Appendices - Biology

Appendices - Biology

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Appendices - Biology

I have a young friend who lives in southern Colorado and is learning mostly at home during the COVID-19 pandemic. Like me, he is endlessly curious, so I offered to help him learn about science topics of his choice. (I also knew I could mine his curiosity for blog post topics, so it’s a win-win.)

The first thing my young friend wanted to learn about was the appendix, a body part he no longer possesses. Most people only notice they have an appendix when it becomes infected. This was the case with my young friend, who needed to have his removed in a hurry because it burst (or as he likes to say, “It exploded!”). An appendectomy (an operation to remove the appendix) is a relatively common surgery that can be done in a short amount of time. I found this training video for surgeons, demonstrating the surgery on a foam model, and we watched it together. My young friend’s surgeon put the incision in his navel, so the scar will be much less noticeable as he grows.

For many years, it was believed that the appendix was a vestigial part—something that served no real purpose. Recently, however, scientists have begun to suspect that it might be a reservoir for good gut bacteria. In the days before good nutrition was widespread, it would have been necessary to repopulate the gut with good bacteria after a bout with food poisoning or diarrhea. A ready supply near the junction of the small intestine and large intestine, in the appendix, would have been an evolutionary advantage.

Although researchers may find that the appendix continues to have a role in our digestive systems, other parts have been shown to no longer serve a purpose in the human body. Many of these vestigial parts lost their relevance as we evolved from our tree-dwelling primate ancestors to hairless, upright, ground-dwelling humans. Other common vestigial parts (some of which are starting to disappear from the reproductive record) are muscles to move the outer ear, our tail bones, and wisdom teeth.

Luckily for humans, there are other body parts they can live without. Our built-in symmetry creates some paired organs, like the lungs, kidneys, eyes, and ears. If one of the pair stops working for some reason, we can manage with just the remaining one. The two halves of the brain can also learn to compensate for each other, to a certain extent. Humans can manage without certain unpaired organs, too, like the spleen, the gallbladder, and the stomach, although there may be quality-of-life issues.

My young friend has already expressed further interest in the nervous system and the heart, so stay tuned for more human body information.

All students learn more when their interests and experiences drive their learning. Online learning may have significant drawbacks, but in my experience, it is leaving more time for students to pursue their own interests. Many of them also now have the means to do that exploration, with access to district-provided tablets and available WiFi. I encourage everyone to find ways to bring out those interests in your budding scientists.

Becky Stewart is a geologist by training and a writer by avocation. She has worked for scientific and educational publishers and is currently a scientific copywriter for a laboratory informatics consulting firm. She enjoys spending time in nature, including in her own garden, which has more and less wild phases depending on the season. Additional hobbies include cooking, woodworking, and minor home improvements.

Appendix 1

The student should enroll in Biology 401-404: Independent Research (or conduct an Excel project) with a faculty mentor in their sophomore or junior year. The possibility of Honors Thesis should be discussed with your research mentor by spring of your junior year. The student should then begin to develop a research plan for the Thesis work in consultation with the faculty mentor and obtain the department head’s permission to enroll in Biology 495: Honors Thesis. Be aware that research conducted for pay (e.g., Excel) cannot also count for academic credit the Honors Thesis research must be distinct in some manner from research experiences for pay.

Summer prior to Senior Year

Work on Honors Thesis Proposal and begin making arrangements for the thesis committee. At the discretion of the faculty mentor, one or more drafts may be required prior to the beginning of the fall semester.

Fall Semester of the Senior Year

Having enrolled in Thesis (Biol. 495), the Thesis candidate begins research, initially by performing a thorough search of the scientific literature, getting experiments underway and finishing the Honors Thesis Proposal (see Appendix 2: Departmental Standards for Written Work Appendix 3 Sample Thesis Proposals). Candidates will receive a copy of the rubric that faculty will use to assess the quality and merit of Honors Thesis research. An Honors Thesis must demonstrate the student’s capacity for quality research and give evidence of mastery of the material. Typically, students meet at least weekly for project discussions and review of several Proposal drafts.

