In completing the Senior Capstone, students should:
- Use primary literature to understand and develop ideas and arguments.
- Understand and think critically about experimental design and data.
- Identify important questions and design new experiments and approaches.
- Integrate material from several courses or sub-disciplines into a coherent whole.
- Consolidate and synthesize basic biological information.
The Senior Capstone has two required components described in more detail below:
- Attendance at 3 either remote or “in-person” seminars; and
- The written portion of the senior capstone: a mini-review on a topic of your choice.
The 400-level Class
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. Choose the one that best fits your interests and your goals.
You must enroll in one of these classes during the normal enrollment period for classes during the spring term of your junior year.
Written Portion for Students Enrolled in Senior Honors
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.
Written Portion for Students Enrolled in Senior Seminar
To complete the written portion of the Senior Exercise, students enrolled in the Senior Seminar will follow the guidelines presented in this document.
Mini-Review for Students Enrolled in the Senior Seminar
The mini-review is a short review paper, typically about 10 pages in length, which covers a focused area of scientific inquiry over a relatively recent period of time. A minireview critically evaluates a current research topic for an audience of other scientists, including those outside the immediate research area. It assesses and synthesizes relevant research, describes its broader significance, points out gaps in understanding, and suggests future work. The journal Neuroscience Letters defines it in this way:
NSL welcomes mini-reviews (usually 10 pages or less within the journal) that cover an important topic in neuroscience in a way that will inform readers, including readers not familiar with the topic. Mini-reviews are meant to be short, punchy, and interesting. Given the constraints on length of articles in NSL, they do not have to be comprehensive or encyclopedic, but they do need to present a topic in a way that accurately reflects the literature and is balanced, interesting and credible.
The Trends journals explain the reviews they publish this way:
Trends journals seek to provide all scientists, from the tenured to the tenderfoot, with concise and curated updates on the latest research. It is our aim to highlight new scientific developments and their impact on the world outside the laboratory. Our high- caliber articles are cutting edge, provocative, yet accessible […]. They are intended not only to bring readers up to speed on recent progress in the field, but also to serve as platforms for debate and to push the boundaries of conventional thinking. The Trends journals offer more than summaries, they contribute insight.
Frontiers in Microbiology describe minireviews this way:
Mini Review articles cover focused aspects of a current area of investigation and its recent developments. They offer a succinct and clear summary of the topic, allowing readers to get up-to-date on new developments and/or emerging concepts, as well as discuss the following: 1) Different schools of thought or controversies, 2) Current research gaps, 3) Potential future developments in the field.
Current Opinions in Cell Biology describes their reviews this way:
The aim of the manuscript is to review recent articles, with particular emphasis on those articles published in the past two years. In addition to describing recent trends, you are encouraged to give your subjective opinion of the topics discussed […]. [T]he review is intended to be a concise view of the field as it is at the moment, rather than a comprehensive overview. Our audience ranges from student to professor, so articles must be accessible to a wide readership. Please avoid jargon, but do not oversimplify: be accurate and precise throughout. […]
Consider these descriptions as useful guides, not absolute rules for how to write your minireview.
Components of the Minireview
Your minireview should have these sections:
- An introduction that summarizes the research question addressed by the review, indicates why the topic is important, and sets it into a broader research and societal context.
- The main body of the review that outlines the recent developments in the field. This section describes the significance of the work, critically evaluates recent papers, and builds a “story” by synthesizing disparate studies. At least 3-4 recent papers should be evaluated in depth. Your analysis must be supported by other primary literature. Use informative subheadings to the degree that is appropriate.
- A section that lays out the future directions that the field might take;
- A brief conclusions section;
- Figures, if needed;
- List of references
All together, the mini-review must be 3000 +/- 100 words without the list of references. Over the course of the Senior Seminar, we will break down the parts of the mini-review into smaller chunks and work on them in discrete steps.
Below is an outline of the steps that we will take in the senior seminar.
Choosing the Topic
In many ways, this is the most critical part of the entire process, for if you choose a topic that interests you, the senior seminar and the senior capstone will be easier.
So, how to choose a topic? You might start by asking yourself what it was that induced you to become a BIOL/MBIO major. Was it something you read when you were younger that you thought really interesting? Or was it a topic covered in one of your Kenyon biology classes that you found fascinating? Or was it a seminar speaker who turned you onto a new idea that grabbed your attention? Choose a topic that will ignite that fire, and that will keep you delving deeper and deeper into the topic.
