STATISTICAL PHYSICS OF BIOLOGICAL
INFORMATION AND COMPLEXITY
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.
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.
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.
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
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.
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
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
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.
- 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.
- 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.
- 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
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.
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
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.
- 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 pageUniversity of Illinois home page
Updated Aug 10, 2001