A Thesis Committee for the student will be approved at the first regularly scheduled department meeting of the semester. The Committee will consist of two department members plus the mentor. An additional member from outside Biology may be appointed at the department’s discretion. The Committee will be formed through discussion, but the department head will have final say on committee composition. The responsibilities of the Thesis Committee are:

  • To meet with the student and review the Proposal during fall semester as well as the Thesis during spring semester
  • To help direct and support the student in pursuing the Thesis both at formal Committee meetings and through informal discussion
  • To insure careful consideration of comments made by all faculty of the department
  • To render to the department a judgment about the acceptability of the Proposal and Thesis.

After the mentor has signed off on the proposal, the completed Honors Thesis Proposal is submitted to the department head for departmental comment and approval by 5 pm of the Friday of the 4 th week of classes in the fall semester. This Proposal must contain the following elements:

  • A maximum of 5 pages of double-spaced text (not including title page, figures, and references)
  • An introduction consisting of a current literature survey, a clear description of the research objective, and how this objective interfaces with the current scholarship within the field
  • A research plan that broadly outlines the specific experiments and/or studies to be done
  • A statement of how living material will be maintained and managed, with particular attention to school breaks
  • IACUC and IRB permits, if appropriate
  • A budget.

Sample Honors Thesis Proposals are included in Appendix 3. The proposal will be circulated to departmental faculty for their comments. Honors candidates are responsible for clarifying with departmental faculty any comments on the Proposal and the Thesis prior to any subsequent meeting of the Committee. Such comments and constructive criticism may affect design and/or conduct of the research project, as well as the interpretation and/or validity of data to be collected.

The student will initiate a Thesis Committee meeting to discuss the Proposal and attendant faculty comments. At this time, any changes to the planned research can be discussed. The Committee also will adjudicate the suitability of the Proposal for producing an Honors Thesis and the acceptability of the Proposal as a whole. If the student and mentor chose to deviate significantly from any proposed elements during the year, they must consult with members of the Thesis Committee for their consensus.

During the last week of October, all students will present and orally defend their Thesis Proposal to the department. The actual presentation will be 5 minutes long there will be 10 additional minutes for questions. At this point, biology faculty can provide input to the student and the Committee regarding any concerns. Students should initiate a discussion with their faculty mentor regarding research plans over the interim session (see below).

Students should use the fall semester wisely regarding completion of experiments, sample analysis, data management, and interpretation of results. It is unlikely that the entire body of research will be completed in one semester, and thus students are unlikely to receive departmental honors if they expect to conduct the majority of the lab- or field work during the spring. Thus, both fall and spring must be utilized for making research progress (see Spring Semester, Item 1, below).

If required by the mentor, the student will write and submit a progress report by the end of classes in the Fall semester.

The student should enroll in Biology 40X: Independent Research for the spring semester.

The Committee’s review of the Proposal, a progress report (if required), and an evaluation of the student’s conduct as an investigator by the mentor will contribute to the grade given in Thesis for the fall semester.

Interim Session

During Interim, Thesis Committee members will meet to evaluate the progress of Honors candidates and to discuss whether the candidate is performing at, above, or below the “acceptable” level in all evaluation categories (refer to Rubric for the Honors Thesis in Biology downloadable here as ThesisRubric_final). After the Thesis Committee renders a decision on truncating or continuing Honors Thesis candidacy, the faculty mentor will communicate that decision to the student.

It is strongly urged that, with the permission of the mentor, candidates elect to use much of their Interim Session on campus doing research, returning early when possible. While not specifically required, engaging in research during this concentrated period can advance progress significantly because the student is free from competing demands of other coursework and activities. This should be discussed by the candidate and mentor well in advance of the intersession.

