Paper Guidelines
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David H.A. Fitch
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GUIDELINES FOR RESEARCH PAPER AND ORAL PRESENTATION
Groups of 3 persons each will select a focused topic, formulate a thesis about this topic, and research evidence supporting and potentially refuting this thesis. The group will write a paper discussing the topic by presenting and discussing the evidence researched by the group. The group will also present their material in the form of an oral presentation before the class during the penultimate two class periods.
 

CHOICE OF TOPIC
 

1. The topic must be within the field of evolutionary biology, either covered in class, in your text books, or perhaps not covered in this course. Above all, choose a topic about which you have developed some interest. The topic may be contemporary or historical, empirical or theoretical, organismal or molecular; but it must involve evolutionary biology. You may use the attached list of suggested topics for ideas, but do not feel that you should be limited to these topics. (For example, you might be interested in "the origin of life on planet Earth".)
 

2. Form a collaborative arrangement with other members in your group. The more collaborative you are, the more that everyone in the group will benefit. Obviously, everyone in your group should agree on a single topic that interests everybody. Your group should meet regularly to discuss the topic.
 

3. Do some preliminary reading about your topic. Bobst Library maintains an excellent collection of books and journals about evolutionary biology (see the attached list of a few of the journals you may wish to peruse). While reading, keep asking yourself if there is a thesis or theme that is being developed and if there are alternative explanations or hypotheses. (For example, some references appear to suggest that life originated de novo on Earth in a "primordial soup", but other references appear to suggest an extraterrestrial origin for life on Earth.) Keep records (e.g., on index cards) of what information came from which reference. (Of course, you may find you that you want to change your topic, or especially to focus and refineyour topic after you have done preliminary readings.)
 

 4. Share and discuss your information with your other group members. It may be most beneficial if everyone in the group reads all the same references and discusses what they mean, how (or if) they fit into your project, how they can or cannot be used as evidence, and so on. Some groups may find it easier to have members specialize in a particular part of the research and present their readings to the group. In the latter (less preferable) case, of course, if the "specialist" doesn't get it exactly right, and the group assumes that the "specialist" is an authoritative expert, the group will suffer as a whole.
 

5. Focus your topic quite narrowly to address a specific thesis or set of alternative theses (as discussed below). (For example, a recent article in the journal Science presented evidence supporting the hypothesis that Earth was "seeded" by meteorites of Martian origin. But there are alternative explanations that suggest the Martian meteorites did not actually contain life forms.) Focused topics are usually much better than broad, general topics (and easier to write about)! The thesis should be a single-sentence statement or proposition about how you view a particularly important aspect of your topic. For example, "the morphospecies concept is a generally practical-but not infallible-means of differentiating species", or "Darwin's interstrain crosses of pigeons demonstrate that several extreme variations may arise at single genetic loci". The thesis statement will be the first sentence of your paper and thus the topic sentence of your first paragraph!
 

6. Collect additional references to probe the depths of existing knowledge about your focused topic. Collect more evidence and questions that address your focused thesis at greater depth. To find additional and more recent references, use Biological Abstracts, Citation Index, Bobcat, the Web, etc. (You may also want to go back and check the original literature cited by your current books or journal articles.)Learn to use your library!
 

7. Test out each piece of evidence that you will use by constructively arguing about it with your collaborators. In what aspect(s) does the evidence fail to support your thesis? What alternative possibilities are definitely and not-so-definitely ruled out by the evidence? (Ruling out alternatives is one good way to support your thesis.) What experiments have not yet been done that you could propose that might fill in some of the details or patch some of the holes in the theory underlying your thesis?
 

WRITING THE PAPER
 

1. Decide if you will write a single paper as a group or if each individual will write his/her own paper. In the first case, all coauthors will be equally responsible and thus will share the same grade.
 

2. Do not just sit down and write your paper!
 

3. Gather and arrange your data, thesis and arguments. You may find it useful to take notes on cards (along with a note about the literature from which you collected your evidence or argument); cards can be shuffled into different orders, allowing you to easily construct and reconstruct different sequences of coherent ideas.
 

4. Construct a fairly detailed outline for your paper. You may find it very useful to actually write a "topic sentence" for each item in the outline that might represent a paragraph in the paper. The organization could be some topic-specific version of the following:
 

I. Thesis paragraph

A. Thesis statement (this is ALWAYS the first sentence of your paper!)

B. How this thesis differs from alternative possibilities

C. The various kinds of evidence we have gathered that support this thesis
 

II. Introductory and background material

A. The main question(s) or problem(s) to be addressed

B. Why this topic is significant (and why testing these hypotheses is important)

C. Observations that led to the thesis (and alternative theses)
 

III. Predictions

A. Predictions of patterns or experimental results that would occur if the alternative theses were true

B. Predictions of patterns or experimental results given my thesis
 

IV. Evidence that supports the thesis and refutes the alternative theses-

For each piece of evidence, cite the appropriate reference and explain how these data both support the thesis and refute alternative theses.

