BIOL 4170 204: Biology Seminar

BIOL 4170 - Biology Seminar

Spring 2025 Syllabus, Section 204, CRN 25577


Instructor Information

Ruvini Pathirana, Ph.D.

Assistant Professor of Microbiology

Email: ruvini.pathirana@tamiu.edu

Office: LBV 379C

Office Hours:
Tue 1030 AM – 1230 PM
Thu 0100 PM - 0200 PM
(may subject to change with notification)

* Note that the office hours (student hours) are walk-ins. No appointments are needed to meet me during the designated student hours and they are on a first-come, first-serve basis.
If you need to meet outside the student hours, please email ruvini.pathirana@tamiu.edu to schedule an appointment.
I have an open-door policy, so feel free to stop by. If my door is closed, I am likely to be in another teaching session, meeting, or busy with research. You may have to return at another time.
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Office Phone: 956-326-2584


Times and Location

R 11:40am-12:35pm in Bullock Hall 208


Course Description

A study of current biological literature and the discussion of research in progress. May be repeated when topic changes. Required of all biology majors in their junior or senior year.
Biology&Chemistry Department, College of Arts & Sciences

Additional Course Information

This is a seminar class series in which we discuss the relevant research, scientific papers, and current events in biology disciplines. Emphasis will be on recent research and new research methodologies. The course endeavors to make students aware of and critically evaluate the primary literature in their area of specialization. This course also focuses on professional development and is incorporated with mini-workshops that prepare you better for a future career in STEM. 

This semester’s topic is “Human Health and Microorganisms.” This course will cover scientific literature search and critical evaluation, current topics in infectious diseases and health-related microbiology, professional preparation for a STEM career, and skills to make learning more efficient and effective in college and beyond.

COURSE MATERIALS

The course materials will be uploaded to the Blackboard (Bb) weekly. There is no assigned textbook for this course. A laptop or iPad that allows access to the internet will be required to participate in in-class assignments and peer evaluations (Bring your device to the classroom !). It is the student’s responsibility to be updated with all the course announcements and materials. Therefore, you should review the course content on Bb frequently to prepare for face-to-face lecture sessions and complete course assignments on time.

COURSE POLICY (Keys to Success)

LECTURE: This is an interactive class; therefore, your participation will be from discussions, written assignments, and peer reviews. This class requires active reading of the course materials (research papers) to succeed. Required reading materials will be uploaded to Blackboard before the class. All students must present a scientific research article (with the approval of the course instructor), lead discussions (as discussion leaders), and participate by asking questions and evaluating the presenters’ work (as discussion participants). The schedule will be uploaded separately on BB.

ATTENDANCE: Attendance is a requirement and vital to participate in class activities that are graded continuously. Attendance is graded. You are expected to come to class on time. You will incur 50% deductions in your attendance for being late. If you are unable to attend a particular class, you must provide a TAMIU-approved excuse within SEVEN days of a missed class. If you have assigned course activities on that specific day, you must reschedule your presentation by swapping with a classmate. You will get an excused or extended deadline (based on the assignment) for a missed class ONLY when a TAMIU-approved excuse is provided. Please refer to the Student Handbook (https://www.tamiu.edu/scce/studenthandbook.shtml): Appendix A. Attendance Rule for acceptable documents for excused absences. 

OFFICE HOURS: Please see the top of page 1 for student (office) hours. I have an open-door policy, so you can stop by anytime. Meeting time can also be arranged by appointment: in person OR (under certain circumstances only) virtually on Blackboard in Virtual Meeting Space.
The second preferred contact method will be by email (at ruvini.pathirana@tamiu.edu).

  • Students must be aware that email communication does not replace face-to-face communication (i.e., meetings during office hours or by appointment). Students must plan their communication with the instructor accordingly and leave enough time to respond.

  • Students should not expect immediate responses, particularly around assignment due dates or exam dates. Failure to leave a reasonable amount of time for an instructor to reply constitutes a failure of the student’s obligation. Students should be aware that faculty (professors, instructors, lecturers, etc.) receive a very high volume of emails daily. Faculty typically teach more than one course while involving other academic activities such as research and/or service. Therefore, respect everyone's time. 

