The only acceptable citation format is author and date.
- One author: (Darwin, 1859) or Darwin (1859)
- Two authors: (Margulis and Schwartz 1998) or Margulis and Schwartz (1998)
- More than two authors: (Bold et al. 1987) or Bold et al. (1987)
4. MATERIAL AND METHODS: Within this section, the authors introduce the organisms examined and the methods employed in the cladistic analysis. In general the Materials and Methods provides adequate background and support (citations) in addition to any modifications made by the authors so that the research could be repeated. This includes identification of instruments, programs, etc.
a. THE ORGANISMS EXAMINED: This section will include all species (or appropriate taxa) under examination, particularly those observed directly in the course. In addition, the authors must include taxa which represent the taxonomic scheme which is under scrutiny. That is, all orders of "Bryophytes" as classified by Holt (2000) must be represented by appropriate species. So, if certain orders are not represented in laboratory, the authors must include species which represent those missing species. All scientific names should be cited for the first time with its authority and year.
The species should be presented in tabular form. Illustrations of particular taxa might be appropriate.
b. THE CHARACTERS EXAMINED: This section will be an introduction to the characters which were considered in the cladistic analysis. The authors will also describe the character states that occur within each character and how those character states are interrelated. The generous use of tables and illustrations would be very appropriate to this section.
c. THE CHARACTER X TAXON MATRIX:
MOLECULAR MATRIX: This table will be generated by the methods outlined in the attachment that gives directions for constructing and generating a molecular tree. You are required to examine a minimum of 5 ingroup taxa per team member. The tree or trees that you generate through PAUP* (following the instructions to run Paup*) will then be used to map the patterns of evolution of states and the distributions of morphological characters (1 character per team member) constructed as a typical, but reduced, morphological matrix and displayed with MacClade.
5. RESULTS: This section will include the tables and figures (including the cladograms) and a description, not analysis, of the cladograms. Save the analysis for the discussion. This section should cite and use all of the figures and tables in the description. The tables and figures should be easy to read and understand within the norms of the research. Also, all tables and figures must be adequately labeled so that they can stand alone.
6. DISCUSSION: This section is a response to the introduction, especially as to how the cladistic analysis causes a rejection or a confirmation of the hypothesis. Like the introduction, the Discussion is citation rich, and should include most of the sources used in the Introduction. The discussion will be in two parts: A PHYLOGENY and CHARACTER EVOLUTION and A TAXONOMY. These requirements are only for the full research paper. For the Research Note, see B (below).
a. A PHYLOGENY: This section presents the proposed phylogeny or evolutionary relationships between the taxa in question as suggested by the cladogram. Then, this section compares the inferred phylogeny with published phylogenies of the groups in question. This also requires an in-depth discussion of the convergences and reversals in the cladogram.
The authors should speculate about the ancestral form from which the groups in question evolved. Since this is the form from which the cladogram begins, it should be described by the primitive characters which were defined in the CHARACTERS section.
Citations of illustrations, figures and tables are necessary components of this section.
b. A TAXONOMY: This section presents the proposed taxonomy of the groups in question (usually to the ordinal level) as suggested by the cladogram. As with the phylogeny, this section compares the proposed taxonomy with published taxonomies.
All taxonomic names of your invention must be explained. Those invented in for the groups within the Plant kingdom, must follow the rules of the International Botanical Congress. Those invented for the Animal kingdom must conform to the rules of the International Zoological Congress.
c. CHARACTER EVOLUTION: This section explores questions of character evolution in more detail. The authors must track changes in the states of all morphological characters in the taxa under examination. In this case, less emphasis may be placed on the taxonomies. Regardless, appropriate tables and diagrams are necessary components of this section. As with the Phylogeny section, this will require a liberal use of the literature.
7. LITERATURE CITED: All documentation will be in the format of the Reference List for this course. Consult that site for any questions about documentation. We will not allow you to cite class notes or encyclopedias in formal papers. Note that the proper use of citations literally allows you to write volumes in every sentence.