Back up each statement with EVIDENCE and the associated citation!
 

V. Explanation of anomalous data or data that might seem to refute the thesis-

If the thesis is true, there should be an explanation for why seemingly anomalous data appear; try to resolve any apparent paradoxes. (For example, Darwin argued that the disjunct distribution of cold-weather species on mountain tops could be explained by the glacial retreat as opposed to migration or special creation.)
 

VI. Conclusion

A. Conclusions and speculations

B. Future prospects

1. Questions or problems that remain unanswered

2. Possible ways of answering or solving them
 

NOTE!-Your outline must be approved by me before you may continue to write your paper! The outline, with a well-focused and written thesis statement, is due Wednesday, October 24, at 9:30 am.
 

5. Write the paper, using your outline as a guide. Use topic sentences to begin each paragraph. In the body of the paragraph, explain and develop the topic sentence using cited evidence or your own arguments. When writing each paragraph, adhere to the topic of that paragraph-do not bring in tangential ideas. At the end of the paragraph, write a sentence that connects the paragraph to the next paragraph. Be as concise yet as complete as possible. Be absolutely certain that you do not plagiarize (you can be expelled for this)!
 

6. Cite specific evidence and construct specific arguments to support your thesis statement. Use data from your library references (books and journal articles) to support your thesis. You should also show what kind of data could refute your thesis. To make your arguments even stronger, you should also explain how the data refute alternative hypotheses. If there are data that are not explained by your thesis, discuss why such apparently anomalous data may exist, even if your thesis is true. Cite appropriate literature in the text whenever you use data or allude to someone else's work (see a journal like Cell for an example of how to do this and the sample paper I have put on reserve in the library). Do NOT cite your literature as footnotes, but list all of your references by author in alphabetical order at the end of your paper (include titles of articles and full citations-again, see Cell for an example).
 

IMPORTANT: You must cite your references each time you use them in the text. For example: "That oxygen is a component of air is shown by heating metal oxides, collecting the resulting gas and testing its ability to support combustion (Lavoisier, 1778:23)", which cites page 23 in a book written by Antoine Lavoisier in 1778. You must also list the references by author at the end of your paper (in alphabetical order withall appropriate information, such as date, title and publisher if a book or title, journal, volume and pages if a journal article). Failure to do so constitutes plagiarism (i.e., the assumption of another author's work as your own).
 

Note: Web references (which are not refereed, by the way, and could be considerably error-prone) should be cited by page author (if known), URL, page title, and date of retrieval. Similar data should be cited for other types of electronic media.
 

7. Type (or word-process) your paper. The body of the paper should be no less and no more than 10 double-spaced pages, 12 point type,NOT dot-matrix, not hand-written (except perhaps for neatly-presented symbols and equations), 1-inch margins, and single-sided pages. Please do NOT right-justify your margins-leave them "ragged" (right-justification results in spaces in strange positions and is distracting to the reader). Please spell-check your work!!! Use regular paper only (like the paper on which these guidelines are printed). Do not use "eraseable" or "onion-skin" papers.
 

8. Include any figures, illustrations or tables (after the literature cited-NOT within the text) that you think are necessary (and which you cite in the text). Cite the original source(s) of these illustrations or tables. If applicable, original computer source code or long calculations (if required, for example, for a proof) should be included as an appendix at the very end.
 

9. Finally, put a cover sheet on your paper that includes the title, your name, the date, and a very brief, 200-word (or less) abstract of the paper. This abstract should be as complete a description of the paper as possible-that is, it must describe your thesis, its relevance to evolutionary biology, and what kinds of evidence you bring to bear on this thesis. Do not merely state that the paper "is about" something. Rather, describe the thesis and the evidence that is used to support it. Number all pages consecutively, beginning with the cover page. (You may wish to make a copy of the paper for yourself before you hand it in-just in case.)
 

DUE DATE (firmly enforced-no exceptions): Wednesday, November 28, at 9:30 AM.
 

ORAL PRESENTATION (held symposium style, December 5 and10)
 

The oral presentation of your topic should involve all 3 members of your group. The goal is to present the material in your paper to your peers (i.e., your classmates), so the presentation must be CLEAR, CONCISE, WELL-PREPARED, and UNDERSTANDABLE. Your peers will be helping to grade you.
 

