MCB422 relies entirely on computer simulations of classical genetic experiments, and features three major topics:
a) Cricket (phage genetics) features classical experiments deducing the nature of genes and the genetic code as originally performed by Seymour Benzer, Sir Francis Crick, and many others;
b) MendelStar ( Mendelian genetics) features the few basic rules of classical genetics first described by Gregor Mendel and some of the more interesting exceptions;
c) PathFinder (yeast genetics) features modern experiments designed to genetically dissect molecular signaling pathways of the yeast cell cycle.
It is your task to solve 18 genetic problems (6 per topic) by developing an experimental strategy and succesfully executing it. You will be assessed not only on successful completion of the task at hand but also on how you documented your experimental findings in your notebook report.

Objectives:
- to acquaint you with the tools and principles of Genetics -- and how to apply them!
- to foster your "critical thinking" skills
- to leave you with understandings that will persist beyond the end of the semester

Philosophy: Teaching is a cooperative enterprise. You'll be lead to water, but you're expected to take responsibility for much of the drinking. Make sure you're playing an active role in your education.

Class time is brief and precious, and the information to be communicated to students is important. Since students are novices and the professor is an expert, it makes sense to tell them what they need to know. With this in mind, the lecture is a common form of university instruction. Lecturing, however, induces passivity of thought and is not necessarily the best way of engaging students in the presented ideas and information.

Note that this course is about "critically thinking" your way through problems. This simply cannot be achieved by having someone else, no matter how knowledgeable or well-intentioned, tell you what to do. We will seek to guide you to realizations and insights, but there's no point in handing them out -- this defeats the purpose of the course and robs you of the opportunity to develop your own critical thinking skills.

This course is not about clicking a "mouse", pushing plates, sterilizing loops. It's about learning how to solve problems and generate new ideas. Expect to invest a lot of brainpower in it, and expect to be frustrated on occasion. We'll do our best to help you past your sticking points, but that's not the same as carrying you and you shouldn't expect intellectual handouts. This is NOT an easy course.

Class/Lab time: Since the problems can be solved from any computer conneted to the web you don't have to be in the lab/class to actually do the work, except for quizzes, which will be given at 9:45 am on the scheduled day.
The main purpose of the lab/class time is helping you to develop a successfull experimental strategy for solving each problem. Keep in mind that the hard part of the task is the development of experiments - not their execution.
- Regard class/lab time similar to an office our - as it provides an open forum for discussing strategies of how to solve any problems you are facing.
- We strongly encourge students to work in groups (>3) so that you can discuss the problems and possible solutions, and help each other to learn how to do various experiments. If you identify yourself as a group, we will assign all group members the same problem, but you must still write up your results on your own.
- The instructors will be in the labs to help you solving the problems by pointing you in the right direction - not by giving you the answer!

Cooperation, teamwork: In general, group study and exploration are fantastic approaches to learning the material. In this class, it is often critical to team up with classmates. Approaching problems by discussing ideas with classmates is highly encouraged and beneficial to all involved. We expect you to teach and learn from your partners the same way we try to teach you.
"Do this" is not an educational advice; guide each other to insights by questioning and discussing. You may also find that you learn as much by teaching as you do from exploring on your own.

Rules of engagement: A short outline describing how we expect to interact with you to help you solving the problems; what we expect of you and what you should expect of us.

Grading: 90-100 = A, 80-89=B, 70-79 = C, 55-69 = D, <55 = E
Final score will be made up from the following components:
Notebook reports: 90%, 18 problems to be solved (6 per module)
Quizzes: 10%, 6 quizzes (2 per module)
There will be no final exam.

Quizzes: Generally 2 per module. These test your preparation to embark on the modules or your comprehension of what's going on in them. Take them serious.

Notebook reports:
For each module, you will have to solve 6 problems by developing and executing an experimental strategy. Grades will be derived on the basis of your notebook reports. You will be assessed not only on successful completion of the task at hand (creation of a strain, identification of genotype/genetic phenomenon, etc.) but also on how you documented your findings in your notebook report. General features are explicitly laid out in a notebook example, and include

Rationale: Explain the logic why and how a series of experiments will allow you to deduce the answer to the problem question at hand. This is not about the experiments themselves; it's about the big idea and the way genetics works and how you can utilize it to gain new insights and solve your problem.
Experimental approach and result: Here you document what you're actually doing and how you are implementing your Big Thinking from the rationale. Basicaly this is a documentation of the individual experiments, their controls, and their results.
Summarize your observations concisely, use data tables if possible. Explain how your results relate to your rationale.
Conclusion: Tie it all up. Document how did you answer the Big Question. Carefully distinguish observations from your interpretation.

