STATISTICAL PHYSICS OF BIOLOGICAL INFORMATION AND COMPLEXITY

Course description:

Topics in biological information and complexity are presented, emphasizing how ideas from statistical physics can be useful in the "century of biology". Topics covered include gene and protein sequence analysis, protein and RNA structure prediction, genomics, population genetics, systems biology, and the evolution of complexity in biological and social systems. Prerequisite: PHYCS 462 or consent of instructor. No prior knowledge of biology is required. 1 UNIT.

Course outline:

You can find the course outline here.  It will be updated as the semester progresses, and I am better able to assess the appropriate rate of coverage.  

Course details:

Nigel Goldenfeld

Time: 9.30-10.20am Mon, Wed, Fri
Place: Loomis Lab 158
Office hour: Wed 1.30pm 256 MRL

Viewpoint: This course is intended for physicists who are looking for challenges in the biological sciences in the post-genomic era. It is relatively easy to invent and solve model problems that are in some sense motivated by biology, such as simplified treatments of protein folding. In many cases, however, this sort of exercise is not useful in advancing biological knowledge, and does not reveal any new physical principles.

Goal: The goal of this course is to attempt to identify problems whose solution would make an impact on biology, and which may require or benefit from physical insights. Key themes that seem to be emerging are the need for analysis of massive data sets, the need to understand the interaction of genes, and the need to create holistic mathematical models of biological systems from elementary parts. Hence, this course focuses on biological information and complexity.

Techniques taught: Mathematical techniques that seem already to be relevant include information theory, extremal statistics, dynamic programming, motif finding, cluster analysis and diagrammatic perturbation theory analysis of simplified models of RNA. Possible applications of dynamical systems theory will be discussed, which may provide a systematic approach for building an integrated picture of biological entities or networks from their basic elements.

Topics that it is planned to cover include: gene and protein sequence analysis, protein and RNA structure prediction, genomics, population genetics, systems biology, the evolution of complexity in biological and social systems.

Prerequisites: PHYCS 462 (or equivalent) or consent of instructor.

No prior knowledge of biology is required.

Announcements

Please register for the email list for the class, so that last minute announcements, class cancellations etc. can be sent to you.  This applies even if you are not taking the class for credit.   Thanks.

Course gradebook is here.

Fall 2001 term essays can be read here.

Homework Assignment One is available here.

Homework Assignment Two is available here.

Homework Assignment Three is available here.

Homework Assignment Four is available here.

Books

There are no required books for this course.   Much of the material is so new that an account suitable for physicists has not yet been written.  The course notes will be made available periodically in the Physics Department library to supplement your own notes from the lectures.  Here are some books that I have found useful, but because they are expensive I do not suggest that you buy most of them, unless you decide to become a "professional". 

• Unraveling DNA by M.D. Frank-Kamenetskii.   This is a wonderful book and is worth buying.  It is the only modern introduction that I have read which approaches the subject in the way that a physicist thinks.
  
  
• Bioinformatics: a practical guide to the analysis of genes and proteins by A.D. Baxevanis and B.F.F. Ouellette.
  
  
• Biological sequence analysis by R. Durbin, S. Eddy, A. Krogh, G. Mitchison.
  
  
• The complete idiot's guide to decoding your genes by L. Tagliaferro and M.V. Bloom.
  
  
• Computational molecular biology by P.A. Pevzner.
  

You can link directly to these books on Amazon, if you wish.

Resources on the WWW

Biology has embraced the internet as it has become a quantitative, data driven and computationally intensive science.   The selections below range from the most elementary to cutting edge sites used by practicing scientists every day.

• Nova program on the Human Genome Project. A good place to start for those who know nothing or want motivation that is comprehensible.
  
  
• APS Virtual Journal of Biophysics.  A compilation of research articles from leading journals at the intersection of biology and physics.  And don't forget to look at Science, Nature and Proceedings of the National Academy of Sciences.   These journals all offer email alerts for the contents of current issues.  A huge number of other online journals are available through this listing of electronic journals.
  
