Principles of Modern Biology/Designing Drugs

Course Overview and Syllabus

Faculty:                                    Dr. Joanne Pratt, AC407
Email:                                        joanne.pratt@olin.edu
Office hours:                            During lab period and by appointment
Lab Specialist:                       Dr. Sadie Aznavoorian-Cheshire, AC406
Email:                                        sadie.aznavoorian-cheshire@olin.edu

Meeting times:
Discussion/Lecture                Tues/Fri 1:30-3:10 AC417
Lab                                           Tue: 3:20-6:00 AC406

Learning Outcomes

Students will learn how to apply concepts and laboratory skills that are currently used in biological research to solve problems in health and disease and drug discovery and development. (competency developed: critical thinking, assessed through homework problems, midterm and final assessments, lab report)

Students will develop technical writing and oral communication skills and demonstrate an ability to utilize scientific resources (literature, databases) to research and present a topic of interest. Students will present their laboratory-based research and literature/media-based research in a variety of written and oral formats. (competency developed: communication, assessed through class discussion, homework problems, lab notebook, lab report, poster, media discussion, global health discussion)

Students will gain experience with the basics of designing, conducting and evaluating laboratory experiments. (competencies developed: design and critical thinking, assessed through lab report, lab notebook, certain exam questions)

Students will demonstrate an understanding of the larger societal context in which biological concepts, tools and research play a role in everyday life and medicine, and how societal context shapes the advancement of research in biology and medicine. (competency developed: context, assessed through oral presentations, certain exam questions)

Students will work in teams throughout the semester. These teams will perform the lab experiments each week, prepare and deliver oral presentations and write lab reports and lab notebooks. (competency developed: collaboration and teamwork, assessed through teammate feedback form, lab report & notebooks)

Course Resources 

Book
Life: The Science of Biology

Website
The course website is found on Blackboard (blackboard.olin.edu).   You will log into the website to complete weekly homework questions. There are many resources available through the site, including links to helpful videos and animations, assignment documents and the lab manual.

Lab
Laboratory Manual for Modern Biology: A manual of general reference information will be made available immediately on Blackboard (Lab tab), followed by weekly installments of upcoming protocols and procedures. Last year’s lab manual is available on the wordpress site, so you can read ahead, but changes may be made to the protocols each week, so Blackboard will have the most up to date information.
Lab notebooks are available at Frank’s.

Assessments and Grading

Final grade will be based on the following:
PIPI                                                                15%
YOGA                                                               5%
Homework                                                   15%
Midterm exam                                            20%
Final exam                                                   20%
Final group lab report                               15%
Lab notebook                                              10%

PIPI

participation, initiative, professionalism and improvement
PIPI counts 15% towards your final grade, and it encompasses critical behaviors that are important for success in any endeavor. It will be determined based on objective measures, including completion of all assignments on time, active participation during class and lab periods and feedback from your lab group members. Some specific factors that may affect PIPI are described below.

Attendance in laboratory sessions is required. Students are also expected to attend each classroom session. Students who opt to miss class meetings are expected to dedicate the equivalent number of classroom hours to advancing their knowledge of biology, and to demonstrate their efforts to the instructors (for example, by giving a presentation to the class, writing a report, creating class materials, etc.) This will directly affect PIPI scores. All of the components of PIPI will factor into the score. For example, a student who participates in class discussions yet demonstrates unprofessional behavior (regularly shows up late, sleeps, works on non-class related activities on their computer) or produces unprofessional assignments (late, sloppy, full of typos, didn’t follow instructions) will receive a poor PIPI grade. A student who attends all class sessions and does well on assignments, but does not participate in class discussions will have below average PIPI score.

Y.O.G.A.

 Your Own Goals Assignment
For this assignment, students set their own learning goals and develop a plan to achieve and assess them. The objective is to give you some control over the outcomes of this course, and you will control one (small) portion (5%) of your course grade. Students enhance their short-term motivation, attain a long-term vision and develop an improved capacity for self-directed learning. This assignment is done in Three Phases: Phase One: Statement of Goals, Phase Two: Revision and Assessment plan, Phase Three: Final Assessment and Reflection.

 

Homework Assignments: Online Quizzes

Online quizzes and class discussion will provide a means to demonstrate understanding of concepts and to identify areas that require more explanation. Students will complete the online quizzes through the blackboard website by midnight each Monday and Thursday, unless otherwise indicated. Students may work with a partner on these quizzes (you must indicate who you worked with on the quiz), and may use books, notes and the internet and spend as much time as needed. These quizzes will count toward your homework grades. In most weeks there will be two quizzes to complete. Students should refer to the syllabus below to see which chapters they are expected to complete prior to each class period.

Important! If you log in to start your homework and then are idle for some time, Blackboard will reset, and you will lose your work. You may want to write your responses in a text or word document and paste them into Blackboard to avoid frustration.

Students will also be assigned specific sections of the lab manual to read prior to lab periods each week. Questions on lab procedures and results will be included in “clicker questions” posed during class periods.