Your topic must be described as a research question, and it must be connected to your coursework, research, or other experiences in biology. You are encouraged to choose a topic where there is some disagreement or controversy.
Early in the semester, you will write a short “pitch” of less than 250 words that explains the research question you intend to address in your minireview, why it is an important subject, and what recent research you will evaluate. The point here is not to have fully developed arguments, but rather to have a strong justification for pursuing the research topic that you have chosen. It’s crucial that you choose a topic with exciting recent literature as well as a strong literature base that supports the recent work. Describe how the research question connects to your prior courses and other experiences in biology, and what topics you will need to learn more about. Your pitch must include references for at least 3-4 papers that you intend to evaluate.
As part of the class, you will put together an annotated bibliography with at least 8 references: these will mostly be primary peer-reviewed scientific journal articles. No more than two references can be review papers. You must identify between 3-4 recent papers that describe the core recent developments you intend to focus on in your minireview.
In an annotated bibliography, the citation is followed by a short description about the paper (see example below), highlighting the main points and the methods used (if applicable). In your annotation, address why this paper will be useful to you as you write your minireview.
Note that as you write your minireview, you will cite additional papers, and some of those included in the annotated bibliography may not ultimately be included in the final version of the mini-review if the ideas don’t fit. Example:
- 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. This paper is relevant to my work because I am interested in reviewing how RNA polymerase initiates transcription, and this structure helps explain the mechanism by which the polymerase engages with DNA.
Writing the Minireview
Like most things in life, writing a longer paper is best tackled by chunking the work into smaller, more manageable parts. Here are some tips on how to go about writing the different parts.
Describe how your research question fits into the breadth of modern biology and how it relates to other fields. Try to frame its historical and biological contexts here. You may wish to write this section last.
The Recent Developments in the Field
This is the body of the paper. Synthesize the recent work in the field in a concise manner. Analyze each paper as you read them, and try to fit them into a “story arc” of how the field is progressing. Address controversies or disagreements. Be critical about the quality of the research, and try to judge the experiments as well as the interpretations of the results.
You may find that a paper is ahead of its time, and makes little sense until other work fills in the gaps: although science is typically presented in a linear, logical manner, it often progresses in stops and starts in a non-linear manner. Scientists present their work in papers in a linear manner to make the story more understandable, but science often is done in a non-linear manner, and the way we write papers sometime does an injustice to the process.
It may also be that there are gaps in our understanding as the work is incomplete; this then gives you an opportunity, as it leads to…
This is the place where you can imagine how the field will progress from this point in time. What are the open questions that you have found? How will you test these questions? What work needs to be done that’s not been done? Point out some future directions and describe experimental approaches that could be taken to explore those directions.
Write a short section that summarizes the research, and form some conclusions about the field with respect to other aspects of biology. This should be no more than a paragraph or two.
If a diagram, figure, graph or table would help explain the concepts in the paper, do include them in the mini-review. However, make sure that you cite the sources of any figures that you use unless you made them yourself.
List of References
A successful senior capstone will cite at least 12 primary journal articles along with any review papers and books. Over-reliance on review papers is not allowed. You must critically evaluate at least 3-4 research articles. Some recent research (within the past three years) must be included, but inclusion of older articles is acceptable.
This final section of your mini-review 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.
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:
- Published papers. Hou WR, Hou YL, Wu GF, Song Y, Su XL, et al. (2011) cDNA, genomic sequence cloning and overexpression of ribosomal protein gene L9 (rpL9) of the giant panda (Ailuropoda melanoleuca). Genet Mol Res 10: 1576-1588. Note: Use of a DOI number for the full-text article is acceptable as an alternative to or in addition to traditional volume and page numbers.
- Accepted, unpublished papers. Same as above, but “In press” appears instead of the page numbers.
- Electronic journal articles. Huynen MMTE, Martens P, Hilderlink HBM (2005) The health impacts of globalisation: a conceptual framework. Global Health 1: 14. Available: http://www.globalizationandhealth.com/content/1/1/14. Accessed 25 January 2012.
- Books. Bates B (1992) Bargaining for life: A social history of tuberculosis. Philadelphia:
University of Pennsylvania Press. 435 p.