No discussions because you "almost" got grade X. Earn the grade you want by starting NOW. Benefit of the doubt and suchlike will already have been given, so we'll have nothing left to offer you if you come up short.

Note that any work turned in with only your name on it is presumed to be solely your work; if you worked as a team, the contributions of your teammate should be clearly delineated. Outside sources of assistance (tutors, etc.) should be clearly and exhaustively acknowledged. Quoted or paraphrased material should be suitably referenced.

Late work:
You snooze - you lose - it's college. Barring a MD-certified or otherwise exceptional and documented excuse, late work will not be accepted. All notebook reports are due by 11 p.m. on the indicated days (see calendar) using electronic submission. Obviously if there is a computer glitch, we'll make allowances. However, risks you undertake by waiting 'till the last moment are yours, not ours.

Resubmissions:
Since writing Notebook reports will require some practice, the first Cricket assignment (problem 3) can be re-submitted for full credit. Cricket assignments 4-5 can be resubmitted for regrading to get half the points lost. Regrades will not be considered for Cricket assignments 6-8, all Mendlestar and all Pathfinder assignments.

Honors: [not available Fall 2006]
To earn honors credit, students must contract to perform advanced scenarios for each module. In Cricket, this constitutes choosing one of several advanced problems in genotype deduction; in Mendelstar, it entails working with pathways of more than a single step, and in Pathfinder, it involves assigning identities 'real' components of the yeast mating type pathway. In each case, scores assigned to the honors scenarios will be averaged in as 15% of the total module score. All other scoring will be exactly as described above.

Instructors:
Konrad: kez@neurobio.arizona.edu
Konrad E. Zinsmaier, Ph.D.
Associate Professor
Arizona Research Laboratories Division of Neurobiology
Gould Simpson Bld, Room 627
phone: 529-1343
Office Hours: "Open-door" policy. Contact me by email and I will try to answer promptly.
Zachary Archer: zarcher@email.arizona.edu
Pat Hollinger: dogmod@email.arizona.edu

Technical support for software:
Konrad: kez@neurobio.arizona.edu
Note: the more complete your description of your last activity, the exact text of error messages, etc. the more likely I will be able to assist you and/or remedy the problem.
Bruce Patterson: patterso@u.arizona.edu (only available as a last resort)

Background: You should be enrolled in or have already taken ECOL320 (Genetics), PL S312 or equivalent.

Textbook: A genetics textbook may be necessary for you to review and read background material for the three modules (particularly Pathfinder which requires understanding yeast genetics and tetrad analysis). Any textbook used recently in Genetics 320 or 325 will be sufficient. The recommended textbook is: Hartl & Jones, 2005, Genetics: Analysis of Genes and Genomes, 6th ed., Jones and Bartlett Publishers.

Absence: Since the problems for each module can be solved from any computer, you don't have to be in the computer lab except for quizzes, which will be given at 9:45 on the scheduled day and cannot be taken except in the lab. However, note that rules for late submission of notebook reports will be strictly enforced.
All holidays or special events observed by organized religions will be honored for those students who show affiliation with that particular religion.
Absences pre-approved by the UA Dean of Students (or Dean's designee) will be honored.

Cheating and Plagiarism:
University of Arizona Student Code of Conduct and other policies apply and can be found in the following website: http://dos.web.arizona.edu/uapolicies/.
Principle: (from the above website) Integrity is expected of every student in all academic work. The guiding principle of academic integrity is that a student's submitted work must be the student's own. This principle is furthered by the student Code of Conduct and disciplinary procedures established by ABOR Policies 5-308 - 5-403, all provisions of which apply to all University of Arizona students. This Code of Academic Integrity (hereinafter "the Code") is intended to fulfill the requirement imposed by ABOR Policy 5-403.A.4 and otherwise to supplement the student Code of Conduct as permitted by ABOR Policy 5-308.C.1. When you sign your name to your work, you are signing that it is solely your work.

Policy against threatening behavior by students: University of Arizona policies apply and can be found in the following website: http://policy.web.arizona.edu/~policy/threaten.shtml.

Disability:  
Students requiring accommodation in testing or notetaking must notify the instructor and must deliver to him the Disability Resource Center faculty letter within the first two lectures of the course. Students who are registered with the Disability Resource Center must submit appropriate documentation to the instructor if they are requesting reasonable accommodations: http://drc.arizona.edu/learn/index.html.

The information in this course syllabus, other than the grade and absence policies, may be subject to change with reasonable advance notice, as deemed appropriate by the instructor.