UCSD BGGN 223 Advanced Genetics
online resources


These resources were developed for the PhD core course in Genetics at UCSD from 1995-2004.
About this course:
The UCSD Biology graduate genetics core course is a fast overview of genetic analysis: how genotype leads to phenotype. It covers model systems (bacteria and bacteriophage, yeast, flies, mammals...), individual topics (Cystic fibrosis, Cancer Genetics) and intellectual techniques (mutational analysis, genomics...). You may have heard that this is a demanding class--it is. We expect you to work hard, and perform at graduate level. The payoff is mastery of the most important subject in modern biology. You can't afford not to understand it.

This page provides you with on-line resources for the course. Nothing here is a replacement for attending lecture but the sites we link may fill in gaps in your background. Remember, you are responsible for filling in the gaps! Try some online problems-- Genetics has an intuitive component and practice really does help.

Questions? Don't wait to speak to the faculty. We are glad to help you and we will arrange office hours to meet with you.

Those who do not stop asking silly questions become scientists.
Leon Lederman.

Contents

Faculty, Text, and Lectures

Course instructors
Lecturerofficetelephoneemail
Lorraine Pillus
Professor
(course director) 		2100A Pacific Hall 822 2442 lpillus@ucsd.edu
Susan Forsburg
Associate Professor 		Salk Institute-MCBL 453 4100 x 1341
Muriel Nesbitt
Associate Professor 		4070E York Hall 534 0564mnesbitt@ucsd.edu
Bill Schafer
Associate Professor 		4402/4401 Bonner Hall 822-0508 wschafer@ucsd.edu
Questions related to individual lectures or individual problem sets should be directed to the appropriate instructor. Issues about the course overall, its logisitics, or other programatic concerns should be addressed to Dr Pillus (course director).

Text
Advanced Genetic Analysis: finding meaning in a genome (20). R.S. Hawley and M. Y. Walker. Oxford: Blackwell Publishing. 239 pp.
This book is available in the UCSD bookstore. It is a nice paperback volume that will be a great reference for your future. It is anticipated that you will use the table of contents to read appropriate sections as necessary without requiring specific assignments Please read Chapter 1 after Lecture 1

Lecture Schedule. Important: this schedule is subject to change!
Classes usually meet Monday and Wednesday 9-12, with some Friday dates as indicated. in 3500 Pacific Hall (P)

datewherewhotopic
31 Mar 04 PPillus
Forsburg 		Course intro and survey
Genetics 101: Mendel and Morgan
7 Apr 04 P Nesbitt Quantitative thinking in genetics
9 Apr 04 P ForsburgBacterial and phage genetics I
12 Apr 04 P ForsburgBacterial and phage genetics II
14 Apr 04 PForsburg Yeast Genetics I
Problem Set I
19 Apr 04 P ForsburgYeast genetics II
20 Apr 04 San Diego Cell Biology Meeting, de Hoffmann Auditorium, The Salk Institute
21 Apr 04 P Schafer Genetic model systems
Problem Set I due
23 Apr 04 PSchafer A case study - C. elegans
Problem Set II
26 Apr 04 P Schafer AFTERNOON Special Behavioral Genetics Symposium
28 Apr 04 P Schafer Mosaic analysis and further thoughts on epistasis
03 May 04 P Schafer
05 May 04P Pillus Mutational Analysis I
Problem Set II due
10 May 04P Pillus Mutational Analysis II
12 May 04P Pillus Mutational Analysis III
Problem Set III
14 May 04P Pillus Genetic Suppression and Epistasis
17 May 04P Pillus Genetic approaches to macromolecular complexes
19 May 04 P Nesbitt Mammalian genomes and karyotype
Problem Set III due
21 May 04P Nesbitt Linkage and mapping
24 May 04P Nesbitt Imprinting
Problem Set IV
26 May 04 P Nesbitt Cancer genetics
TBDProblem Set IV due

Homework policy

Understanding genetics means understanding how to solve problems and design genetic strategies for testing hypotheses. Therefore, your evaluation in this course will be based on problem-solving abilities demonstrated through the completion of problem sets given as homework assignments, rather than through a formal exam. You must pass this class to satisfy your course requirements.

Grades
1 Outstanding
2 Very Good
3 Satisfactory
4 Unsatisfactory
5 Poor
6 Very bad

 There will be four graded homework assignments. These will sample the array of topics covered during the course. Many of the questions are modeled after past first-year exams, so it pays to put your effort into doing them. Expect the problem sets to be challenging, but to build on the principles presented in lecture. Information about where and when to turn in assignments will provided in lecture.

To complete this course successfully(ie, pass the class) you must attend lecture and pass these assignments. If you know you are going to miss an assignment, or you miss one because of illness, be sure to talk to the faculty about makeups! Grades are based on the numerical average of the four homework assignments. 1.0 - 3.0 is passing, greater than 3.0 is not. If you fail more than one assignment, you will not pass the class.

You are welcome to study together on the problems, which is often helpful, and you are encouraged to consult with the faculty. However, the work you hand in must be identifiably your own. Discuss the problems in your study group and then go home and write up your answers alone. Do not look for or copy answers to problem sets from old keys; do not copy information from other sources. Cheating, plagiarism, or dishonesty will not be tolerated in this course , just as it is not tolerated in science. You may wish to review the UCSD Policy on the Integrity of Scholarship. If you have any questions, please speak to one of the faculty.

