Physics 498: Statistical Physics of Biological Information and Complexity

Nigel Goldenfeld


Homework 2

Due date: This assignment is due Wed Oct 31, 2001 or earlier.  There will be a penalty for late entries.  If you know that you will be unable to make this deadline for a good reason, e.g. you have beam time at Argonne or something like that, let me know ahead of time so that we can arrange a mutually agreed upon deadline. 

HW 2--1: This assignment is a chance for you to play with some web based bioinformatics tools, in an open-ended way.

(a) Please go to the Biology Workbench web site and open an account for yourself.  It is completely free.  The Biology Workbench is an integrated point-and-click environment for doing bioinformatics tasks simply and quickly.

(b) Go to this exercise on phylogenetic trees and work through it.  When you are done, you will have figured out whether neanderthals were direct ancestors of human beings.  Hand in your final results for the trees you build, and any supporting documentation necessary to understand your conclusions.


HW 2--2: Write a brief paper about any aspect of molecular phylogenetics that you find interesting.   A few examples of topics that you may wish to consider are:

My examples above were split between uses and methods of tree building.  I hope that you can come up with many other interesting aspects to write about connected with molecular phylogenetics or bioinformatics.

You do not need to restrict yourself to a literature review.  Feel free to perform an exercise similar to HW 2--1 and present that as your paper.  You can find other examples on the web.

Length of paper: No less than 2 single spaced 12 point typed pages.  No more than 4 single spaced 12 point typed pages.  This will be strictly enforced (I will not read more than 4 pages).   Figures should be attached separately, i.e. they will not count in the length limitation. 

Dissemination of papers: A few selected papers will be subject to a brief 10 minute presentation by their author later on this semester.   I will endeavour to collect all the homeworks and term paper together in a book for all those taking this class.

Further details:

I expect that you will use the web resources on the course's home page, and/or scan recent issues of Proceedings of the National Academy of Sciences, Science, Nature, Physical Review Letters, the appropriate online preprint archives, or more biologically technical journals, such as Cell.

The paper should have a bibliography.

You should imagine that your reader is one of your classmates.

Format: Your paper should have approximately the following structure.  Here are some suggestions for the sorts of questions your paper should address to make it most useful to the reader.  As you will see, the purpose is not to focus too much on technical details.

Introduction and Background:

What hypotheses are being tested in this paper?

What information induced the authors to perform the experiments/theory?

What new methods or insights brought to bear on the problem?

Why did you chose to write about this topic? 

Why is this interesting or important?


What are the critical methods of the paper?

What enabling technologies are used?

What are the weaknesses of the methods used?

Are there other or better approaches that could be used?

Results and Discussion

What are the primary conclusions of the paper?

Did the authors prove their hypotheses?

What novel information or directions come from this work?

What control experiments were performed? (If appropriate)

What assumptions still remain in the work?

How could these assumptions be tested?

What other explanations for the observations are still possible?

What would you do next to advance this field?