In completing the Senior Capstone, students should:
The Senior Capstone has three required components that are described in more detail below:
Each semester, the Department sponsors five or six seminars. These seminars, usually by outside speakers, expose students to methods and thinking used in biology. Attending these seminars promotes all of the goals of the Senior Capstone. More information about seminar attendance can be found on page 11 of this document.
You are required during the senior year to attend four of the seminars as part of the senior capstone. You should aim to complete this during the first semester of the senior year, but it must be completed no later than the end of February 2018. Do not make the assumption that all seminars will be given as scheduled, as illness and bad weather can result in cancellations.
Try to get to the seminars earlier in the year if possible, as the winter seminars sometimes result in cancellations. It is your responsibility to sign the attendance list for each seminar you attend and only seminars for which you have signed in can be counted towards the requirement. Students who have conflicts with meeting the required seminar attendance because of participation in intercollegiate athletics or other commitments should contact the Chair of Biology.
The Educational Testing Service Subject Exam is designed to test your cumulative knowledge in the field of Biology, and serves the Biology department as a useful assessment of both individual students and our overall programs. We ask that you DO NOT study for this exam, as we are interested in finding out what you know overall. However, you do need to take the exam seriously, as it is a graduation requirement. Scores will be sent to you after spring break.
Enroll in a 400-level class for the fall of your senior year. The choices are the Senior Seminar in Biology (BIOL 475) or Senior Honors (BIOL 497). One function of these classes is to help you with the process of completing the written portion of the senior capstone. There will be two senior seminar sections, each with a slightly different focus within biology. Choose the one that best fits your interest and your schedule.
You must enroll in one of these classes during the normal enrollment period for classes during the spring term of your junior year.
The completed honors thesis serves as the written portion of the senior capstone for students enrolled in Senior Honors (BIOL 497). If you enroll in BIOL 497 in the fall and decide not to complete honors, the written portion of your senior capstone will be a copy of the honors thesis introduction that will have been completed by the end of the fall term for BIOL 497.
To complete the written portion of the Senior Capstone, students enrolled in the Senior Seminar will follow the guidelines presented in this document.
The written portion of your senior capstone includes a 500 word summary and three essays based on a published journal article. In the first part you will describe, evaluate, and critique the experimental design and data of the article. In the second part you will place the article in a broad biological context, relating it to the other sub-disciplines of biology and explaining the overall significance of the work. In the third part you will describe future work that addresses important questions that arise from the article.
Choosing an article: Choose a recent research study that will lend itself to the type of analysis required in the essay. The article must have been published in a well-respected journal (see suggestions below) within the last five years, and cannot have been used in the context of a different course.
During the senior seminar, you will submit three journal articles for approval. In consultation with the seminar instructor, one article will be selected from those submitted. For your guidance, a list of well-respected journals is provided below. Note that this list is not exhaustive, and that you are not limited to the journals suggested here.
Suggested journals: Animal Behavior; Am. J. Physiol.; American Naturalist; Behavioral Ecology; Biophysical J., Cell (and other Cell journals), Development; Developmental Biology; Ecological Applications; Ecology; EMBO; Evolution; Genes and Development; Genetics; J. Bacteriology; J. Biological Chemistry; J. Cell Biology; J. Comp. Phsyiol (A, B, or C); J. Neurosci; J. Virology; Molecular and Cellular; Biology; Molecular Microbiology; Nature; Oeecologica; Plant Cell; Plant Cell and Environment; Plant Journal; Plant Physiology; Planta; PLoS journals; Proc. Natl. Acad. Sci.; Proc. Royal Soc. B; Science; Toxicol. Sci.; Virology.
As part of the senior seminar, an annotated bibliography will be due. The annotated bibliography demonstrates your ability to identify additional sources related to your journal article and represents a start on your literature search. In your subsequent work, you will almost certainly cite additional papers, and some of those included in the annotated bibliography may not ultimately be included in the final senior capstone.
The annotated bibliography must include at least 15 references, and these must mostly be primary peer-reviewed scientific journal articles. No more than 5 references can be review papers. Use the citation guidelines described on page 8 of this document, and follow the citation with a short (2 or 3 sentence) description about the paper. In your annotation be sure to address why this paper will be useful to you as you write your essays.
1. Gibbons BJ, Brignole EJ, Azubel M, Murakami K, Voss NR, et al. (2012) Subunit architecture of general transcription factor TFIIH. Proc Natl Acad Sci U S A 109: 1949- 1954.