Spring Semester of the Senior Year

  1. With approval from the committee and a grade of “A” in Biol. 495, the candidate will switch from Biol. 40X to Honors Thesis (Biol. 496) and continue the research project. As the semester wears on, curricular matters other than research will rear their heads (e.g., midterm examinations, term papers, and final examinations in other courses post-graduate plans, etc.) planning and executing successfully all necessary experiments/field work/analyses will become very important. For this reason, it is prudent to schedule completing necessary investigations by early in the spring semester. A reasonable target is that, by the Mid-Term Grade due date, the student has assembled the bulk of the final form of the Honors Thesis, including drafts of figures (graphs, diagrams, or photographs) and tables, and most statistical analyses.
  2. At the beginning of the spring semester, the student, mentor, and committee will agree upon due dates for important materials (e.g., thesis drafts). In particular, the committee should agree upon the date by which the candidate should circulate to the committee the near-final draft of the thesis that will be evaluated during the review meeting (see next item). This timeline is at the discretion of the committee, and failure to adequately meet deadlines may affect the student’s candidacy.
  3. By 5 pm of the Friday of the 12 th week of classes (count of week includes spring break), the Thesis Committee will meet with the Honors candidate to review the Thesis and probe the student’s understanding of the research. At this time, the Committee will make a judgment on the quality and suitability of the Thesis and decide whether the candidate can submit the Thesis to the department and stand for defense of the Thesis in a public presentation. If the thesis is approved, the Committee also will determine what changes, if any, must be made in the final draft of the Thesis. The specific format of this Committee meeting will be at the discretion of the mentor.
  4. By 4 pm of the Wednesday of the 13 th week of classes, the candidate will submit a final draft of the Honors Thesis to the Department Head for faculty comment as well as for distribution to outside examiners from other departments on campus and beyond the College. Again, comments from faculty and outside reviewers must be considered by the student, and further discussion with the faculty mentor may again be necessary.
  5. During the last week of classes (typically that Friday afternoon), Honors candidates will publicly present and defend their thesis research (see below). If the Thesis and the Defense are acceptable, the Thesis Committee will move acceptance, and the department will vote to recommend the candidate for Graduation with Honors in Biology. If the department does not make this recommendation, the decision will be communicated to the candidate by the mentor, and students will earn completion of another course in Independent Study.
  6. The candidate should ensure that the mentor submits a completed Approval of Thesis form to the Academic Progress Committee as soon as possible after the presentation, but certainly no later than the date for submission of Senior Grades.
  7. An electronic PDF copy of the Honors Thesis, incorporating any and all changes as directed by the Committee, outside examiners, or Department members, are submitted to the Department Head and the mentor before the end of the final examination period.

Presentation of Honors Thesis and Defense

During the last week of classes (typically that Friday afternoon), all Thesis students will present in a public venue their thesis work to the Biology faculty, one or more outside examiners, and any students and invited guests. Students must keep in mind that many in the audience will not be familiar with the research jargon that is peculiar to their sub-discipline and should make every attempt to clearly and simply present their results and conclusions. The Thesis presentation is not just a reading of a scientific paper in a format suitable for publication, but is aimed more broadly at a scientifically literate audience.

Typically, 15 minutes are allowed for presentation of each Thesis and 15 additional minutes are allowed for questions and answers. After the Thesis is presented, the outside examiner(s), then Biology faculty, and then other audience members may ask questions. We expect students to demonstrate mastery of their research area, understanding of the basis and execution of methods employed, and how their particular research findings fit into the larger body of knowledge in the research area. Here is a sample PowerPoint thesis defense slide show.

Following the Thesis presentation, the student also must be able to defend it against reasonable criticism in the form of questions from the audience. This is a critical part of securing Honors in Biology, and it is your task to convince the biology faculty and outside examiners with pertinent evidence. Admission of ignorance is never a sin, and if the answer to a question will not come to you, do not despair. Faculty are noted for their gentle attempts to lead thesis students toward a correct or, at least, acceptable response to a difficult question.

Successful presentation of the Thesis by the student, submission of an acceptable final draft of the Thesis during the final examination period, and earning grades of A in Thesis (Biol. 495/496) will satisfy the departmental requirements for graduation with Honors in Biology, provided the candidate also meets the College-wide GPA requirements. During the last faculty meeting of the academic year, the Academic Progress Committee moves that the faculty recommend to the Board of Trustees that all successful Honors candidates be allowed to graduate with Departmental Honors and, unless there are objections, the faculty passes the motion. When the trustees accept this recommendation at their last meeting of the academic year, a notation of “Graduation with Departmental Honors” is made on the transcript of each student so designated students graduating with departmental honors also are noted on the commencement program.