 1. Your oral presentation must be about the topic, thesis and evidence that you present in your paper. However, you will not be able to present everything in as much detail as in your paper because your talk will be limited to 10 minutes with 2minutes to answer questions.
 

2. A typical presentation could begin by providing an abstract of your work, similar to the abstract on the cover page of your paper. Make sure you clearly state the thesis, possible alternatives, the evidence you feel supports your thesis and refutes the alternatives, possible problems, and your conclusion. Other than that, the specific format of your presentation will depend on your topic and your own creativity. For example, although many people will wish to present in a straight lecture-type format that is known to work well, a really creative group might wish to present its material as a mock debate, "trial", or news interview. In any format, the important criteria for your evaluation will be clarity of presentation and success at persuasion.
 

3. Support your presentation with visual aids. Figures, tables or other visual materials should be SIMPLE, CLEAR, and well-organized. If you plan on using anything other than transparencies, please tell me what kind of media you plan to use at least a week before your presentation!
 

 4. The group should get together to practice their presentations to make sure (1) it fits within the 10-minute limit, and (2) that it's good! The grade of each individual is based on the grade of the group, so if the group looks bad, so will you.
 

5. You will have 2 minutes to field questions from the audience. How well you answer these questions is also considered in your grade. The only way to prepare for these questions is to know everything you can about your topic and dream up possible questions yourself and try to answer them during your practice sessions. You will also be a member of the audience, and your participation in asking questions will also contribute to your individual evaluations.
 

Suggested topics and topics of successful papers in past classes-
 

The phylogenetic origin of HIV

Poor fidelity in HIV reverse transcriptase is an adaptation to the host immune system. (Note that this is also an excellent example of a thesis statement.)

Cystic fibrosis has persisted in human populations because heterozygotes have a selective advantage. (Another excellent thesis statement.)

Molecular data is better than morphological data for phylogenetic inference. (A good thesis, but one that was not successfully proven by the last author.)

Polymorphism has been maintained for tens of millions of years at the Major Histocompatibility Locus by means of "overdominant selection". (Great thesis statement with lots of potential molecular data.)

Mechanisms of recent evolution of antibiotic drug resistance in malaria or tuberculosis

What does "homology" really mean, and can it really be identified?

Transposable element evolution: lineal or reticulate?

Evolution of development

"Altruistic" behavior in social insects

Cooperative behavior in wolf packs: individual or "group" selection?

Undulapodia of eukaryotic cells resulted from endosymbiosis. (A good example of a thesis statement about the evolution of motility in eukaryotic cells.)

Biogeography of camelids

Natural selection as a useful tool in computer algorithms to solve multivariate problems

Natural selection as a useful algorithm in modern drug design by high-tech companies like "Molecular Evolution"

The relationships of tetrapods: are birds more closely related to "reptiles" or to mammals?

The real reason dinosaurs went extinct

Fungi are more closely related to animals than to plants. (A thesis statement.)

Ancient gene duplications resolve the root to the tree of life. (Another thesis statement.)

Evolution of color vision in vertebrates (lots of excellent material here!)

The relationship of humans to other primates

Phylogenetic evidence for the coevolution of nematode parasites and their mammalian hosts

Darwin was not the first to propose Natural Selection as the main agent of evolutionary change. (Again, a thesis statement-the history of evolutionary science is also a perfectly legitimate topic!)

Mapping genetic loci involved in the evolution of Drosophila head shape

Genetic loci involved in Drosophila reproductive isolation (and thus speciation)

Computer simulations of evolutionary genetic principles

The evolution of sexual dimorphism, or of sex itself

How did flight evolve in birds (or insects, mammals or reptiles)?

How many times did flight evolve in mammals? (There are two major bat lineages; did they evolve independently?)

The evolution of eyes: Convergence or ancient sharing of developmental mechanism?

The evolution of eyes: Evidence for developmental constraint provides evidence against design. (Yet another thesis statement.)

Even though he "lost" the great Académie debate of 1830 to his student, Geoffroy's proposal of typological homology between the body plans of insects and vertebrates (i.e., vertebrates are upside-down insects) has been vindicated by recent molecular evidence. (Or has it?) (Another thesis statement-one that combines a famous problem of classical importance with recent molecular evidence!)
 

List of some evolutionary journals available in Bobst Library-
 

Evolution (QH301.E9)

Molecular Biology and Evolution (QH506.M642)

Molecular Phylogenetics and Evolution (QH367.5.M56)

Journal of Molecular Evolution (QH431.A1J6)

American Naturalist (QH1.A5)

Nature (Q1.N3)

Science (Q1.S32)

Systematic Biology

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