- Book chapters. Hansen B (1991) New York City epidemics and history for the public. In: Harden VA, Risse GB, editors. AIDS and the historian. Bethesda: National Institutes of Health. pp. 21-28.
In text citations should use (author, date) format. The words in the citations will be counted in the word limit for the minireview.
- Single author papers: (Cruz, 1976)
- Two-author papers: (Takamata and Artisomov, 2012)
- Multiple author papers: (Liu, et al., 2017)
General Bits of Advice
Be sure to clearly delineate each sub-section of this essay. Many students find subheadings to be useful. Use informative headings wherever possible.
Develop the necessary expertise to critique the work. To write an effective mini-review, you must consult and cite relevant papers that flesh out the field.
As you write, think about both the strengths and weaknesses of each paper.
Effective language use will be critical to your success. The 3000 +/- 100 word limit puts your prose on a tight budget. Organize the paper by preparing an effective outline; ideas and paragraphs should flow logically. Avoid wordiness, and use care with sentence structure. Don't obscure your meaning with multiple clauses and overly complicated constructions.
Address several subdisciplines of biological knowledge that are biologically relevant to the topic of your paper. Make explicit links and connections with other areas. Describe and compare experimental data and approaches whenever possible.
You may not describe experiments that have already been published as your future work, and it is your responsibility to know the literature well enough to avoid previously published experiments. Reference relevant literature to support your future directions and experiments.
Due Dates and Mechanics
All work will be submitted electronically on Moodle. Original written work is screened by turnitin.com. Due dates and times will be strictly enforced. You will submit portions of your senior capstone as assignments in the senior seminar. Key due dates include:
- Sept. 20 [Sunday, 11:59 p.m.] Pitch of mini-review due
- Oct. 4 [Sunday, 11:59 p.m.] Annotated bibliography due
- Nov. 2 [Monday, 11:59 p.m.] Complete manuscript version of mini-review document due. Also submit pdfs of the 3-5 papers that you focus on.
- Dec. 18 [Friday, 4:30 p.m.] Revised mini-review due.
The deadlines for your senior capstone complement due dates in the senior seminar. Keeping up with assignments means you get the benefit of interacting with your peers as you write your senior capstone.
In case of illness: If you cannot attend class or complete work due to illness or COVID-19 related circumstances contact the appropriate college officials and let me know of the disruption to your academic work as soon as possible. Note that you are not obligated to disclose any specific health or private information. We will work with you and college officials to determine needed adjustments.
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 professor 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. Please see the course catalog for details.
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).
Organization of the Complete Minireview
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.
- Title page. The title page must include your name and the word count for the paper;
- Recent Developments in the Field;
- Future Directions;
- Figures (optional);
- References Cited.
Your senior capstone will be read by one of the other BIOL475 instructors who will serve as a “second reader.” Thus, 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 e-mail and/or letter of the decision of the Department regarding satisfactory completion of the written portion of the Senior Capstone. Decisions will be made by the end of January. Should you not pass the written portion of the senior capstone, you can attempt the capstone again in the second semester by submitting a revised version by 1 March 2021. Should you not satisfactorily complete all components of the senior capstone in biology you cannot graduate.
Senior Capstones receiving Distinction are usually marked by originality and outstanding scientific writing, analysis, organization and flow of discussion, and use of primary literature. Distinction is awarded when your work is judged to be of “A” quality. The minireview will be assessed on the following criteria:
- Explanation. Minireviews should accurately explain the underlying biological concepts and details of research articles.
- Evaluation. Minireviews should assess the strengths and weaknesses of several research articles.
- Synthesis. Minireviews should synthesize multiple research articles into a coherent picture of a current research topic.
- Breadth. Minireviews should address and connect multiple organizational levels.
- Significance. Minireviews should address the significance of the work by forging links to other areas of biology and practical implications.
- Future work. Minireviews should identify knowledge gaps and propose further work to address them.
Biology Seminar Series: Information for Students
Why do we require seniors and research students to attend seminars?
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.
What sort of information is presented in a seminar?
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.
What are the benefits to the speaker and the audience?
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. Students can benefit by seeing an actual example of how scientists interact with each other in the real world.
How can I enjoy and benefit from my seminar attendance?
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.