  • All student emails will be answered within THREE business days of receiving the email. Send a courtesy reminder if you do not receive a response email after three days. Emails received over the weekend will be answered by the next business day.

  • To help prioritize emails, include the course code and a short subject line in each email. Also, remember to mention your name (first and last name) and TAMIU student number in the signature line.

CELL PHONE USE: Please MUTE cell phones or keep silent mode during lectures.  If the occasion should arise where an individual must use their cell phone as a courtesy to their fellow students and the instructor, please excuse yourself from the classroom. Under no circumstances should a cell phone be used during an examination.

SYLLABUS: Any changes to the syllabus/course information, or schedule will be updated on Blackboard promptly.

IN-CLASS ACTIVITIES & ASSIGNMENTS: Complete and submit all assigned coursework by the scheduled due date.  Communicate immediately issues that impede your ability to participate/complete assignments. Deadlines are time-sensitive, and your immediacy in communicating with me will be critical to your success. *Note: 10% of the earned points will be deducted for late submissions. 

ARTIFICIAL INTELLIGENCE (AI) USE POLICY

Any assignment required to submit must be your own. Reading and Writing is integral to thinking. It is also challenging. Part of treating others with respect is giving appropriate credit for ideas and scholarly work. Therefore, prompt-based generative AI tools like ChatGPT or CodePilot (and many more) are not PERMITTED in this course to generate new content. 

You are free to use spell check, grammar check, and synonym identification tools such as Grammarly, ProWritingAid, MS Word, etc. to enhance the clarity and readability of your writeup. 

In any case of suspicion, the instructor reserves the right to request an oral explanation of the write-up/answers and additional supportive assignments.

Program Learning Outcomes

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Student Learning Outcomes

This course aims to enhance students’ awareness and proper use of scientific research publications to enhance skills in handling personal, professional, and societal issues.

Upon the successful completion of this course, students will be able:

1. To integrate factual and conceptual information into understanding scientific data in a specific area of interest.

2. To effectively communicate scientific understanding orally and in writing.

3. To engage in active reading and critically analyze a scientific article

4. Acquire an interest in learning more about medical microbiology and put the knowledge to good use in your future career and personal life.

Important Dates

Visit the Academic Calendar (tamiu.edu) page to view the term's important dates.

Textbooks

Other Course Materials

To go to the bookstore, click here.

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Grading Criteria

GRADE PERCENTAGE
A 90 - 100
B 80 - 89.9
C 70 - 79.9
D 60 - 69.9
F Below 60

Course Grading

ASSIGNMENT CRITERIA PERCENT CONTRIBUTION
Active Participation (Attendance, Discussions) 10 %
Written Assignments & Peer Evaluations 30 %
Professional Preparation (CV, Cover Letter, Personal Statement) 20 %
Presentation of a Scientific Paper 40 %

Schedule of Topics and Assignments

Day Date Agenda/Topic Reading(s) Due
Thu 1/23 Syllabus
Introduction (Elevator Pitch)
Student Grouping
What is scietific literature? How to retrieve scientific information?
Reading Assignment 1
Thu 1/30 Research Seminar Reading Assignment Homework DUE
Thu 2/6 Student Presentation 1
Thu 2/13 Student Presentation 2
Thu 2/20 Student Presentation 3
Thu 2/27 Student Presentation 4 Reading Assignment 2
Thu 3/6 Professional Preparation: CV, Cover Letter, Personal Statement Reading Assignment 2 Homework DUE
Thu 3/13 SPRING BREAK - No Class
Thu 3/20 Student Presentation 5 CV, Cover Letter, Personal Statement DUE
Thu 3/27 Student Presentation 6
Thu 4/3 Setting SMART Goals
Professional Preparation: STEM Jobs
Thu 4/10 Student Presentations 7
Thu 4/17 Student Presentations 8 Reading Assignment 3
Thu 4/24 Student Presentations 9
Thu 5/1 LAST CLASS DAY
Research Seminar
Reading Assignment 3 Homework DUE

University/College Policies

Please see the University Policies below.

