Course Syllabus


Genome Evolution Across the Tree of Life

A wealth of genomic data has been gathered from broadly diverse research organisms in recent years. Articles analyzing this body of information now dominate the pages of the world’s leading scientific journals and herald the dawn of a new approach to biological inquiry. Strategies for exploring the fundamental processes governing living organisms are no longer based merely on a trait-by-trait or a gene-by-gene research paradigm, but are now conducted on global, whole-organism and genome-wide scales. How can we make sense of the flood of new information produced by genomic studies? An excellent way to become familiar with the grand scheme of genome biology is to approach the topic from a comparative and evolutionary perspective. Although genomic projects are generally designed to help us to better understand individual research organisms, collectively they provide a tremendous resource to explore and understand basic questions surrounding genome architecture, content, function and evolution. Over the semester we'll become familiar with the latest developments, research strategies, and modes of analysis used in comparative genomic research. Additionally, we’ll discuss articles drawn from the recent literature in the field that illustrate the range of extant genome diversity and elucidate the mechanisms by which genomes have evolved from the pre-cellular earth to the present.

PBIO 8800
Andrew Paterson
Fall 2006


Principal Course Assignments:

Strategies for exploring the fundamental processing governing life are no longer based merely on a trait-by-trait or a gene-by-gene research paradigm, but are now conducted on global, whole-organism and genome-wide scales. The terminology, experimental logic, and modes of analysis integral to genomic research have become essential tools for any student who wishes to be competitive for a career in 21st century, biology-related fields. However, as always, fundamental talents, such as analytical reasoning, critical thinking, effective writing, and oral presentation skills remain essential qualities for both undergraduate and graduate students. This course aims to familiarize students with the latest developments, research strategies, and modes of analysis used in comparative genomic research. Additionally, it provides considerable practice in critical thinking, analytic, and communication skills through reading, interpretation, and inquiry-based discussion of scientific papers drawn from the recent literature. Students enrolled at both the undergraduate and graduate levels will have opportunity to express their ideas more formally through strategic writing assignments and to revise their work in light of critical feedback from course instructors. Students enrolled at the graduate level will prepare a comprehensive, original review, in proper journal format, of a topic closely related to the subject matter covered in the course.

Specific Course Requirements for Grading:

Participation: Undergrads 40 pts (max. 4 per class for the 10 student-led discussions). Grads 30 points (max. 3 per class for the 10 student-led discussions). An important component of this advanced stage in your career development (graduate school) is to become a good scientist and colleague. This involves a major transition, from the 'information recipient' role that we often play as undergrads (and earlier), to the 'information contributor and integrator' role that gains us respect as professionals. Courses such as this one are an excellent venue in which to make this transition, and much of your grade will be based on our assessment of your progress toward this goal. You participation in the weekly discussions should reflect the standards that you expect of yourself as a scientist and as a good colleague, to: 1) stay current on the literature (here, thoughtfully read the assigned papers each week); 2) communicate actively with fellow scientists about mutual interests (here, provide useful and interesting comments in class and ask thought-provoking questions); 3) make novel contributions to the research community (here, do some careful thinking before and during class and share some original insights not presented in the assigned papers - occasionally you should 'go beyond the call of duty' and read an extra article or two and bring those insights into the discussion). A good scientist is never embarrassed about asking basic questions to ensure that he or she fully understands the research being discussed. A good colleague appreciates the insights offered by others and strives to 'pay back' the community by contributing his or her own novel insights. The following scale will be used for undergrads (grads): 4 (3): Active participant in discussion; demonstrated synthesis/analysis of ideas in discussion or paper; clarification of ideas in paper/discussion; or comparison to other research. 3 (2): Active participant in discussion, demonstrated understanding of subject area. 2 (1): Participated at least once in discussion. 1 (0): Attended class 0: Absent. Grads will make up the difference by an additional required critical commentary, see below. If you'd like to see how your participation grade looks during the semester, contact one of the professors. Discussion/Facilitation: 40 pts Pick a topic and date. Select a primary research article (see list, or check with instructor for permission to deviate from list); identify article to instructor for distribution to class (as pdf); read and analyze article; read related background articles; consider the impact of the primary article on our understanding of the research area. Prepare a brief (10 min) oral introduction to the article. Bring in a handout for the class that briefly summarizes useful background. Prepare thought-provoking questions that reveal the merits and implication of each article, as well as its shortcomings. Guide that weeks discussion, ending on time. Critical commentary: Undergrads 20 pts. Grads 30 pts. Undergrads to write a minimum of 2 per semester, grads to write a minimum of 3 per semester (hence 30 points). Either can opt to write one more and we’ll drop your lowest score. Prepare a brief critical commentary (maximum 3 pages firm) on a research article that we discuss (not a review article and not the article that you used for your discussion/facilitation). Include a complete reference to the article in the first sentence. Briefly summarize the problems or questions being addressed, the methods being used to address them, and the main findings. Evaluate the intellectual contributions of the article and propose an experiment or analysis that would further advance our understanding of the topic. Write in essay format (complete sentence and proper paragraphs – see perspectives, news of the week, news and views articles in Nature and Science for examples of similar writing). Commentaries are due the day that we discuss the article covered, and will usually be returned the following week.

Grading Policy:

As detailed in course requirements for grading (above).

Attendance Policy:

Attendance is required, and will be reflected in grading together with the degree of participation in discussions.

Required Course Material Including Texts:

The course will use readings from the primary literature that will be provided as pdfs.

Makeup Exam Policy:

By arrangement.