Summary Timeline

The summary timeline below is a resource intended for those who have already read all of the above information. If you do not pay strict attention to the information above, you risk missing important information that will eliminate you from consideration for Honors.

Spring semester junior year

Summer between junior and senior year

Fall senior year

  • After the mentor has signed off on the proposal, the completed Honors Thesis Proposal is submitted for departmental comment and approval by 5 pm of the Friday of the 4 th week of classes.
  • During the last week of October, candidate presents and orally defends the Thesis Proposal.

Interim senior year

  • Candidate works on thesis
  • Thesis committee decides whether the candidate can enroll in BIOL 496

Spring senior year

  • If approved, the candidate enrolls in BIOL 496
  • The student follows the committee-specific timeline regarding submission of drafts and other materials.
  • By 5 pm on Friday of the 12 th week of classes (count of week includes spring break), the Thesis Committee will meet with the Honors candidate to review the Thesis and decide whether the candidate can submit the thesis to the department and stand for defense.
  • By 4 pm on Wednesday of the 13 th week of classes, the candidate will submit a near-final draft of the Honors Thesis to the Department Head for faculty comment.

During the last week of classes, the Honors candidate will publicly present and defend the thesis research.

Appendix 4

The honors thesis is written in the general form of a scientific paper with additions peculiar to the thesis format. Thus, it has several discrete parts that serve different purposes. These parts are listed and discussed below. Departmental honors theses are available in Skillman Library and in the Biology Department Office, and students should refer to them for examples of acceptable form and style. Sample honors thesis are available in Appendix 3.

Title page. This lists in separate paragraphs the title of the honors thesis, its author and the thesis adviser.

Biographical sketch. This section is peculiar to the Lafayette honors thesis and is not usually included in a scientific paper submitted for publication. Refer to the examples provided in recent theses in the department office.

Table of contents.

Abstract. An abstract is a terse, one-paragraph statement of the major findings of the study it is not a summary of the entire thesis. The abstract should begin with a statement of the purpose of the study and then present the major findings. A good abstract ends with a one- or two-sentence summary of the significance of the findings.

Introduction. The purpose of the introduction is to present the reader with a concise summary of what was known about the subject to be investigated at the start of the study. This section has a historical perspective and is often two or three times the length of the introduction of a standard scientific paper written for the more narrowly focused audience of a specialty journal. In order to write such a summary, the student will have to find, read, and digest the literature on the subject.

Materials and Methods. In this section of the thesis, the student describes the identity, source, and maintenance of the organism(s) studied, methods used in data collection, identifies important pieces of equipment, chemical analyses and any other special tests or methods used. Sufficient detail must be included so that another scientist could repeat the study if he or she wished to do so.

Results. Data are presented in turn as serially numbered figures and tables, and the major trends of the data are pointed out to the reader. Note that the figures and tables are presented in separate sections at the end of the thesis. Not all data require their own figures or tables in some cases it is appropriate to simply mention a single important datum or observation in a separate paragraph.

Discussion. The findings of the study are discussed within the larger context of what is known about the subject and a synthesis of the new facts with the old ones is attempted. As with the introduction, the discussion section of a thesis is usually significantly longer than that of a standard scientific paper. In the last paragraph of the discussion, it is appropriate to suggest directions for further research.

Acknowledgments. This is the place to credit those who have helped you in the experiments, in the preparation of the thesis, and in its presentation. Use complete names and indicate the exact nature of the assistance. Be certain to acknowledge any financial support from grants.

Literature Cited. Here the student lists, in alphabetical order by first author, all of the published or unpublished works, personal communications, etc., which were mentioned in the text of the thesis. Note that italics are used for genus and species names, journal or book titles, and volume and issue numbers.

Tables. Here the tables are presented in numerical order on separate pages in their own section, complete with legends.

Figures. The figures are grouped together in this section in numerical order on separate pages, again, complete with legends.

Watch the video: Jai faim plus que Alain (February 2023).