This paper presents the cryo-EM structure of TFIIH. By combining these data with
previous x-ray structures of individual subunits, a well-defined model of this general
transcription factor was determined, contributing important information for the overall
understanding of the architecture of the RNA pol II pre-initiation complex.
The purpose of the summary is to demonstrate your understanding of the paper’s content, approach, and findings. The summary should function much as an abstract does by relating key information on the question, experimental design, and results presented in the paper. The summary should be no more than 500 words. A revised version must be handed in with the final version of your senior capstone.
The purpose of the first essay is to demonstrate your ability to understand and think critically about both experimental design and data. Your overall objective is to evaluate the primary experiments and analyze the results.
Experimental Design. A well-done essay will reflect a thorough understanding of the overall objective and specific experimental aims of the paper. The essay should clearly define the model system and techniques employed, as well as the relative strengths and limitations of other approaches to the same question. Are the model system and experimental design(s) appropriate? Why or why not?
Data and Interpretation. Focus your data analysis on the two or three most important figures or tables. For papers with complicated multiple-panel figures, you may choose specific graphs or panels. Attach these figures to the back of your document (they do not count against the 1100- word limit). We expect you to deal concretely with the data, for example by pointing out particular features of the figures or tables, and by making numerical comparisons.
Strong essays will identify and discuss both the strengths and limitations of the data in individual experiments. An understanding of the logical framework of the paper will also be evident. How do the results of each experiment lead to the overall conclusion? To what degree do the data support the authors' claims? Are there particularly clever or innovative strategies for resolving uncertainties? Discuss alternative interpretations, experiment designs, or relevant controls that would refine or improve the conclusions of the paper.
The purpose of the second part is to demonstrate your ability to place your paper in the context of what you know about biological systems. In doing so you will focus on two primary questions: how does your paper relate to other sub-disciplines of biology that you have studied and what is the overall biological significance of the work? For the latter, consider how previous studies have influenced your paper as well as how your paper has influenced subsequent work in the field of biology.
In composing this essay, draw upon your knowledge of biology and related disciplines as well as your reading of the literature relevant to your paper. In your analysis pay special attention to the different levels of biological organization. For example, if the main focus of your journal article is population biology, you might aim to relate it to landscape ecology, organismal biology, and population genetics. If the main focus of your journal article is cellular biology, you might aim to relate it to organismal biology, molecular biology, biochemistry, and/or evolution. As a strategy you might think first about the implications of your study at one level of biological organization below and one level above the focus of your paper. What insights can you glean from the paper when thinking about larger or smaller levels of biological organization? In light of this, why are the results of this paper significant?
The purpose of the third part is to demonstrate your ability to identify important questions and to design experiments. Your overall objective is to describe the future work that needs to be done to address the next important questions that arise from your article.
You should describe at least three distinct experiments or research questions in your 1100 word essay. You may describe experiments that extend or confirm the findings of your article. You may also describe other approaches to explore the fundamental research questions in your article. Finally, you may propose new research questions and describe how they might be investigated.
You must describe your proposed future work in detail. Present a research question or specific aim along with a hypothesis. Describe the experimental system and the specific techniques and methods that will be used to test the hypothesis. Where appropriate, describe the control groups and the data analysis that will be employed. State what results would support or contradict the hypothesis. Indicate potential problems that might arise during the experiments and suggest alternate strategies where possible.
All work will be submitted electronically on Moodle. Original written work is screened by turnitin.com. Due dates and times will be strictly enforced. See instructions below for specific deadlines.
You will submit portions of your senior capstone as assignments in the senior seminar. Key due dates include:
Due dates are non-negotiable. If any deadline is not met, the Dean for Academic Advising will be notified, and you may be required to re-do the written portion of the senior capstone with a new journal article. Comments by your faculty mentor will generally be returned within one week following each deadline.
All drafts submitted must show professional English style and usage throughout, including page numbers and proper reference format. If deficiencies appear, you will be required to work with a scientifically literate tutor at the Writing Center or your faculty mentor before submitting the revised manuscript. Revised manuscripts that still show serious deficiencies in style will not satisfy the senior capstone.
Academic honesty and plagiarism: You must write in your own words. Relying on close paraphrasing of other’s work does not constitute “in your own words”. Ask your mentor about paraphrasing if in question, particularly regarding methods, introductory comments from research papers, and discussion comments. DO NOT use direct quotations in your essays. You should describe the work of others in your own words and cite the work properly in text and in listed references. Turnitin.com automatically checks for plagiarism. Results of this check are available to you prior to each deadline. Collegiate standards for academic honesty will be followed to the letter. Please see the course catalog for details on plagiarism.