  
  THE MOLECULES OF LIFE
  
  
• Overview of single molecule experiments on DNA, from Oct 2001 Physics Today.
  
  
• RNA folding.  mfold and a quick getting started guide with some RNA examples to try.
  
  
• RNA folding: The Vienna package web server.
  
  
• RNA world, a collection of RNA related links.
  
  
• Software and links to perform comparative analysis of RNA secondary structure.
  
  
• Ribosomal Database Project II (RDP) which has online rRNA databases, sequence comparison and phylogenetic tree generation.  A tutorial for much of the functionality is here.   A neat tool for displaying phylogenetic trees on the web is at the Phylodendron web site.
  
  
  BIOINFORMATICS
  
  
• The Biology WorkBench is an integrated web environment for doing many bioinformatics routine tasks such as sequence alignment, multiple sequence alignment, phylogenetic tree construction etc.  It is a point-and-click environment linking software and databases.  You can access it here, and must register to get a free account.
  
  
• A simple example of bioinformatics in action.
  
  
• The single most cited paper in all of science during the last decade: Basic Local Alignment Search Tool (BLAST).
  
  
• Karlin and Altschul's paper on the statistical significance of sequence alignments.
  
  
• Fisher and Tippett's paper (1.2Mb in PDF format) on extremal statistics.  Proc. Camb. Phil. Soc. 24, 180-190 (1928).
  
  
• Statistical Physics and Biological Information Program at the Institute for Theoretical Physics, Santa Barbara has much good pedagogical material that heavily influenced this course.
  
  
• A worldwide list of courses on bioinformatics is here.
  
  
• US National Center for Biotechnology Information.  The key computational resource for researchers in bioinformatics, featuring sequence comparison tools and much more.
  
  
• European Bioinformatics Institute.
  
  
• Nature's Genome Gateway, with many original papers and expositary articles.  And the Nature Physics Portal section on Biology for Physicists.
  
  
• Fiction: Jorge Luis Borges' short story The Library of Babel which is reminscent of some of the themes of this course.
  
  
• An unusual application of genetic analysis: the case of the remains of St. Luke.
  
  
  BIOLOGICAL COMPLEXITY
  
  
• Complexity Digest -- a virtual journal of complexity, which is always interesting.  Note that you can also sign up to receive weekly email alerts about newly published articles on complexity topics.
  
  
• Systems biology workbench project - an integrated environment to enable researchers to model holistically biological systems.
  
  
• The E-cell project: a simplified simulation of a cell.
  
  
• The Systems Biology Institute, and interdisciplinary institute for the study of systems biology.
  
  
• Mark Borisuk's thesis on the dynamical system study of the frog cell cycle.  Includes a clear introduction to bifurcation theory.
  
  
• John Tyson's Computational Cell Biology Lab and their Dec 2001 review on network dynamics and cell physiology.
  
  
• Leland Hartwell et al's article on modular cell biology.

The Los Alamos archive frequently has articles of relevance to biological information and complexity in the condensed matter  and physics sections. 

Here are some examples of searches that you can do to find recent articles of relevance to this course:

• Click here to find all articles on either sequences, RNA or DNA.
  
  
• Click here to find all articles in the Biological Physics sub-section.
  
  
• Click here to find all articles with DNA or RNA in the title.
  
  
• Click here to find articles with ecology or biology in the abstract.
  
  
• Click here to find articles with protein in the title.
  
  
• Click here to find articles with genome in the title or abstract.

Some of the modern applications of statistical physics ideas are to complex dynamical systems in economics, sociology, computer networks etc. Good resources are the Santa Fe Institute and the New England Complex Systems Institute.

Nigel Goldenfeld

Telephone: (217)-333-8027

Office: 3-113 ESB
Office hour: Wed 1.30pm or by appointment

Nigel Goldenfeld's Home Page

Department of Physics home page
University of Illinois home page