Research in Biology

Independent Study (Bio 390 & 490) & Summer Fellowships

For many students who participate, independent research is the culmination of their undergraduate experience. You will engage in proposing hypotheses, devising ways to test them, developing experimental methods, analyzing data, and writing and rewriting your paper. You will take an active part in your education by working on a research project being carried out in the laboratory of one of the Biology Department faculty. No matter what your future career, this intense intellectual experience will be superb preparation.

The Biology Department facilities in the Barshinger Life Sciences and Philosophy Building feature 12 student-faculty research laboratories, greenhouses, and animal rooms. Specialized facilities and research equipment include a liquid scintillation counter for radioisotope studies, a gas chromatograph, a fluorometer, preparative and ultracentrifuges, electrophoresis equipment, a dark room, a cold room, a DNA sequencer, a quantitative thermal cycler and controlled environment chambers. A variety of equipment is also available for terrestrial and aquatic field studies. All equipment is available to students in courses; our research students learn to use even the most complex instruments.

The department's Digital Imaging Processing Laboratory provides 8 Power Mac work stations, several Nikon compound microscopes, a fluorescence microscope and an inverted phase contrast microscope. All are supported by digital imaging video equipment had a flatbed scanner. The facility is directed by Profs. Fluck and Triman. They received an ILI grant to set up the laboratory.

The Biology Department also houses a specialized computerized photosynthesis monitoring and analysis apparatus. This was obtained by Profs. Pike and Richardson also through the ILI grant.

Following is a brief description of the research opportunities for students in the Department of Biology. The Department believes that research is an integral component of the study of biology; this is why courses in the Department have a laboratory component. Furthermore, the Department urges all majors to have a research experience as part of their major program.

Independent Study

Students may enroll in Bio. 490 (seniors) or Bio. 390 (juniors), Independent Study, for one or two courses of elective credit towards the Biology major (see the College Catalog). Independent Study is typically performed with a professor as an adviser, and involves an independent research project performed in that professor's laboratory. The exact nature of the project is outlined in consultation with that professor but typically involves the continuation of on-going research. (See the list of Department faculty on p. 2 for a brief description of our research interests.) Some independent study projects result in a published journal article, some of which are on display in the lobby of Fackenthal Laboratories. Different professors require different amounts of written work from the independent study student, but the Department requires a thesis at the end of the project, and a progress report at the end of the first semester in the case of two-semester projects.

In a typical year, up to a third of the senior biology majors will enroll in Bio. 490. Students who complete a two-semester project and who meet other requirements may be candidates for Departmental Honors; a successful oral defense of the project is required for Honors in Biology (see below).

Any student with an interest in Bio. 390 or 490 should talk to faculty about the possibility of doing research. You will not be committing yourself! You may decide that research is not for you; that's fine. But don't hesitate to discuss the possibilities. You should think about one semester (fall or spring) or two semester projects. Talk to several faculty members about their work if you do not have a fixed idea of the area you wish to study. The specific project you do is not as important as the interactions you have with the faculty member who is sponsoring your research, and the opportunity to actively participate in your own education. You should think about your preferences for level of biological organization (population, organism, cell, molecule), the kinds of tools used in particular areas, and the styles of student/professor interaction that different faculty have. We also encourage you to talk to students who are currently enrolled in Bio. 390 or 490 or who have done summer research projects. Descriptions of student research projects are also on display in the cases just inside the front door of the Fackenthal Laboratories. Most faculty members will advise two or at most three independent study students at a time. Students in Bio. 390 or 490 must ordinarily have achieved a 3.0 average in major courses, but we have waived this requirement for students who have a strong commitment to research or who have shown improvement in their course work. If this policy affects you, don't hesitate to discuss your situation with potential research advisers.

The scope and variety of undergraduate research is indicated by the following samples, selected from projects pursued in recent years. The results of some of these studies have been incorporated into articles published in scientific journals or have been presented at national scientific meetings, with the student listed as co-author.