You may cite very few web sources without an instructor's prior approval. Those that may be cited include the Tree of Life Project, GenBank, papers from the Journal of Systematic Biology at SU, and the data sheet descriptions of taxa on this web site. Before you take a possible web citation to an instructor, you must complete the attached Request Form.
As a minimum, we expect the team to cite at least 15 references. In addition, we require that each team include at least one appropriate reference that has been published within the past 6 months and a citation from our in-house publication, the Journal of Systematic Biology (formerly, the Journal of Evolutionary Botany). Please note that these are MINIMUM requirements.
BEFORE YOU SUBMIT YOUR WORK, SAVE IT WITH A NAME THAT FOLLOW THESE CRITERIA: TEAM NAME 0. AFTER WE REVIEW YOUR PAPER, THE REVIEWED VERSION WILL BE NAMED BY US TEAM NAME 0H OR 0I (H: HOLT, I: IUDICA). CONSECUTIVE VERSIONS WILL BE TEAM NAME AND 1, 2, 3, ETC. PLEASE FOLLOW THESE GUIDELINES WHEN NAMING YOUR PROJECT.
RESEARCH NOTES (PROJECT 2)
For a designated unit each team will divide into two small groups of 2 or 3 students each and write two notes instead of one full journal article. The outline for the note will be somewhat truncated from that above. It will include:
The team will work together to make a common cladistic analysis, thus the Materials and Methods will the be the same for the two small groups, For teams of four, each small group will be two students and the note will explore the evolution of one character. However, if the small group is three students, its note will explore the evolution of two characters.
B. REVIEW PAPERS (PROJECT 3)
For project 3, all teams will contract with the instructor to write a review paper about the taxa being studied (members of the Supergroup Planta). In this case, the paper will explore a larger question that deals with the origin of the kingdom, patterns of evolution in the kingdom, and/or evaluation of taxonomic-systematic means to organize the kingdom. The focus also could be quite narrow if the topic warrants it (e.g. origin of the flowering plants).
The general outline of the review article is simpler than that of the journal article. As before, it will have a title, abstract, and introduction. In the review article, however, an introduction could expand to be an extended exploration of the history of the topic. The discussion section will explore current views (especially their explanatory strengths and weaknesses) on the topic. Thus, this review will present multiple published opinions. The literature cited will have a minimum of 25 sources. As with all formal work, the literature must be dominated by primary and secondary literature.
At the end of the semester, students will make a contract with the instructor about a topic related to some aspect of the course (e.g. evolution, cladistics, phylogeny, taxonomy, or systematics). Your essay should be a second look at your answer to one or more of the questions that you considered on the first day of class. How has your understanding of the question and the formulation of an answer changed through your experiences in Systematic Biology? In other words, your essay should not be written as an evaluation of the course, but as an evaluation of your growth as a Biologist or Ecologist. We hope that you got more from the course than a catalog of living things. Experiences like your projects, the museum, collecting fossils, analyzing leaves and forests require the integration of course material whose understanding transcends simple answers to quizzes. Furthermore, Systematic Biology has at its foundation the underlying themes of evolution (particularly the evidences that Darwin used in Origin), as well as the major themes of the history and philosophy of your chosen discipline.
We expect the students to write a minimum of 600 words in a personal (first person) style. We expect adequate support from the literature for the essay. Also, we expect the writing to reflect particular experiences that the student had in the course (as well as BI:101-102-201). This essay will be due at the time of the final examination period. Click here for further discussion on the Personal Essay.
D. THE TEAM MEETING AND CONTRACT:
The Title, Abstract, Character X Taxon Matrix, Cladogram, and Literature Cited sections are ordinarily written or compiled through a group effort. Also, consensus within the team should be reached in order to determine what non-trivial features to explore, and the resulting phylogeny and taxonomy. In recognition of the group effort, ordinarily 20% of each team member's grade will be based on the whole paper.