COVID-19 Related Policies

If you have tested positive for COVID-19, please refer to the Student Handbook, Appendix A (Attendance Rule) for instructions.

Required Class Attendance

Students are expected to attend every class in person (or virtually, if the class is online) and to complete all assignments. If you cannot attend class, it is your responsibility to communicate absences with your professors. The faculty member will decide if your excuse is valid and thus may provide lecture materials of the class. According to University policy, acceptable reasons for an absence, which cannot affect a student’s grade, include:

  • Participation in an authorized University activity.
  • Death or major illness in a student’s immediate family.
  • Illness of a dependent family member.
  • Participation in legal proceedings or administrative procedures that require a student’s presence.
  • Religious holy day.
  • Illness that is too severe or contagious for the student to attend class.
  • Required participation in military duties.
  • Mandatory admission interviews for professional or graduate school which cannot be rescheduled.

Students are responsible for providing satisfactory evidence to faculty members within seven calendar days of their absence and return to class. They must substantiate the reason for the absence. If the absence is excused, faculty members must either provide students with the opportunity to make up the exam or other work missed, or provide a satisfactory alternative to complete the exam or other work missed within 30 calendar days from the date of absence. Students who miss class due to a University-sponsored activity are responsible for identifying their absences to their instructors with as much advance notice as possible. 

Classroom Behavior (applies to online or Face-to-Face Classes)

TAMIU encourages classroom discussion and academic debate as an essential intellectual activity. It is essential that students learn to express and defend their beliefs, but it is also essential that they learn to listen and respond respectfully to others whose beliefs they may not share. The University will always tolerate different, unorthodox, and unpopular points of view, but it will not tolerate condescending or insulting remarks. When students verbally abuse or ridicule and intimidate others whose views they do not agree with, they subvert the free exchange of ideas that should characterize a university classroom. If their actions are deemed by the professor to be disruptive, they will be subject to appropriate disciplinary action (please refer to Student Handbook Article 4).

TAMIU Honor Code: Plagiarism and Cheating

As a TAMIU student, you are bound by the TAMIU Honor Code to conduct yourself ethically in all your activities as a TAMIU student and to report violations of the Honor Code. Please read carefully the Student Handbook Article 7 and Article 10 available at https://www.tamiu.edu/scce/studenthandbook.shtml.

We are committed to strict enforcement of the Honor Code. Violations of the Honor Code tend to involve claiming work that is not one’s own, most commonly plagiarism in written assignments and any form of cheating on exams and other types of assignments.

Plagiarism is the presentation of someone else’s work as your own. It occurs when you:

  1. Borrow someone else’s facts, ideas, or opinions and put them entirely in your own words. You must acknowledge that these thoughts are not your own by immediately citing the source in your paper. Failure to do this is plagiarism.
  2. Borrow someone else’s words (short phrases, clauses, or sentences), you must enclose the copied words in quotation marks as well as citing the source. Failure to do this is plagiarism.
  3. Present someone else’s paper or exam (stolen, borrowed, or bought) as your own. You have committed a clearly intentional form of intellectual theft and have put your academic future in jeopardy. This is the worst form of plagiarism.

Here is another explanation from the 2020, seventh edition of the Manual of The American Psychological Association (APA):

“Plagiarism is the act of presenting the words, idea, or images of another as your own; it denies authors or creators of content the credit they are due.  Whether deliberate or unintentional, plagiarism violates ethical standards in scholarship” (p. 254).  This same principle applies to the illicit use of AI.

Plagiarism: Researchers do not claim the words and ideas of another as their own; they give credit where credit is due. Quotations marks should be used to indicate the exact words of another. Each time you paraphrase another author (i.e., summarize a passage or rearrange the order of a sentence and change some of the words), you need to credit the source in the text. The key element of this principle is that authors do not present the work of another as if it were their own words. This can extend to ideas as well as written words. If authors model a study after one done by someone else, the originating author should be given credit. If the rationale for a study was suggested in the discussion section of someone else's article, the person should be given credit. Given the free exchange of ideas, which is very important for the health of intellectual discourse, authors may not know where an idea for a study originated. If authors do know, however, they should   acknowledge the source; this includes personal communications (p. 11). For guidance on proper documentation, consult the Academic Success Center or a recommended guide to documentation and research such as the Manual of the APA or the MLA Handbook for Writers of Research Papers. If you still have doubts concerning proper documentation, seek advice from your instructor prior to submitting a final draft.