  • Developmental effects of UV irradiation in the medaka fish egg (Oryzias latipes).
  • Microfilaments and the formation of the blastodisc in medaka (Oryzias latipes), a teleost, during ooplasmic segregation.
  • The spatiotemporal pattern of microtubules in parthenogenetically activated medaka (Oryzias latipes) eggs.
  • Cell counts of blastocysts cultured under different CO2 concentrations.
  • Cell counts of blastocysts cultured with or without calf serum.
  • Effects of creatine monohydrate ingestion on the maintenance of sprint performance in college age men.
  • Rana pipiens detects hypertonic NaCl solutions on hydrated surfaces: taste or thirst?
  • The effects of body size on the resting metabolism and locomotor performance of the ornate box turtle, Terrapene ornata.
  • The role of ammonia in pattern formation in slugs of Dictyostelium discoideum.
  • Effect of ammonia on the chemotactic response of prestalk cells of Dictyostelium discoideum to cyclic AMP.
  • Blanching responses of prestalk and anterior-like cells of Dictyostelium discoideum to pH and ammonia as indicators of strength of proton pumping into acidosomes.
  • Inhibition of elongation via auxin induced ethylene prodution in pea stem tissue.
  • Fatty acid acylated chloroplast proteins of Arabidopsis thaliana.
  • The effect of light on auxin uptake in hypocotyl segments of Cucurbita pepo.
  • Correlation of genotype and phenotype in monozygotic twins clinically discordant for MERRF (myclonic epilepsy and ragged red fibers).
  • Random segregation of the mutant mitochondrial tRNA leu(UUR) gene in monozygotic twins discordant for MELAS (mitochondrial myopathy encephalopathy, lactic acidosis and stroke-like episodes).
  • A translation product fingerprint for mitochondria containing the MELAS tRNA leu(UUR) mutation compared to the fingerprint from normal mitochondria.
  • Relationship of cliff flora to soils and bedrock in southcentral Pennsylvania.
  • Site-directed mutagenesis to restore basepairing at position 513/538 in 16S rRNA of Escherichia coli .
  • Development of single cell isolation technique to characterize a deoxygalactose resistant strain (SB 210) of Tetrahymena thermophila .
  • Microscopic detection of filamentation in ribosomal protein S12 mutants of Escherichia coli .

Department Guidelines for Independent Study

The following guidelines are Department of Biology policy regarding student Independent Research in Biology.

  • All interested students who possess at least a 3.0 grade point average in biology courses (We have waived this requirement for students who have a strong commitment to research or who have shown improvement in their course work.) and who are preparing to register for the 5th, 6th, 7th, or 8th semester, should consult the members of the Department regarding research opportunities available.
  • Students who secure the consent of a potential research adviser will also be reviewed by the entire Department.
  • Credit for Bio. 390 or 490 will be given only for research conducted under the direct supervision of a member of the Department of Biology.
  • A student may not enroll for two credits of Bio. 390 or 490 in a single semester.
  • A student may satisfy only two of the five required biology electives with Bio. 390 or 490.
  • All Bio. 390 and 490 projects will culminate in the final semester in a written report (see 3. Instructions for Written Reports) which is to be reviewed by at least one member of the Department (called the second reader) in addition to the adviser, prior to submission of the grade for the course. The adviser and the second reader consult on the grade for the work in all cases. In some cases, the second reader will be involved in a consultative role during the design and implementation of the project, but this is not required for all projects. This paper must be completed by the last day of classes.
  • In certain circumstances, an independent study report will include work from more than two semesters or from a summer and two semesters. This is fine, but please make clear when each part of the work was done.
  • Students registering for a second semester of Bio. 390 or 490 must submit a progress report (see 3. Instructions for Written Reports) by the last day of classes of the first semester. This report will be reviewed by the adviser and one other member of the department, or--if the student is a candidate for honors--by the whole staff.
  • Regular grades will be given for all semesters of Bio. 390 and 490. The P/NP option may not be exercised. The grade for work in independent study is decided by the independent study adviser in consultation with the second reader. The second reader brings to the negotiation an opinion of the quality of the written work (progress report or final paper), while the adviser also brings knowledge of the quality and amount of work done by the student and the degree of independence shown by the student. As a rule of thumb, the grade on the written paper is one half the grade for the course and the second reader contributes half the grade on the written paper.

How to Enroll in Independent Study

Enrollment in Independent Study requires that a professor agree to sponsor you, and the Department must agree that your record supports the probability of a successful independent study experience. Thus, you must begin to plan your independent study during preregistration for the semester in which you wish to begin it. You should speak to the Chair of the Department about the possibility of doing independent study, you should speak to students who are doing independent study and examine the display of research opportunities in the lobby of Fackenthal Laboratories and on bulletin boards around the building, and you should speak to several professors about doing independent study in their laboratories. After you have done this, you should choose a professor with whom you wish to do independent study and ask him or her to sponsor you.

Special Registration Instructions

Enrollment in Independent Study requires a special form you must obtain from the Registrar. This form includes a brief description of your research project, and must be completed during the first two weeks of the semester you begin your study. A copy of the form is on the following page.

