This course is about how cellular behaviors lead to the generation of tissue and animal forms during development. The goal of this course is to provide the background necessary to ask critical questions both about what is thought to be understood, and about what is thought to be unknown about the molecular and cellular mechanisms of pattern formation.
I will cover material in Gilbert's textbook, review articles taken from the scientific literature, and original research articles.
1. Attendance and class participation. This is highly recommended, as 14% of the grade will be based on class participation.
2. Weekly assignments. Each week I will give you an assignment. Most weeks I will simply ask that you pose a few questions about that week's material. After doing the reading, these assignments should take no more than 15 minutes. Assignments are due in class on the day they are listed as due. No extensions will be given. I will not thoroughly grade all the assignments, but will spot check about half of them. Doing these assignments is guaranteed to very marginally help your grade (in total aggregate, they account for <10% of your grade). More importantly, they are designed to help you prepare for participation in class, and also for the midterm (which together account for about 40% of your grade). Therefore I would strenuously encourage you to complete them.
3. Class presentation. Pairs of students will present one or two research articles and lead a discussion. The research article(s) will be assigned, and be related to material of that week. Each pair of students should be prepared to present for about 20 minutes, allowing 10 minutes for class discussion.
**A meeting with me is mandatory the week before the presentation.**
4. Midterm. There will be a midterm in class on October 18th, consisting of multiple choice and short essay questions. This will be closed book. No early, late, or make up exams will be offered, except in emergency situations (as verified by a note from your dean).
5. A Perspective Paper.Topic: Pick one that you are interested in. The topic should be broader than a single research paper, but do not attempt to cover too large an area. "Xenopus gastrulation" is too broad, but "The role of Integrin tyrosine phosphorylation in Xenopus gastrulation" is too narrow; "Differences between frog and fish in the requirements for Integrin function" might be appropriate. You may do your review paper on a topic related to your class presentation. Be creative, topics that explore links between different research areas (such as cell, molecular, evolution, genetics, physiology, ecology, plant biology, etc), and developmental biology are especially encouraged.
Sources: Your paper should have at least 4 citations to the primary literature (original research papers), it will also likely have citations to review articles and perhaps book chapters. There are two approaches to finding research papers. The first is to read something more general, and pay close attention to the citations. For example, our textbook has hundreds of citations to good papers, and individual papers each have dozens of citations. The second approach is to use PubMed to do a literature search.
Due dates: I want to see an abstract or outline by November 22nd. I will not grade this, but I will provide comments. The abstract or outline should sketch out the major point(s) you will be making in your paper, and provide key sources so that I know you have found material to work from. Papers are due by December 6th.
Format: I am not overly concerned about length, 8-10 pages (double spaced) would be nice. There is no reason to pad; try to write concisely (hint: examine each word and ask yourself if it is really necessary for the point you are trying to make). If it is shorter than 8 pages and clearly reviews an important research area, hooray!!! If it is longer than 10 pages, there should be a very good reason (ie, you have a brilliant idea and no matter how succinctly you write, it cannot be expressed in fewer pages). How (and even whether) you subdivide the paper is up to you and might vary depending on the topic you have chosen. A typical 8 page paper might include 2-3 pages introducing the broad subject matter, 1 page providing a specific introduction to the research topic, 3-4 pages describing and analyzing the results, and 1-2 pages summarizing, putting the results into a broader context, and suggesting areas for further research. Document the sources you use by providing citations in the text and including a bibliography at the end. I encourage you to use figures if they help the paper.
Suggestions: Click here to see my thoughts on Science Writing. A good paper will introduce a topic, focus on the results in one research paper, and then conclude with what might be done next; small, simple drawings can be used to help the reader follow the writing.There are other possibilities for good term papers, if you want to bring together disparate topics and unify them with your own hypothesis, that might require discussing several different research papers each in not as much depth as you would if you are discussing primarily one. Some of the review papers assigned to you for reading are particularly good examples for how to structure your paper: Perrimon (2001), the short review article on Squint as a morphogen, and Shubin (2004), the short review on Stickleback evolution
The Outline or Abstract should include at least two citations, with a description (2-3 sentences) of what you take from each paper. This is due November 22nd.
6. Experimental Techniques Handbook. As the class proceeds, we will learn experimental techniques as part of learning developmental biology. I will highlight the experimental techniques as we go along and provide an explanation in class. Based on that explanation, and your own readings in the book and on-line, I expect you to provide a short overview of the technique. This overview does not need to provide buffer recipes and concentrations and temperatures and times (it is not a protocol), but it should include the critical reagents, an outline of the steps needed, and a description of the nature of the results (is it a number, a size, a picture, what?). Please email me PART I (on September 29), in Word format, so that I can make comments directly on your document. You will have a chance to correct/enhance the techniques in Part I and improve your grade for the complete Experimental Techniques Handbook.
7. The final exam has not yet been scheduled. It will be closed book, comprehensive (about 70% 2nd half, 30% 1st half), and include multiple choice questions as well as essay questions. No early, late, or make up exams will be offered. There will not be separate sections for 1st and 2nd half semesters, most of the first half material will be contained within questions that also deal with 2nd half material. I will post possible exam questions before the end of classes.
Small weekly assignments (2 points each)
Techniques handbook I
Techniques handbook Complete
Scott F. Gilbert. Development Biology, 9th Ed.
Additional Readings: you will also be responsible for reading review articles and original research articles. Most of these are available as PDF files on the web (links from the syllabus). Those few that are not will be photocopied for you and handed out in class. .
Web: Some weeks I will assign material on the Web for reading.
Office Hours: Tuesdays, 2:30-4:30 PM
Office Location: Shanklin 306
Office Phone: x3461
My policy to provide reasonable accommodations to students with documented disabilities. You, however, are responsible for registering with Disabilities Services, in addition to informing me in a timely manner of your requests. If you require accommodations in this class, please make an appointment with me as soon as possible [during the 2nd week of the semester], so that appropriate arrangements can be made.
Procedures for registering with Disabilities Services