The Introduction, the Materials and Methods, the Proposed Phylogeny, and the Proposed Taxonomy of the Research Article ordinarily will each be the responsibility of individual group members. A week prior to the submission of the first draft, each team will present to the instructor what the individual responsibilities will be. In addition, the team will negotiate as to the relative importance of the whole paper grade. We will regard the results of this negotiation as a contract that defines the responsibilities of the individual members, the team leader, and the team as a group. We will use the contract for the Research Article in determining individual grades for the paper.
We will ask for similar contracts in the case of Review Papers. The review papers will follow a looser format that will be determined by the contract negotiation with the instructor. Also, the review paper contract will specify other responsibilities.
E. THE FIRST DRAFT:
The first drafts are due at the times scheduled in the syllabus. They must be in finished form (this means completed and written using MS Word).
1. DIALOGUES: are those sections in which the instructors and the students entering into a conversation that is based upon the assigned readings. Much of the conversation would be about different taxonomic groups. However, we will assign other readings (e.g., origin of species, path of science, etc.) that will be part of the conversation.
2. Dialogue will began with a brief quiz (two questions). One question will be answer by the entire team (1 point) and the other will be answered by each individual (2 points). That will be followed by a conversation in which the instructors may pose questions to which you may respond. You may post question to which the instructors or other student will respond or you may make a comment that is appropriate to the topic being explored (2 points). We expect each student to make at least one contribution per dialogue and will keep a record of those contributions as they are made. Therefore, full credit for any dialogue will be 5 points per student.
3. The dialogues will determine 10% of your final grade. We will count only the best 24 dialogues per student.
II. PAPER SCHEDULE (very important DUE DATES):
22 FEB FIRST DRAFTS OF THE ANIMAL-BACTERIA (PROJECT 1) PAPERS DUE.
29 FEB FIRST REWRITES OF THE ANIMAL-BACTERIA PAPERS DUE.
21 MARCH - WE WILL NOT ACCEPT DRAFTS OF PROJECT 1 AFTER THIS DATE.
28 MARCH FIRST DRAFTS OF THE PROTIST-FUNGI (PROJECT 2) PAPERS DUE.
4 APR FIRST REWRITES OF THE PROTIST-FUNGI PAPERS DUE.
18 APRIL - WE WILL NOT ACCEPT DRAFTS OF PROJECT 2 AFTER THIS DATE.
25 APR DRAFTS OF THE PLANT PAPERS (PROJECT 3) DUE. (NO REVISION ACCEPTED).
2 MAY (08:00 TO 10:00) GAME & DIALOGUE, ESSAYS (add link to Portfolio).
III. THE FINAL GRADE FOR EACH PAPER WILL BE DETERMINED AS FOLLOWS:
A. PAPERS ARE GRADED ON A 0-10 SCALE.
B. IF THE PAPER IS AWARDED A "PUBLISH" AT THE SUBMISSION OF THE FIRST REWRITE, IT WILL RECEIVE A 10.
C. IF THE PAPER IS AWARDED A "PUBLISH WITH MINOR REVISIONS" AT THE SUBMISSION OF THE FIRST REWRITE, IT WILL RECEIVE A GRADE OF 5 IF IT IS NOT FINISH ON TIME. STUDENTS MAY REWRITE THEIR PAPERS UP TO THREE MORE TIMES TO ACHIEVE A "PUBLISH." THE GRADE WILL BE DETERMINED ACCORDING TO THE FOLLOWING SCHEDULE:
PUBLISH AFTER THE SECOND REWRITE: 9
PUBLISH AFTER THE THIRD REWRITE: 8
PUBLISH AFTER THE FOURTH REWRITE: 7
D. IF THE PAPER IS AWARDED A "DO NOT PUBLISH" AT THE SUBMISSION OF THE FIRST REWRITE, IT WILL RECEIVE A GRADE OF 0. AS ABOVE, STUDENTS MAY REWRITE THEIR PAPERS UP TO THREE TIMES TO ACHIEVE A "PUBLISH."