Instructions for Written Reports

Standardized Title Page

The title page should include:

informative title
full name of student
department to which the paper is being submitted
name of advisor
name of course
indication if the paper is for departmental honors
date paper was submitted
expected graduation date

The Progress Report

The Progress Report, submitted on the last day of classes of the first semester of a two-semester project, is a concise statement of the project at midstream. Although brief, it serves as a significant part of the first-semester grade, since staff members other than the adviser rely almost solely upon this statement as a basis for evaluating the student's performance. How well the progress report is written is as important as the results it may contain. This being so, it is strongly advised that preliminary drafts of the report be gone over carefully by student and adviser before the final version is prepared. The following specifications should be explicitly followed:

Length. The text of the report should be no more than six pages, double-spaced. In addition, space is allowed for a list of references cited in the text, and three pages for figures and tables. If desired, a bibliography of literature read but not cited can be prepared as an appendix, but this normally is not expected. These length restrictions are meant to enforce conciseness, clarity, and careful choice of material to be included.

Content. The progress report should include:

Introduction (i.e., purpose and a brief background)

Methods and Results to Date

Discussion and Future Plans

Literature Cited

As its name implies, the report should be both backward- and forward-looking.

Style and neatness of text. Margins should be wide (1 1/2 inches on left, 1 inch on right) to allow room for written comments. One inch of space also should be left at the top and bottom of each page. The report should be typed and double-spaced, and a cover sheet with an informative title provided. Other aspects of text style, including the mode of reference citation in the text and the form of the bibliography, shall follow the guidelines for biology papers in A Short Guide to Writing About Biology by Jan A. Pechenik. In addition, grammar and sentence structure must be correct and ideas must be expressed clearly.

Figures and tables. Figures should be carefully drawn. Axes should be labeled, and a title and explanatory legend provided. The student should consider carefully how a given set of data should best be graphed, and should consult with the adviser if uncertain whether points should be connected, curves smoothed, etc. Tables should be provided with an explanatory legend. All figures and tables should be referred to in the text, but should be labeled sufficiently to be understandable by themselves. Please see A Short Guide to Writing About Biology by Jan A. Pechenik.

The Final Report

The preparation and guidelines for the final report are the same for one-semester or two-semester projects. There is no limit on length, but the contents should be subdivided under appropriate headings. The final report should contain:

Abstract
Introduction
Materials and Methods
Results
Discussion
Literature cited
Acknowledgments

In addition, the guidelines given above for the progress report should be followed with regard to the style of the text, and the figures and tables of the final report. The care that should go into the preparation of the final report is reflected in the concept that communication of the results of research is as important as the research itself. This being the case, adequate time should be reserved for the writing of the report, including drafts to be gone over by the adviser. In the case of one-semester projects, the expectations of the student in terms of the final report's quality remain the same. Please see A Short Guide to Writing About Biology by Jan A. Pechenik for advice and formatting information.

Criteria Used in Evaluation of Independent Study Reports

These comments attempt to clarify the goals of Bio. 390 and 490 as we perceive them, and to alert you to what we will be thinking about as we read your reports. We intend here to clarify the aspects of your research and written reports that we value most highly. We hope these comments are useful to you as you think about your research, and later as you prepare your progress report and final report.

  • Degree of difficulty of the project.--Some projects are "safer," more narrow in design, or tread more familiar ground than others. Where your project fits in this continuum is not something you should worry about--in large part it is your adviser's responsibility to help you find a project that is not impossible to do in the time available, and to ensure that it is challenging, asks interesting questions, and has clear focus. Evaluators recognize that some projects are higher risk ventures than others, and make allowance for this in their evaluation.
  • Actual importance or novelty of findings.--Although some projects may lead to publication and be blessed with beautiful, definitive results, this is a very minor criterion of a successful Bio. 390 or 490 project. You may actually learn more from a project in which the findings are very modest and inconclusive, and your evaluators may be more impressed by the way you wrestle with such results than by less thoughtful treatment of "beautiful" results. Bio. 390 and 490 are supposed to help you become a scientist in your approach, analysis and thought processes, and your project will be judged on the evidence that you have progressed in that direction. Importance or novelty of findings, in and of itself, is no real criterion of that progress.
  • Adequate analysis and understanding of your data and their significance.
  • Larger perspective on the questions being asked.--These criteria are much more important in evaluation of your project than the first two. Do not forget this in your rush to amass data! Evaluators will be looking for evidence that you have thought about your findings, about how they bear on your original questions, and about the larger picture into which your project fits.
  • Adequacy of literature search.--It is expected that you do a conscientious job here, and to the extent possible make connections between the work of others and your own. The relevant literature will be much more extensive in the case of some projects than others; do not worry about the number of entries in your "literature cited" list, so long as you have made a real effort to find literature and use it. Your evaluators will be rather discerning in this regard.
  • Clarity of presentation, grammatical writing, and careful organization.
  • Care in preparation of tables, figures, and typescript.
  • Careful adherence to prescribed guidelines.--These last three criteria are relatively easy to apply to any written report, and you will be badly hurt if you do not pay adequate attention to these aspects. It is easy for evaluators to recognize a sloppy job, and it is easy for you to avoid a sloppy job, simply by saving enough time at the end of your project to do a careful final preparation. Clear writing and organization will come more easily to some of you than others, but whether you consider yourself a good writer or a poor one, do not expect one draft to be all you will need!