Homework Assignments: Media Discussions

Each lab group will be responsible for leading a discussion on a topic in contemporary biology, e.g. identified from news or science journal reports. Groups will email their article to all class members by 12 PM (noon) on the day prior to their discussion. All class members are expected to read the article(s) and to come to class prepared to discuss them. Student presenters/discussion leaders are expected to have some additional background knowledge of the topic to be discussed. Media discussions will last approximately 20-30 minutes. A handout with more information will be distributed.

Homework Assignments: IQI and Other

In addition to the online quizzes, there will be several other homework assignments throughout the semester. Other assignments include (but are not limited to) a bioinformatics assignment, a global health presentation, and an optional poster presentation. More information on these assignments will be distributed.

Assignments that involve watching a video or listening to a podcast may include an IQI (Insights, Questions, and Implications) component. IQI is an approach to learning that allows for more lively discussion and learning in the classroom.  When you are asked to read an article or watch a film outside of class, you should be an investigator and observer who yields between 6-10 insights, questions and implications to be shared in class as discussions start to evolve that your curiosity and depth of thinking.  It will also confirm that you are actively engaged in outside work. These will be graded as P/NR, and not sending these in might have a negative impact on your class participation grade.

Exams

There will be a midterm and final exam to measure learning during the semester. These will be untimed take-home exams. Textbooks, notebooks, lab manual, Google, etc. may be used to find information during the exams. Discussing the exam with anyone during the exam period is not allowed. Emphasis will be placed on your understanding of concepts, ability to apply this understanding to solve problems and your ability to find relevant information and communicate your understanding, rather than memorization of facts. The exams will cover material presented in the textbook, lab and covered in class, including media discussions.

 

Laboratory notebooks and lab reports

The laboratory grade will have two major contributing components. A final group lab report is due the week following completion of the lab activities. The final lab report is based on the entire lab project and counts 15% toward your final grade. A document describing the components of the lab report will be available. A midterm lab report that covers the first half of the laboratory project, namely the cloning, transformation, DNA preparation, restriction digest, PCR and agarose gel electrophoresis results will be due the week after these procedures are completed. This lab report will count as two homework grades.

In addition each team will keep a lab notebook. This must be a hard copy; writing on the electronic lab manual, then printing it out at the end of the semester, is not acceptable. This will be a record of all experimental steps taken during regular lab hours or between lab sessions. Lab notebooks will be read periodically by lab instructors, TAs and your peers, and will be assessed two or three times during the semester. Completed lab notebooks are due immediately after the completion of lab activities, at which time they will receive an official grade. They count 10% toward your final course grade.

Academic Integrity and Expectations

Students who do not attend classes are responsible for all materials presented or discussed in class and for announcements made during class. You should check the Bb site or ask classmates for information that you may have missed. Portable computers may only be used in class to take notes or to engage in assignments that are integral to the class session. Email, messaging in class, surfing the internet, etc. are expressly not permitted as a classroom activity. This will be strictly enforced.

All students are expected to behave with high levels of academic integrity. This includes the following:

  • Not presenting the work of others as one’s own. This includes presenting the work of others with no or minimal changes (plagiarism)*.
  • Providing appropriate citations for all information presented. This includes print-based, web-based and personal communications. Citations are required for both text and figures.
  • Sharing credit with collaborators (and refraining from working with others if you have been requested to work independently).
  • Preserving integrity of laboratory data, including using appropriate data collection and recording methods, and not falsifying or fabricating results.
  • Adhering to the Olin Honor Code.

*This entire section on academic integrity was borrowed from Debbie Chachra’s syllabus.

Topics to be addressed

Emphasis will be on structure, function, and regulation at the molecular level. For example, the structure and regulation of genes, properties and synthesis of proteins, the organization of the cell and multi-cellular systems will be studied in detail. These topics will be applied to understand the molecular differences between organisms, the molecular basis of disease and the molecular approaches to drug development.

5 core concepts in Biology have been identified in a study conducted by AAAS and NSF (visionandchange.org) as central to undergraduate life science education, and these concepts will be unifying themes throughout the semester.

  1. EVOLUTION: The diversity of life evolved over time by processes of mutation, selection, and genetic change.
  2. STRUCTURE AND FUNCTION: Basic units of structure define the function of all living things.
  3. INFORMATION FLOW, EXCHANGE, AND STORAGE: The growth and behavior of organisms are activated through the expression of genetic information in context.
  4. PATHWAYS AND TRANSFORMATIONS OF ENERGY AND MATTER: Biological systems grow and change by processes based upon chemical transformation pathways and are governed by the laws of thermodynamics.
  5. SYSTEMS: Living systems are interconnected and interacting.

In addition to the content covered in the ebook, the following topics will be covered:

  • Drug discovery, development and clinical trials
  • Natural Defenses against Disease: Innate and adaptive immunology
  • Scientific Ethics and Ethical Implications of Biological Research
  • Global health
  • Bioinformatics
  • Cancer research and treatment
 A detailed weekly schedule can be found here:  Weekly Schedule_ModBio

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