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MOLECULAR EVOLUTION SYLLABUS 480

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					                                           SYLLABUS
                                  MOLECULAR EVOLUTION MB437
                                              and
                             ADVANCES IN MOLECULAR EVOLUTION MB537

                                 FROM THE BIG BANG TO BIOINFORMATICS
                                FROM THE PRIOMORDIAL SOUP TO BIOETHICS

                                            Marcie McClure, Ph.D.
                                        mars@parvati.msu.montana.edu
                                                   994-7370
                                         Fall, 2007, Tu/Th 11:00-12:15
                                                 Lewis Hall 110

                                                 *********

Lecture 1    8/28/07     Comments. Organization & Introduction
Lecture 2    8/30/07     Evolution: the Big Picture
Lecture 3    9/4/07      The BIG BANG and formation of the elements necessary for life.
Lecture 4    9/6/07      Biogenesis I: The primitive earth and the prebiotic soup.
Lecture 5    9/11/07     Biogenesis II: Self-assembly, Energetics and Bioinformational Molecules.
Lecture 6    9/13/07     Biogenesis III: Protein or Nucleic Acids first? RNA or DNA?
Lecture 7    9/18/07            open discussion
Lecture 8    9/20/07     The RNA world: the three Domains of life and LUCA or LUCC.
Lecture 9    9/25/07     Origin of the Genetic Code and more on LUCC
Lecture 10   9/27/07     Genomes: Content and Architecture
Lecture 11   10/2/07     Mutation: nucleotide substitutions and amino acid replacements.
Lecture 12   10/4/07     Methods: Analyzing sequences: rates/patterns.
Lecture 13   10/09/07    mid-term I?????
Lecture 14   10/11/07            open discussion
Lecture 15   10/16/07    Molecular Phylogeny I: History, terms, definitions, and limits.
Lecture 16   10/18/07    Molecular Phylogeny II: How to determine a phylogenetic tree.
Lecture 17   10/23/07    Molecular Phylogeny III: Improvements and Extensions to Genome Trees.
Lecture 18   10/25/07    WHATS NEW? Bayesian and HMM Approaches to phylogenetic reconstruction.
Lecture 19   10/30/07     Deviation from Tree-like behavior: horizontal transmission of information.
Lecture 20   11/1/07      mid-term II?????
Lecture 21   11/6/07      Convergent Evolution: the antifreeze story.
Lecture 22   11/8/07      Evolution of Viruses.
Lecture 23   11/13/07     Retroid Agents: eukaryotic hosts and disease states.
Lecture 24   11/15/07     Do viral RNA polymerases share ancestry?
Lecture 25   11/20/07     Bioethics of the Human Genome Project/ Introduction to Bioinformatics.
                  11/21-23/07                    THANKSGIVING HOLIDAY
Lecture 26 11/27/07
Lecture 27 11/29/07
Lecture 28 12/4/07
Lecture 29 12/6/07




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                                  MOLECULAR EVOLUTION MB437
                                              and
                             ADVANCES IN MOLECULAR EVOLUTION MB537

            FROM THE BIG BANG THROUGH THE CHEMICAL FACTS OF LIFE TO BIOINFORMATICS

                                           Marcie McClure, Ph.D.
                                       mars@parvati.msu.montana.edu
                                                  994-7370
                                       Fall, 2006, Tu/Th 11:00-12:15
                                                 Cooley-B2



Text: Fundamentals of Molecular Evolution by Li and Grauer

Purpose of the class:
        The objectives of this class are to provide advanced, upper division undergraduates and
graduate students with a basic introduction to molecular evolution. This is a survey class. Some
topics will be covered briefly as they are a class unto themselves.

Requirements and Expectations:
        All students will answer a short quiz and survey. This is an anonymous questionnaire that
will fulfill two purposes: 1) indicator of your knowledge level, and 2) feedback to MM about
expectations of the class.

       All students are expected to attend all lectures, take notes and participate in classroom
discussion.

        All students will participate in a project and report. The nature and content of these projects
will be discussed in full in a few weeks.


Handouts of the slides will be distributed at the beginning of each lecture. They are also available
on my webpage which you can find at the Microbiology website.

I have not given permission for anyone to take notes in my class to be distributed in any manner to
anyone. If you obtain notes from my class that you have not acquired by attending the class and
taking them yourself I am not responsible for the content. Be advised that lecture material is the
intellectual property of individual faculty members and as such cannot be used or disseminated in
any form without express permission of said faculty.


CELLULAR PHONES MUST BE TURNED OFF IN THE CLASS -- IF YOURS RINGS YOU
WILL BE DISMISSED FROM THE CLASS -- NO EXCEPTIONS.

IF YOU HAVE A DOCUMENTED DISABILITY THAT MAY REQUIRE ASSISTANCE, YOU
WILL NEED TO CONTACT ME AND ADVISE ME OF ANY NECESSARY COORDINATION
IN YOUR ACADEMIC ACCOMMODATIONS.




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FYI from the MSU Student Conduct Code

Behavioral Expectations

Montana State University expects all students to conduct themselves as honest, responsible and law-abiding members of
the academic community and to respect the rights of other students, members of the faculty and staff and the public to
use, enjoy and participate in the University programs and facilities. For additional information reference
www2.montana.edu/policy/student_conduct/cg600.html

Collaboration

University policy states that, unless otherwise specified, students may not collaborate on graded material. Any
exceptions to this policy will be stated explicitly for individual assignments. If you have any questions about the limits
of collaboration, you are expected to ask for clarification.


Plagiarism

Paraphrasing or quoting another’s work without citing the source is a form of academic misconduct. Even inadvertent
or unintentional misuse or appropriation of another's work (such as relying heavily on source material that is not
expressly acknowledged) is considered plagiarism. If you have any questions about using and citing sources, you are
expected to ask for clarification.

Academic Expectations

Section 310.00 in the MSU Conduct Guidelines states that students must:
A. be prompt and regular in attending classes;
B. be well prepared for classes;
C. submit required assignments in a timely manner;
D. take exams when scheduled;
E.    act in a respectful manner toward other students and the instructor and in a way that does not detract from the
       learning experience; and
F. make and keep appointments when necessary to meet with the instructor.

In addition to the above items, students are expected to meet any additional course and behavioral standards as defined
by the instructor.




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 behavioral standards as defined
by the instructor.




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Jun Wang Jun Wang Dr
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