Course Description: 

In this course, we will read, analyze and discuss original research papers involving modern molecular and biochemical methods. These papers will be chosen to cover a variety of topics of high current interest. Papers will range from topics such as the discovery and reconstitution of essential biological pathways to disease mechanisms through fundamental principles of genomic organization and control.  In all cases, the emphasis will be on underlying biochemical mechanisms and experimental approaches. The class periods will involve a mixture of discussions (both in large and small groups) and interactive problem solving and analyses. 

Course goals and learning outcomes:

• Demonstrate an understanding of selected biochemical principles as they apply to real situations
• Demonstrate an understanding of how fundamental mechanisms at the molecular level can contribute to phenomena at the organismal level
• Demonstrate an understanding of the applicability, strengths and weaknesses of major methods in molecular biochemistry
• Demonstrate the ability to analyze molecular and biochemical information critically, including analysis of the experimental logic, the effectiveness of methods, the meaning of observational and experimental data, and the appropriateness of the conclusions
• Effectively communicate biochemical information in both oral and written form
  
• The advantages of teaching a course based on the scientific literature are many:
• The primary literature provides detailed concrete examples, which are often more interesting and give better insight than simplified text-book examples. The real world is amazingly complex, and getting a feel for complex, real problems is an important step in your intellectual development.
• Analysis of experimental logic will teach you critical thinking skills that are useful for dealing with complex, real-world problems.
• The methods of modern molecular biochemistry are the tools of the 21^st century. It’s a good idea to gain a deep understanding of their power and limitations.

Block I : The first block will focus on critical analyses of papers. We will start with paper anatomy and the peer review process to set the stage of the nuts and bolts of publishing work.  You will also present a paper in preparation for your final grant presentation (see below).  Together we will discuss and dissect strengths and weaknesses of papers which will allow you to propose future directions in preparation for your final grant proposal (see below) and grant panel critique.  We will examine seminal genomics papers and current therapeutics papers as key examples. 

Block II: The second block will focus on scientific application and significance. As such, we will read and discuss papers that use biochemistry for purposes related to energy and materials science. These discussions will allow us to think ‘outside the box’ of some traditional uses of biochemistry and will help you to formulate your own application/ justification for your final grant proposal (see below).

Course requirements

Attendance and Participation: Because this class depends on interactions, attendance is expected as is regular contribution to the class discussions. If you will be unable to attend a class, notify us in advance by email or voicemail. Anyone who is present every day and is involved in the class meets expectations (see scoring on next page). Deductions will be made for unexcused absences, if it appears that a student is not contributing to discussions, or for unacceptable work on writings and presentations.

Graded writings and quizzes: There will be at least one writing assignment each week.  The writing assignments will focus on analyses (goals 1-4). Writings involve exercises such as analyzing or commenting on a scientific paper, suggesting further experimental approaches, or considering the broader implications of some finding. You will not be expected to memorize the details of particular papers but rather to understand experimental studies. 

Weekly Presentations: Each week a pair of students will be responsible for preparing an oral presentation of a paper we are reading. The presentations should be brief (roughly 10-15 min) and focused, and will serve as a launching point for discussion. You will turn in your powerpoint presentation. You will be evaluated on presentation depth of understanding, clarity and style. In addition, you will be given feedback on your presentation for continued improvement over the course of the semester in preparation for your grant proposal presentation. 

Grant Proposal: Your final semester long project will be a formal grant proposal. You will chose one primary paper and write a grant proposal expanding on a specific aspect of that paper (i.e. a new direction with proposed experiments, or parallel experiments in a new organismal system chosen for a specific purpose, etc.) We will help you to focus the scope of your proposal. This will be a semester-long assignment; the final grant proposal will be due at the end of the semester with deadlines for individual sections throughout the semester. Details for the format will be provided in class.

Final Presentation: There will be a final presentation to accompany the grant proposal at the end of the semester. Each student will give a 15 minute presentation with 5 minutes for questions explaining the background and significance of their proposal, as well as their specific aims and proposed research plans. These presentations will be peer-evaluated. Each presentation will be ‘scored’ on whether or not it should be funded; funded proposals are eligible for a prize!

Grading:

Class Participation                  20%

Graded Writings and quizzes 15%

Weekly Presentations              15%

Grant Proposal                        25%

Final Presentation                   25%

Grades will be given based on whether the student met the expectations of the assignment, using a scale of 0 – 3 as follows:

3 = Exceeds goal.  Performs the task at the level expected of a professional in the field.  There are no significant errors or misunderstandings, the work is clear and comprehensive, and it demonstrates sophisticated thinking (insight, analytical ability, integration etc…).

2 = Meets goal.  The work is performed with minimal errors or misunderstandings and is of overall good quality.  It could be improved, however, with increased analysis, integration, sophistication or rigor.

1 = Approaches goal.  The guidelines of the assignment were followed and the work shows evidence of progress towards meeting the goal.  Nevertheless, it may be unclear, partially incorrect, or reflect misunderstandings.

0 = No evidence of achieving goal.  The work was either not done, or done so poorly that one cannot discern sufficient progress towards achieving the goal.

These grades correlate loosely to letter grades as follows:

A         Meets the goals of almost all assignments, occasionally exceeding the goals (2.3+)

A-/B+  Meets the goals of all assignments (~2)

B         Meets the goals of most of the assignments (~1.7+)

C         Typically approaches goals, only occasionally meeting them (~1.3)

D         Approaches goals, but on too many assignments shows no evidence of achieving goals (0.5-1)

F          No evidence of achieving goals on more than half the assignments (< 0.5)

We take into account progress over the semester.  We typically expect students to have more trouble meeting the goals early in the semester, but as their skills develop, they can meet the goals more easily.  Demonstrating full ability to meet the goals at the end of the semester carries a lot of weight in the grading.

Students with disabilities:

In compliance with Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act, reasonable accommodation will be provided to students with documented disabilities on a case-by-case basis. Students must register with Student Disability Services with the Office of Academic Support Services (607-274-1005, TDD 607-274-7319, acssd@ithaca.edu) and provide appropriate documentation to Ithaca College before any academic adjustment will be provided. 

Academic Honesty:

All the work in this class must be your own, unless stated otherwise.  For many of the assignments, it is expected that you will discuss ideas with your classmates.  Nevertheless, the final work must be your own, and must reflect your own analysis and interpretation. 

Confirmed instances of academic misconduct will result in a zero for that assignment/quiz and referral to the school judiciary system.  Please refer to the Student Handbook for a detailed description of the policies regarding student academic conduct.  If you have a question about what constitutes plagiarism, refer to the following web site:  http://www.ithaca.edu/library/htmls/plagiarism.htm