If you encounter difficulties on the problem sets, seek help sooner rather than later! The faculty is more than willing to assist you in developing problem-solving strategies. Most students who have had problems in this class do so because they did not seek assistance soon enough. Be proactive.

A false statement of fact, made deliberately, is the most serious crime a scientist can commit.
C. P. Snow, The Search (1959)

Problems

Problem setsPractice Problems
Problem Set 1 (Forsburg; pdf format)Practice problem ) (Forsburg; will be solved in class 19 Apr)

Overheads and reading lists 20

Reading and background
Powerpoint and figures

Recommended seminars

You are strongly encouraged to attend the Wednesday Biology seminars (4pm in the CMG Conference Room), and/or the Thursday seminars at Salk (4pm in the de Hoffmann Auditorium) regularly. Several scheduled seminars in the Departmental series are especially relevant to the course and you are required to attend these.
DateSpeakerTitle
07 Apr 04
4pm, CMG Auditorium		Adam Kuspa Genomics and Genetics in Dictyostellium
14 Apr 04
4pm, CMG Auditorium		 John Collier Anthrax Toxin Biology
21 Apr 04
4pm, CMG Auditorium		 Richard Novick Staph Biology
5 May 04
4pm, CMG Auditorium		Rex Kerr Kamen Prize Lectureship: Sensory Neuron Activity in C. elegans

What is genetics?

This article gives a vivid description....

What is genomics?

We generally think of genetics as the relationship between genotype and phenotype: the identification and charcterization of mutants and their effects on the cell. Classical genetics is a viable tool even in the absence of molecular biology or knowledge of gene sequences; molecular genetics provides us with additional information about DNA sequence and gene expression. With the completion of genome sequencing, there is now a discipline called genomics. This is the analysis of DNA sequence at the genome-wide level. Rather than analysis of phenotypes related to a process of interest, this is a large-scale effort to compare all genes equally to one another. In the terms of the article cited above, genomics would be the roll-call of all the workers in the car plant, the time they come to work, where they stand in the factory, and whether any of them are related to one another. It tells you a lot, though it doesn't tell you what any worker does.

Background

Do you need more background information? Here are some resources for studying genetics on the web. If you are feeling lost, you should check these sites out for a refresher. You should also be able to do the online genetics problems. Also, check our links to sites for individual genetic systems and associated lecture topics (e.g., coli, worms, etc).

Basic Information and overviews

General genetics course notes: These can be very useful for alternative ways of describing the concepts that come up in class. Sometimes all it takes is a different description...

Classic papers

Terminology

Meiosis

Need more?

The great tragedy of Science - the slaying of a beautiful hypothesis by an ugly fact.
T. H. Huxley

Systems/Topics

Prokaryotic genetics Yeast genetics
Drosophila genetics
C. elegans Arabidopsis: Human genetics resources Other vertebrate systems:

Methods and Technology, including genomics

The science of life is a superb and dazzlingly lighted hall that can only be approaached through a long and ghastly kitchen.
Claude Bernard, Introduction to Experimental Medicine (1865)

The tools

Here are some additional tools and resources relevant to graduate study in molecular genetics, in no particular order:

Local Info

Ockham's Razor

Non sunt multiplicanda entia praeter necessitatum. (Entities are not to be multiplied beyond necessity)
Or to put another way,
Frustra fit per plura, quod fieri potest per pauciora. (It is vain to do with more what can be done with less)

Ockham's razor is not an excuse or an explanation for biology as it is. It is a philosophical strategy for solving problems! Start with the simple, and let the data lead you to the complexity. If the data do not fit the simple model, then it is the simple model that is wrong, not the data. That is, you can't use Ockham as an excuse to ignore the outlying data. However, if the data fit the simplest model, then Ockham says you have no reason to develop a more complex model. At least, not yet--not until you have more data!

What happens in biology is that we keep doing experiments even when we have a model. That is because our role is always to challenge the hypothesis (never to prove it, always to disprove it). Inevitably the simple model will fall, because biology is not simple and eventually we get data that do not fit.

That's all Ockham tells us--but it's a great deal. In practical terms, what Ockham's razor means is that we develop hypotheses by determining the most parsimonious, uncomplicated model that is consistent with all of our data. Then we bootstrap ourselves to a more complicated model by vigorously challenging the first one.

"William of Ockham, a Franciscan monk, was born around 1290 in Surrey, and died in Munich. He studied at Oxford University and wrote extensively on the theological and philosophical issues of the time. By the principle later known as 'Ockham's Razor,' he insisted that ' what can be done with fewer.... is done in vain with more'. Denounced as a heretic to Pope John XXII, he was summoned to Avignon in 1324 where he got into further hot water and entirely rejected the secular authority of the papacy. William fled to the service of the Emperor Louis of Bavaria in 1328, almost certainly dying of the plague that ravaged Europe in 1349." from http://www.eclipse.co.uk/pens/folder1/ockham.html

send email to the webmaster to make comments or suggest links.

3/24/04   revised and updated.
© S. L Forsburg

Made on a Macintosh.