E. EXPLANATION OF THE CATEGORIES
PUBLISH means that the paper can be accepted as is with no revisions or corrections in spelling, grammar or formats.
PUBLISH WITH MINOR REVISIONS means that the science is sound and well supported but the spelling, grammar, and/or formats need work. (this category do not apply to the last paper).
DO NOT PUBLISH means that the paper requires extensive revision with regard to the science and the writing.
V. THE JOURNAL:
A tangible goal of this course is the production of a book or collection of papers which can be bound and put on reserve for future years' study. The book is actually organized as a journal called The Journal of Systematic Biology. The journal has 3 issues, each corresponding to one of the papers which you will write.
The journal will serve as model papers for future Systematic Biology classes. Also, a collection used in this way will allow the students to have an audience that is larger than their instructor.
Only those papers which receive a publish will be included in the future issues of the journal.
VI. THE STUDENT EDITOR:
The student editor will be available to meet with the teams to discuss aspects of grammar, scientific writing and the science in the papers. Your meetings will have to accommodate the editor’s schedule, so try to set up meeting times as far in advance as possible.
Also, the editor’s job does not involve rewriting your papers. Editor does not mean a ghost writer.
Each week include a quiz game which covers the preceding week's material. The game will have questions of different categories such as recognition, taxonomy, structures, tissues, organelles, life histories, etc. Within each category, there will be 1, 2, and 3-point questions. The class elects the category and point-values until the total points possible reach 10. The 1 & 2-point questions will be answered by the teams; 3-point questions will be answered individually.
We will provide a running taxonomy with appropriate taxa as presented in class. It will have only the names of the taxa and an indication of the hierarchy. NO DESCRIPTIONS WILL BE INCLUDED. Group members may consult this taxonomy at anytime during the games. As a consequence, spelling counts.
The last game will cover material from the last week of class and will be played at the time of the final examination. The results of all the games will determine 15% of the final grade.
VIII. UNKNOWNS AND OTHER ASSIGNMENTS:
UNKNOWNS
Each week, your group will be given an unknown alga or tree which you are expected to key out (trees to species, algae to genus). Begin your determination by carefully observing the unknown organism. Only after a thorough examination should you begin to use your key. The unknown is due before the end of the respective class period.
Your unknown determination is considered complete after you have finished an outline drawing which illustrates the important key characters (Be sure to use a size bar). For plants, give the family, genus and species according to the taxonomy of Cronquist (1981) or other (as specified). List phylum, class, order, and genus of unknown protists according to the taxonomy as presented in class. Add the proper authority name and year.
OTHER ACTIVITIES
We will have pdf files accompanying each activity on the course schedule. You will access these files through the Weekly Assignments pages. Be sure that your browser has Acrobat Reader for this. Most times we expect you to use the files as guides for observation during the activity. However, sometimes we will take up the completed sheet and apply grades to the accumulated unknowns grade. Nevertheless, questions for The Game will be drawn from the activities.
KEYS (4)
At the end of each of the first three weeks, student teams will be given a set of taxa to arrange into a dichotomous key, which will be due on the next Monday. At the end of the semester, students will write a dichotomous key to all of the bird species that they observe through the semester.
BACTERIA PROJECTS (2)
Students will observe bacteria as communities through two different long-terms projects: The Hay Infusion and the Winogradsky Column.
FOREST ANALYSIS AND VARIATION PROJECTS
During the last two weeks, students will do a forest analysis (species diversity and island biogeography) and explore variation in a species of your choice.
The unknowns and other assignments comprise 10% of your final grade.
This semester we require that you (the continuing Biology majors) continue the portfolio that you started in Genetics (BI:201). Because this is a universal course requirement, those students who did not have Genetics will create a portfolio or add appropriate items as required. This will determine 5% of the final grade. On your essay, you will include a link to your portfolio.
This page maintained by Jack R. Holt and Carlos A. Iudica. Last modified: 04/21/08