Developed by Joseph Travis, Florida State University

Introduction

A thesis paper develops a critical argument in favor of a thesis on an unsolved biological question. A "thesis" is the hypothesis or answer to the unsolved question that, in your paper, you assert to be the correct one. The support for your thesis will come from the original literature in the field in which your question resides (e.g. evolutionary biology, ecology, phylogeny of insects). The range of questions on which you might focus will vary among your courses and may be defined in various ways by the instructor. For example, in the mid 1980's, I prohibited any paper from addressing whether dinosaurs were "warm blooded"; the topic had proven so popular that I lost the ability to distinguish levels of quality among the many papers produced on the topic each semester. 

Writing a paper of this kind, especially a scientific one, may be a new experience for you. It will certainly be different from papers you have written in other courses. It might therefore be useful to review what your paper should and should not be, offer some reasons why students receive poor grades on papers, and provide you with some information that would allow you to move forward.

There are many things your paper should not be. It should not be a book review; it should not be an evaluation of one or two original papers on a topic; it should not summarize my lecture on a topic. It should not be a commentary on an idea or a polemical diatribe. It should not be based on outdated literature; its author should not have ignored or overlooked important recent work on the topic. It should not be less than 6 double-spaced pages or more than 8 such pages. It should not be typed or printed in any font smaller than 10-point. It should not be written in colloquial style and should not include puns or jokes unless they are truly witty, original, and funny. It should not contain grammatical errors, misspellings, or typographical mistakes because these will be integrated into your grade for the paper and not in a positive fashion.

Your paper should have several attributes. It should be written well and written succinctly; it should contain citations of books or papers that substantiate any facts that you claim to be true and that are not common knowledge. It should draw from and include citations of at least 6 original papers, all of which ought to have been published within the last 6 years. It may include citations of many, many more papers, including classic books or papers that were published more than 6 years ago. It should have a clear point of view (the thesis), and it should reflect your most critical thinking.

The point of this exercise is to help you learn to develop your powers of critical thought and to express a critical opinion by marshalling evidence in support of a position. It is also designed to expose you to the original scientific literature so you can appreciate how science actually works. You are expected to take a position on the topic and argue for it.

Preparing Your Thesis: An Example

Let's consider how you might prepare your thesis this if your topic were the hypothesis that the dinosaurs were driven to extinction by the after-effects of an asteroid impact.
You would begin by asking the teaching assistant or me for some initial guidance: is this a reasonable topic and, if so, where might you begin to seek information. After this consultation, you would begin your own work by reading one or two general discussions of the "asteroid-impact" theory and then proceed to read 3-5 original articles that addressed the evidence for and against the idea. You might find that, in the end, you examine more than a dozen papers, even though you find that only 5 of them contain useful information that you can clearly understand. At this point you decide that the asteroid-impact theory is wrong; that is, there was an asteroid impact, its after-effects were clearly detrimental, but, ultimately, it was not why those charming behemoths went extinct.

Your thesis can be stated plainly: the effects of an asteroid impact were not the ultimate cause of the extinctions of the dinosaurs. You should then outline the lines of evidence in support of this thesis.

These might be the following points:

• that many dinosaur groups had already gone extinct or were well on their way to extinction before the end of the Cretaceous;

• that iridium anomalies occur on either side of the critical K-T boundary;

• that other groups of organisms, which should have suffered from the effects of any asteroid impact, did not suffer similar mass extinctions; 

• that climatic change and increasing land-mass fragmentation were likely to be playing major roles in the demise of the dinosaurs.

You should have a few sentences that elaborate on each line of evidence and should be able to note which papers that you read offer the evidence for each of the arguments.

The Paper Itself: Example Continued

You are almost ready to begin to write your paper. Before you write, you prepare an outline of the paper, which might look like this:

Introduction (1/2 page)

• Topic: Asteroid Impact Theory and Dinosaurs

  • Brief statement of the topic

  • Brief statement of its importance (deals with a major mass extinction, produced a major change in nature of species of land animals)

• Thesis: Asteroids Were Not Responsible

The Asteroid Impact Theory (1 page)

• The Impact Theory

  • Origin of the idea

  • How it portrays events and their consequences

• Support for the Theory: Lines of Evidence

  • Rapid extinctions

  • Iridium anomalies

  • Crater evidence

The Asteroid Theory Is Wrong (3 pages)

• Many groups already disappearing

• Iridium anomalies not always coincident with K-T boundary

• Extinctions in other groups?