TAMIU has penalties for plagiarism and cheating.

  • Penalties for Plagiarism: Should a faculty member discover that a student has committed plagiarism, the student should receive a grade of 'F' in that course and the matter will be referred to the Honor Council for possible disciplinary action. The faculty member, however, may elect to give freshmen and sophomore students a “zero” for the assignment and to allow them to revise the assignment up to a grade of “F” (50%) if they believe that the student plagiarized out of ignorance or carelessness and not out of an attempt to deceive in order to earn an unmerited grade; the instructor must still report the offense to the Honor Council. This option should not be available to juniors, seniors, or graduate students, who cannot reasonably claim ignorance of documentation rules as an excuse. For repeat offenders in undergraduate courses or for an offender in any graduate course, the penalty for plagiarism is likely to include suspension or expulsion from the university.
    • Caution: Be very careful what you upload to Turnitin or send to your professor for evaluation. Whatever you upload for evaluation will be considered your final, approved draft. If it is plagiarized, you will be held responsible. The excuse that “it was only a draft” will not be accepted.
    • Caution:  Also, do not share your electronic files with others. If you do, you are responsible for the possible consequences. If another student takes your file of a paper and changes the name to his or her name and submits it and you also submit the paper, we will hold both of you responsible for plagiarism. It is impossible for us to know with certainty who wrote the paper and who stole it. And, of course, we cannot know if there was collusion between you and the other student in the matter.
  • Penalties for Cheating: Should a faculty member discover a student cheating on an exam or quiz or other class project, the student should receive a “zero” for the assignment and not be allowed to make the assignment up. The incident should be reported to the chair of the department and to the Honor Council. If the cheating is extensive, however, or if the assignment constitutes a major grade for the course (e.g., a final exam), or if the student has cheated in the past, the student should receive an “F” in the course, and the matter should be referred to the Honor Council. Additional penalties, including suspension or expulsion from the university may be imposed. Under no circumstances should a student who deserves an “F” in the course be allowed to withdraw from the course with a “W.”
    • Caution: Chat groups that start off as “study groups” can easily devolve into “cheating groups.” Be very careful not to join or remain any chat group if it begins to discuss specific information about exams or assignments that are meant to require individual work. If you are a member of such a group and it begins to cheat, you will be held responsible along with all the other members of the group. The TAMIU Honor Code requires that you report any such instances of cheating.
  • Student Right of Appeal: Faculty will notify students immediately via the student’s TAMIU e- mail account that they have submitted plagiarized work. Students have the right to appeal a faculty member’s charge of academic dishonesty by notifying the TAMIU Honor Council of their intent to appeal as long as the notification of appeal comes within 10 business days of the faculty member’s e-mail message to the student and/or the Office of Student Conduct and Community Engagement. The Student Handbook provides more details.

Use of Work in Two or More Courses

You may not submit work completed in one course for a grade in a second course unless you receive explicit permission to do so by the instructor of the second course. In general, you should get credit for a work product only once. 

AI Policies

Your instructor will provide you with their personal policy on the use of AI in the classroom setting and associated coursework.

TAMIU E-Mail and SafeZone

Personal Announcements sent to students through TAMIU E-mail (tamiu.edu or dusty email) are the official means of communicating course and university business with students and faculty –not the U.S. Mail and no other e-mail addresses. Students and faculty must check their TAMIU e-mail accounts regularly, if not daily. Not having seen an important TAMIU e-mail or message from a faculty member, chair, or dean is not accepted as an excuse for failure to take important action.