Your final report--and your progress report--are too important to simply be thrown together. Care in writing, attention to details, adequate analysis of your results and careful thought about their meaning--these, together with evidence of careful planning and procedures, are the criteria that are really important in the ultimate evaluation of your project. Except for your adviser, those evaluating your work will be basing their judgment almost entirely on your write-up (together with your oral defense, if you are an honors candidate). If you think far in advance about what is expected in your write-up, you will undoubtedly turn out a stronger product.

Expectations of Independent Study Students

Following is a copy of a memorandum that Prof. Fluck gives to each of his independent study students. It is a highly personal document that sets forth his expectations for the independent study students he advises. It is included here to give you an idea of what to expect from an independent study project with him or another professor.

To: Biology 490 Students
From: Richard A. Fluck
Re: Independent Study in my Laboratory

Introduction:

Students pursue independent study for various reasons. Some of you have done research before, have liked it, and want another chance to work on a research problem. Others of you have never done research and want to find out what it's like, whether you like it, and whether you can do it. Some of you look forward to the challenge of working independently and to the possibility of discovering something. Some of you find our standard courses too confining and would like the freedom you think Bio 490 will give you. Probably all of you know that Bio 490 will look good on your record.

I need to know why you want to pursue independent study, because to some extent I will tailor my advising to meet your wishes. What are your goals in pursuing Bio 490? What do you hope to find out about yourself? What do you hope to accomplish?

My philosophy and expectations:

If you work in my laboratory, I will treat you as an apprentice--not as a technician to do my own research. However, except in very unusual circumstances, you will work on a research problem closely related to the ongoing project in my laboratory. Biological research--probably any kind of research--is complex, and it is usually foolish to jump into a new problem without the necessary background. My students and I have been working on various aspects of medaka development since 1974, and in that time we have learned a lot about the medaka embryo and have developed a number of standard procedures that you can use to get started on your own project; these procedures will give you a good base onto which you can add your own protocols.

At any one time, we are usually pursuing several lines of investigation in the laboratory--some of them are old lines, while we have just opened others. I will do my best to describe for you the overall objectives of the study and to describe the alternative projects that you may choose to pursue yourself. I will have pursued each line enough to know that 1) it really is a problem worth pursuing, and 2) there are no major technical problems that will hinder you from pursuing the problem. You and I will then agree that one project is the best one for you to pursue, taking into account your background, interests, and time commitment (one or two semesters); and the likelihood of "success."

Once we have settled on a project, it becomes your project. I will advise you, but you must take responsibility for the project--the literature search, the research, and the writing. And just as I will not come into the laboratory to do your experiments for you, I will not write your thesis or progress reports for you. These are primarily your responsibility; I am here to advise you. I will do my best to give you feedback about your performance and progress along the way. If you are doing well, I'll tell you. If you seem to be slacking off, I'll tell you that. But I will not ride you to get you to work. Frankly, I have better things to do.

The Biology Department's "Department Guidelines for Independent Study" and "Criteria used in Evaluation of Independent Study Projects" contain useful information about independent study. You should read both documents carefully. I would like to state some additional expectations I have:

I expect you to work on your project at least fifteen hours per week. This includes weekly meetings with me and also time spent reading, working in the laboratory, and writing. In fact, most students have found they must work more than fifteen hours if they hope to make reasonable progress. Many of the experiments you will perform will require large blocks of time--up to 10 hours at a stretch; you should plan your schedule accordingly.

I expect all my students to share the routine work in the lab: feeding and otherwise caring for adult fish; collecting, cleaning, counting, and growing embryos; cleaning up after themselves, including washing and putting away their own glassware.

I expect you to meet with me at least one hour each week. The agenda for these meetings is up to you and can include reviewing data, discussing the primary literature, going over experimental protocols, working on drafts of paper, etc.