• Continental fragmentation and climate change

Conclusions (1 1/2 pages)

• Counter-arguments to my thesis

  • Problems with evidence I used

  • Problems with interpretation

• Synthesis and Conclusion

When you have finished this outline, you are ready to write the paper, using your notes from your reading and your outline of your arguments and supportive literature to guide you in turning the outline into clear prose.

This same process should work for nearly any topic you choose. For example, if you find the notion of the "mitochondrial Eve" intriguing, your paper should offer a thesis that the data support the hypothesis that all extant humans are descended from a single matriarchal line that came through a population bottleneck in such-and-such a place this-many years ago. Or you could offer the thesis that this hypothesis is unsupported by the data and should be rejected. Your paper should not just tell the reader about the hypothesis. If you love lungfish, your paper might argue the thesis that tetrapods are descended from an ancestor shared with modern lungfish and not from one shared with rhipidistian crossopterygians. If you hate lungfish then argue the opposite. Regardless of what you investigate, take a stand. It is less important which position you take, or which thesis you advance, than that you advance a thesis that you can support with sound arguments and up-to-date information.

How To Get a Poor Grade

My top ten reasons for poor paper grades are:

10. Student chooses topic that is very complicated and never asks for help or guidance, and the paper is a muddle of mistaken conclusions.
9. Student chooses a topic that is covered in depth in lecture and does little more than summarize the lecture.
8. Student never asks for help, waits until the weekend before the paper is due to begin, and then finds no useful information or finds that all of the books that he/she wishes to read are checked out.
7. Student cites only two papers, and the instructor knows that there are many, many more readily available papers on that topic that contain critical information.
6. Student cites only review papers (these are thesis papers written by professional scientists and should be your starting point, not your only references).
5. Student rewrites a classmate's thesis paper but not well enough to disguise the obvious plagiarism.
4. Student rewrites a review on the topic that was published in a journal, but not well enough to disguise the obvious plagiarism.
3. Student uses the Encyclopedia Britannica as the sole source of information.
2. Student cites no papers or books published after 1928.
1. Student copies, verbatim, one of the student papers on reserve in the library, retypes it, and submits it as his/her own.

Don't laugh; every one of these has actually happened.

As the top reasons for poor grades imply, excellent papers from previous years will be on reserve in the library for you to examine. You should have a clear idea of what is expected of you and what you will have to produce in order to receive a good grade.

Topics

You are free to devise your own topic. I offer the following list of topics that are appropriate for the Evolution course (PCB 4673) to give you some ideas about the level of question that you should be addressing, with the hope that one of these topics will strike your fancy or that it will help you find your own topic. Feel free to talk to the teaching assistant or me to get some help in finding a topic or developing an idea in which you are interested into a genuine, operational thesis-paper topic.

• The regularity of protein evolution: is there a molecular clock?

• Mechanisms for concerted evolution

• Evolution of human subpopulations and its relation to linguistic evolution

• How should adaptations be defined and recognized

• Why was Darwin's notion of selection received so poorly?

• The definition of homology and its importance for evolutionary biology

• How should phylogenies be reconstructed?

• Are modern anthropogenous extinctions comparable to the mass extinctions of geologic history?

• Are birds truly the closest extant relatives of the extinct giant "reptiles"?

• Tetrapod origins: lungfish or someone else?

• Evolutionary patterns in the mechanisms of mitosis

• Antibiotic resistance in pathogenic organisms

• Does evolutionary biology have a lesson for understanding and controlling HIV?

• Parasite and host coevolution and the impact of host-switching in pathogenic organisms

• Evolution of the sex ratio

• Pesticide resistance and its impact on agronomic practice

• Gene for gene evolution in crop plants and their pathogens

• The lessons from evolution for the idea of phage therapy for controlling bacterial diseases

• Were the mass extinctions also selective?

• Evolution of intervening sequences in eukaryotic genes

• Complex adaptations and their evolution

• Why do stable hybrid zones exist (or do they)?