Students, faculty, and staff are encouraged to download the SafeZone app, which is a free mobile app for all University faculty, staff, and students.  SafeZone allows you to: report safety concerns (24/7), get connected with mental health professionals, activate location sharing with authorities, and anonymously report incidents.  Go to https://www.tamiu.edu/adminis/police/safezone/index.shtml for more information.

Copyright Restrictions

The Copyright Act of 1976 grants to copyright owners the exclusive right to reproduce their works and distribute copies of their work. Works that receive copyright protection include published works such as a textbook. Copying a textbook without permission from the owner of the copyright may constitute copyright infringement. Civil and criminal penalties may be assessed for copyright infringement. Civil penalties include damages up to $100,000; criminal penalties include a fine up to $250,000 and imprisonment. Copyright laws do not allow students and professors to make photocopies of copyrighted materials, but you may copy a limited portion of a work, such as article from a journal or a chapter from a book for your own personal academic use or, in the case of a professor, for personal, limited classroom use. In general, the extent of your copying should not suggest that the purpose or the effect of your copying is to avoid paying for the materials. And, of course, you may not sell these copies for a profit. Thus, students who copy textbooks to avoid buying them or professors who provide photocopies of textbooks to enable students to save money are violating the law.

Students with Disabilities

Texas A&M International University seeks to provide reasonable accommodations for all qualified persons with disabilities. This University will adhere to all applicable federal, state, and local laws, regulations and guidelines with respect to providing reasonable accommodations as required to afford equal education opportunity. It is the student's responsibility to register with the Office of Student Counseling and Disability Services located in Student Center 126. This office will contact the faculty member to recommend specific, reasonable accommodations. Faculty are prohibited from making accommodations based solely on communications from students. They may make accommodations only when provided documentation by the Student Counseling and Disability Services office.

Student Attendance and Leave of Absence (LOA) Policy

As part of our efforts to assist and encourage all students towards graduation, TAMIU provides
LOA’s for students, including pregnant/parenting students, in accordance with the Attendance Rule (Section 3.07) and the Student LOA Rule (Section 3.08), which includes the “Leave of Absence Request” form. Both rules can be found in the TAMIU Student Handbook (URL: http://www.tamiu.edu/studentaffairs/StudentHandbook1.shtml).

Pregnant and Parenting Students

Under Title IX of the Education Amendments of 1972, harassment based on sex, including harassment because of pregnancy or related conditions, is prohibited. A pregnant/parenting student must be granted an absence for as long as the student’s physician deems the absence medically necessary. It is a violation of Title IX to ask for documentation relative to the pregnant/parenting student’s status beyond what would be required for other medical conditions. If a student would like to file a complaint for discrimination due to his or her pregnant/parenting status, please contact the TAMIU Title IX Coordinator (Lorissa M. Cortez, 5201 University Boulevard, KLM 159B, Laredo, TX 78041,TitleIX@tamiu.edu, 956.326.2857) and/or the Office of Civil Rights (Dallas Office, U.S. Department of Education, 1999 Bryan Street, Suite 1620, Dallas, TX 75201-6810, 214.661.9600). You can also report it on TAMIU’s anonymous electronic reporting site: https://www.tamiu.edu/reportit.

TAMIU advises a pregnant/parenting student to notify their professor once the student is aware that accommodations for such will be necessary. It is recommended that the student and professor develop a reasonable plan for the student’s completion of missed coursework or assignments. The Office of Equal Opportunity and Diversity (Lorissa M. Cortez, lorissam.cortez@tamiu.edu) can assist the student and professor in working out the reasonable accommodations. For other questions or concerns regarding Title IX compliance related to pregnant/parenting students at the University, contact the Title IX Coordinator. In the event that a student will need a leave of absence for a substantial period of time, TAMIU urges the student to consider a Leave of Absence (LOA) as outlined in the TAMIU Student Handbook. As part of our efforts to assist and encourage all students towards graduation, TAMIU provides LOA’s for students, including pregnant/parenting students, in accordance with the Attendance Rule and the Student LOA Rule. Both rules can be found in the TAMIU Student Handbook (https://www.tamiu.edu/scce/studenthandbook.shtml).