Citations and references: Appropriate credit must be given to the author(s) of any reference material you use in your paper. If an idea is not your own, you must correctly attribute credit, even when the wording is your own. Citations are given in (author, date) form in the body of the text in parentheses (see formatting guidelines, below).
A successful senior capstone will cite at least 12 primary journal articles overall and include cited works in each of the three essays. Overreliance on review papers is explicitly discouraged. This final section of your manuscript is an ordered list of the references cited in your paper. Include all those specific references cited in the text. Do not include references that are not cited. A single References Cited section should be provided that covers the references for all three essays and your summary.
Use a citation manager program to format your citations. Citations must be in the format of a major journal in the discipline of your focal paper. They must include: authors, title, journal, volume, pages, and year. The following examples come from the PLoS web site:
In text citations should use (author, date) format. The words in the citations count towards the 1100 word limit for essays 1-3.
All work must be double-spaced in 12-pt font with one-inch margins. Include numbers on every page. Submit your complete manuscript and revised complete manuscript with the following sections.
The Department will assign a second reader. Each Senior Capstone will be read by at least two faculty members and the department as a whole will approve the final evaluation.
You will be notified by the Department Chair by email and/or letter of the decision of the Department regarding satisfactory completion of the essays. Decisions will be made by the end of the first semester. Should you not pass the written portion of the senior capstone, you can attempt the exercise again in the second semester, according to a schedule arranged by your mentor and the department chair. Should you not satisfactorily complete any component of the senior capstone in biology you cannot graduate in May.
Senior Capstones receiving Distinction are usually marked by originality and outstanding scientific writing, analysis, organization and flow of discussion, and use of primary literature. The results of your ETS exam are a pre-requisite to earning distinction on your senior capstone. Distinction is rewarded when your work is judged to be of “A” quality on all the essays and the ETS exam is completed satisfactorily.
The following is a list of criteria that the Biology department uses when assessing senior capstone essays. Students should refer to the full senior capstone guidelines for detailed instructions for each essay. We share this with students as a supplementary indication of our expectations. We caution against use of this list as a simple checklist. Simply addressing each criterion does not necessarily guarantee a satisfactory senior capstone.
The seminar series is an important part of our departmental emphasis on the process of science. Just as you have learned about the process of science by reading research papers in classes, you will also learn about how science works by attending seminars.
Seminars are a common means for communicating scientific information, and being comfortable with this format is an important skill for biologists.
The seminar series is also an important opportunity for both students and faculty to interact with scientists from other institutions. We often invite students to have lunch or dinner with seminar speakers — if you’d like to be invited, let us know.
In a typical research seminar, the speaker will present findings and ideas that are not yet published. Thus, the content in a research seminar may be less polished or less finished than the final product that is printed in a peer-reviewed journal.
Speakers benefit by presenting their work at an early stage. They receive important feedback from the audience, usually in the form of questions during or after the seminar.
The audience benefits by hearing about results before they reach print form. Students can benefit by seeing an actual example of how scientists interact with each other in the real world.
Prepare beforehand. If you have the chance, read a paper written by the seminar speaker or read a review article on the topic. Having an understanding of the topic before the seminar will greatly enhance your enjoyment and understanding.
Take notes. Generally, research seminars move fast and speakers often lapse into the jargon of their discipline. It is possible to get swamped by a tsunami of vocabulary. The beginning of a research seminar usually contains background on the research area, similar to the Introduction section of a paper. It helps to jot down unfamiliar names and acronyms.
Later in the talk you might forget that eNAC stands for epithelial sodium channel, that TEWL is total evaporative water loss, or that a pika is a short-eared mammal that lives at high altitudes. Having your notes to remind you, you'll be able to keep up with the talk.
Think critically. When reading a research paper, scientists try to critically evaluate the evidence that is presented. Try to do the same during a seminar. Look carefully at the data. Do they support the stated conclusions? Even if you miss some of the details, you can always assess the quality of the data that are presented.
Understand what you can. You may not understand every aspect of a research seminar, especially if it is outside of your major area of biology. Don't worry about it. Probably only a few experts in the field understand the work entirely. And even the speaker may not exactly know how everything fits together. Remember that speakers often present research in progress and there are almost certainly aspects that are still not understood.
Observe how effectively the speaker presents the seminar. You can learn a lot by watching how scientists present their work. Are the slides clear? Did the speaker give enough background information? Are the data presented effectively? Even if you don't understand a word of the science, you can learn how to effectively present your work. You might also note some mistakes and vow never to make them yourself.
Ask questions: You are encouraged to ask questions at seminars. Our students often do, and speakers are appreciative and impressed.