I usually ask my students to prepare a literature review(s) in the area of their project. Due fairly early in the first semester, these reviews get you into the literature, make you think carefully about your project, and get you started writing. These literature reviews have often formed the basis for the introduction of a thesis.

I expect you to submit drafts of all your documents and to submit them early enough that I have time to study them carefully. We will agree on a series of due dates early in your project and then try to adhere to them. You will write all your documents on a Macintosh computer.

Honors:

Just a few words about honors. I believe that honors is something that is granted retrospectively. That is, a faculty committee looks at a thesis, the research it represents, and a thesis defense and then decides whether the work is worthy of Honors in Biology. I do not believe that honors should be a major goal of independent study. In fact, if an important reason for you pursuing independent study is that you may qualify for Honors in Biology, I'd rather not work with you. My experience is that this is not a good reason to do research. I love doing research, I have fun doing it. It's worthwhile in and of itself. If your work qualifies you for honors, fine. But honors should not be your major goal.

If you want to have your project considered for Honors in Biology, it is your responsibility to make it worthy of consideration--to make both the research and the writing worthy of honors. I will not repeatedly edit your writing to get it into shape for a suitable thesis. It seems to me that your ability to do this is part of what the committee evaluates.

In evaluating your project, the committee and I will look at two semesters of work--not one semester. Too often students slack off in the fall and then come on strong in the spring, hoping that a strong finish and good thesis will carry them into an honors defense. I will not permit you to do this; I expect you to put in two semesters of good work if you want me to support you application for honors.

Graduation with Departmental Honors

Honors in Biology are awarded to students who successfully complete two semesters of independent study and pass an oral examination given by a committee of faculty, (see the College Catalog for more information). Copies of student research papers which have received Honors in Biology are sent to the College Archivist for deposit into the College Archives.

The following guidelines are Department of Biology policy regarding the award of Honors in Biology.

  • Departmental Honors will not be granted for one-semester research projects.
  • Students are nominated for honors by the faculty supervising their independent study project. This nomination must have the student's approval and it typically takes place between semesters of a two semester independent study project. The faculty of the Department read and discuss the progress report and approve or disapprove the continuation of the project for honors within 14 days of the beginning of the second semester.
  • Honors defense committees should be formed enough in advance of the defense that the members have time to thoroughly read the final paper. The final paper is due on the last day of classes. The defense is publicized and open to the public. Typically, honors defenses are held during Reading Days or Finals Week in the semester the independent study research is completed.
  • The committee should have 3-5 members in addition to the adviser. At least one member must be from outside the Biology Department. At least two members, and a majority of members, must be faculty in Biology. Faculty in Biology should be a mix of junior and senior faculty. The adviser is not a voting member of the committee.
  • Honors candidates will defend their thesis before their examining committee during the period specified by the College. The Honors Defense involves an oral presentation and an oral defense of the research findings and their implications. Candidates for Honors in Biology will be examined on their thesis topic and are expected to be conversant with all aspects of their study very broadly defined. Honors is awarded for excellent quality work in the laboratory, for initiative and enterprise in the performance of research, for an excellent thesis and presentation, and for a significant understanding of the research results and their implications.
  • The procedure for the defense is as follows.
    • The defense starts with a very brief introduction by the adviser. The student then makes an approximately 15 minute professional meeting-style presentation of his or her research to the committee. This presentation should include visual aids if appropriate.
    • The student is then questioned by the public audience. When these questions are completed, members of the public audience may leave, or they may stay if they wish to observe the examination by the committee. The committee members then ask questions, and they may go by turns or not. The adviser does not participate in the questioning or in the answering of questions. It is considered bad form for the student to defer to the adviser for an answer to a question or for the adviser to ask a question that might lead the student to the answer of another question. When all members of the committee are satisfied, the adviser will ask the student and any remaining members of the public audience to leave the room. The student should be asked to stay close at hand.
    • Behind closed doors, the committee then discusses the quality of the paper and of the presentation and defense in order to reach a decision on whether or not to recommend the student be granted honors in Biology. The adviser is present for this discussion but does not participate although the committee may ask the adviser for information. A formal vote is taken. The adviser does not vote. The committee may require or suggest that changes be made to the paper before honors is granted or before it is sent to the archives and stored in the department records. After a decision is reached, the adviser informs the student of the decision. The adviser should also inform the student of the nature of the criticisms of his or her work and should oversee the changes to the paper required by the committee.
  • Successful honors candidates will submit one unbound copy of their final revised thesis to the College Archives and one unbound copy to the Department. These copies will become part of the permanent collections of the College and the Department.

Exceptions to the above may be made upon petition to the Department of Biology.

 

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