Anti-Discrimination/Title IX

TAMIU does not discriminate or permit harassment against any individual on the basis of race, color, sex, religion, national origin, age, disability, genetic information, veteran status, sexual orientation or gender identity in admissions, educational programs, or employment. If you would like to file a complaint relative to Title IX or any civil rights violation, please contact the TAMIU Director of Equal Opportunity and Diversity/Title IX Coordinator, Lorissa M. Cortez, 5201 University Boulevard, Killam Library 159B, Laredo, TX 78041,TitleIX@tamiu.edu, 956.326.2857, via the anonymous electronic reporting website, ReportIt, at https://www.tamiu.edu/reportit, and/or the Office of Civil Rights (Dallas Office), U.S. Department of Education, 1999 Bryan Street, Suite 1620, Dallas, TX 75201-6810, 214.661.9600.

Incompletes

Students who are unable to complete a course should withdraw from the course before the final date for withdrawal and receive a “W.” To qualify for an “incomplete” and thus have the opportunity to complete the course at a later date, a student must meet the following criteria:

  1. The student must have completed 90% of the course work assigned before the final date for withdrawing from a course with a “W”, and the student must be passing the course;
  2. The student cannot complete the course because an accident, an illness, or a traumatic personal or family event occurred after the final date for withdrawal from a course;
  3. The student must sign an “Incomplete Grade Contract” and secure signatures of approval from the professor and the college dean.
  4. The student must agree to complete the missing course work before the end of the next long semester; failure to meet this deadline will cause the “I” to automatically be converted to an “F”; extensions to this deadline may be granted by the dean of the college. This is the general policy regarding the circumstances under which an “incomplete” may be granted, but under exceptional circumstances, a student may receive an incomplete who does not meet all of the criteria above if the faculty member, department chair, and dean recommend it.

WIN Contracts

The Department of Biology and Chemistry does not permit WIN contracts. For other departments within the college, WIN Contracts are offered only under exceptional circumstances and are limited to graduating seniors. Only courses offered by full-time TAMIU faculty or TAMIU instructors are eligible to be contracted for the WIN requirement. However, a WIN contract for a course taught by an adjunct may be approved, with special permission from the department chair and dean. Students must seek approval before beginning any work for the WIN Contract. No student will contract more than one course per semester. Summer WIN Contracts must continue through both summer sessions.

Student Responsibility for Dropping a Course

It is the responsibility of the student to drop the course before the final date for withdrawal from a course. Faculty members, in fact, may not drop a student from a course without getting the approval of their department chair and dean.

Independent Study Course

Independent Study (IS) courses are offered only under exceptional circumstances. Required courses intended to build academic skills may not be taken as IS (e.g., clinical supervision and internships). No student will take more than one IS course per semester. Moreover, IS courses are limited to seniors and graduate students. Summer IS course must continue through both summer sessions.

Grade Changes & Appeals

Faculty are authorized to change final grades only when they have committed a computational error or an error in recording a grade, and they must receive the approval of their department chairs and the dean to change the grade. As part of that approval, they must attach a detailed explanation of the reason for the mistake. Only in rare cases would another reason be entertained as legitimate for a grade change. A student who is unhappy with his or her grade on an assignment must discuss the situation with the faculty member teaching the course. If students believe that they have been graded unfairly, they have the right to appeal the grade using a grade appeal process in the Student Handbook and in the Faculty Handbook.

Final Examination

All courses in all colleges must include a comprehensive exam or performance and be given on the date and time specified by the Academic Calendar and the Final Exam schedule published by the Registrar’s Office. In the College of Arts & Sciences all final exams must contain a written component. The written component should comprise at least 20% of the final exam grade. Exceptions to this policy must receive the approval of the department chair and the dean at the beginning of the semester.

Mental Health and Well-Being

The university aims to provide students with essential knowledge and tools to understand and support mental health. As part of our commitment to your well-being, we offer access to Telus Health, a service available 24/7/365 via chat, phone, or webinar. Scan the QR code to download the app and explore the resources available to you for guidance and support whenever you need it. The Telus app is available to download directly from TELUS (tamiu.edu) or from the Apple App Store and Google Play.