• Why does Haldane's rule seem so general?

• The "good-genes" hypothesis for female choice: mutation purging or fitness enhancing?

• The evolution of virulence and pathogenicity: will things always get worse (for the hosts)?

• Senescence and its evolutionary explanation

• The evolutionary consequences of overfishing

• The evolution of eukaryotic gene control

• How evolutionarily labile are different kinds of traits?

Where to Look

Modern database services like BIOSIS and others available through FirstSearch in Dirac Library can help you locate papers on topics with great ease and convenience. They also provide the abstracts of those papers. These services can help you start to investigate a topic, acquire a sense of how much material is available on a topic, and help you find potentially useful papers in the current literature that you might not have found by starting with even a recent review paper.

But remember that reading abstracts and relying solely on database searches are not substitutes for reading the actual papers and perusing the scientific journals. The abstract is what the author wants you to believe about his/her study. I think its best to draw one's own conclusions because the quality of scientific work is not uniformly high. I also think that authors tend to put the rosiest glow on their work in the abstract, and sometimes things are not what they are claimed to be, if you get my drift.

You should also remember that the indexing of papers depends on the authors' thoughtfulness in preparing the key words that these services use for their indexing. Frankly, the key words are the very last things most authors write, and some of those authors appear to have written them hastily if not outright furtively. One often finds gems of information in papers whose key words might not have led a reader to them immediately. 

The database services are not terribly helpful unless you already know something about the topic you wish to investigate. The best way to get that initial knowledge is to read recent review papers or position papers in the scientific literature on that topic. These occur either in journals dedicated to such papers or in specialized edited volumes on those topics. Some of the journals in which you would find such articles useful for the topics embraced by my courses are these:

Nontechnical articles (good for getting ideas but don't ever cite them as scientific literature)

• American Scientist
• Natural History
• BioScience
• Scientific American
• National Geographic
• Smithsonian

General "News" Journals (excellent for initial references to a topic)

• Nature
• Science
• Trends in Ecology and Evolution

Review Volumes (listed as "books" in our library; excellent for overviews and summaries, "road maps" to complicated topics, and initial references)

• Advances in Ecological Research
• Annual Review of Genetics
• Advances in Genetics
• Evolutionary Biology
• Annual Review of Earth and Planetary Sciences
• Annual Review of Ecology and Systematics

It can be harder to find the edited volumes on a subject. This is an area for which the indexing service of LUIS in the FSU library is very helpful. This is also an area in which the instructor and teaching assistant can be very helpful; we can usually point you toward a recent volume. These edited volumes consist of several papers on the subject, each written by different authors. The "author" of the book is actually the person or persons that assembled the authors of the individual papers and collected their work into a single volume.

Ultimately you will be reading papers that report the results of original research on a topic. These can also represent good starting points for a topic if, in perusing a journal, a particular paper captures your attention and engages your imagination. The journals in which the material covered by my courses is most likely to be found include these:

Journal Articles Reporting Results of Original Research (these should be the bulk of your citations)

• American Journal of Botany
• Hereditas
• American Naturalist
• Heredity
• Animal Behaviour
• Journal of Animal Ecology
• Behavioural Ecology
• Journal of Ecology
• Behavioral Ecology and Sociobiology
• Journal of Evolutionary Biology
• Biological Conservation
• Conservation Biology
• Journal of Molecular Evolution
• Ecology
• Molecular Biology and Evolution
• Evolutionary Ecology
• Molecular Phylogenetics
• Functional Ecology
• Oecologia
• Genetical Research
• Oikos
• Genetics
• Paleobiology
• Systematic Biology
• Theoretical Population Biology

A Note on "Using the Internet"

We live in a wonderful age; anyone with an idea or opinion on a subject can construct a site accessible through the World Wide Web to promote that idea. Unlike papers in scientific journals, however, such sites do not have to be reviewed by peers for accuracy of content before becoming established. Thus they are not considered to be acceptable scientific references. Of course, there are electronic scientific journals and other legitimate electronic sources that are acceptable references. You must be careful to use information only from legitimate scientific sources; consult the teaching assistant or me if you need help in deciding whether a particular electronic source is acceptable.