Brian White

I am a professor in the Biology Department at the University of Massachusetts, Boston.

My official UMB Web Page.

Background

I received a BS in Biology from MIT in 1985 and PhD. in Biological Sciences from Stanford University in 1992. From 1992 to 1997, I worked in the Biology Department at MIT; from 1997 to the present, I have been at UMB.

Activities

I teach the two-semester introductory biology series of courses for Biology Majors. I also develop educational software and conduct research in Biology and Biology Education. More information on these can be found at the links to the left.

General Biology MOOC

In 2013, I teamed up with Eric Lander from MIT's Broad Institute to develop a Massively Open On-line Course (MOOC) in General Biology called "7.00x: The Secret of Life". This free on-line course includes lectures, problem sets, exams, and more. It uses the software I have developed in the problem sets and exams. It can be found at edX. The MOOC will be integrated into Bio 111 starting in Fall 2013.

A Problems Approach to Introductory Biology

In 2006, Michelle Mishke (MIT) and I published a book of practice problems for Introductory Biology courses. This book is sometimes called “The Problems Book” or “APAIB”. It contains problems on Genetics, Biochemistry, Molecular Biology, and problems that integrate all three components. It also included a set of very detailed solutions to all of the problems in the book. The book also makes extensive use of software simulations for practicing with these materials.

In 2012, the book went out of print. Fortunately, the publisher (ASM Press) was generous enough to allow us to post the content on-line for free. It is available from the links below:

Software

I am part of the BioQUEST Curriculum Consortium and through this I develop software for teaching biology. I work in close collaboration with Ethan Bolker of the UMB CS department and his students to develop much of this software.

These are designed to allow students to explore biological phenomena through interactive simulations.

All are freely-available from the links below, open-source, and subject to the GNU Public License (GPL).

All are written in Java, which is freely-available at this link.

Many also have javascript versions that will run in most browsers (especially Google Chrome). These versions lack some of the features of the stand-alone Java programs, but many allow on-line grading.

If you use this software for teaching, please let me know. That way, I can collect feedback for further development and document uses for grant-development purposes. THANKS!

Aipotu. An interactive simulation linking Genetics, Biochemistry, Molecular Biology, and Evolution.
The Virtual Genetics Lab. An interactive simulation of Mendelian Genetics. jsVGL is a javascript version of VGL that runs in a web browser.
The Gene Explorer. An interactive simulation of gene expression. jsGenex is a javascript version of Genex that runs in a web browser.
The Protein Investigator. An interactive simulation of protein folding that allows you to fold proteins of your own design. jsPI
jlogP. Calculates the hydrophobicity and molecular formula of molecules drawn by the user. jsMolCalc is a javascript version of MolCalc that runs in a web browser.
jsPedigrees. A tool for exploring pedigree genetics. Students can draw a pedigree and then the software will determine which modes of inheritance are compatible.
The Phylogenetic Tree Constructor. A tool that allows students to select organisms for constructing trees using molecular phylogeny software.
Tree Building Applet. Allows students to draw a phylogenetic tree of 20 familiar organisms.


Teaching Materials

I have also developed several other pieces of Biology Curriculum.



Research

My research program has two main threads. The first is Biology Education research; the second is the role of the Genetic Code in evolution.

I am currently looking for graduate students to work on these projects as well as others. Interested students should contact me by e-mail brian.white@umb.edu; information on applying to the UMB Biology Graduate Program can be found here.

Education Research

This part of my research program focuses on the development and evaluation of materials (often, but not always software) for teaching Biology at the undergraduate level.

Current projects include looking at students' abilities to construct phylogenetic trees of familiar organisms using the Tree Builder software we have developed.

Some sample trees are shown below. What do they show about students' understanding of the structure and meaning of phylogenetic trees?

Possible projects include:

Past projects have resulted in the following publications:


Biological Research

This part of my research program focuses on the role of the genetic code in the evolution of model proteins.

There is evidence that the standard genetic code is not random - that the arrangement of particular codons minimizes the effects of point mutations on the polar requirement of the amino acids encoded. The average effect of point mutations on the polar requirement of the amino acids encoded by a given genetic code is specified by a parameter called MS(0) (work by Stephen Freeland et al.). Studies by Freeland and others have shown that the standard code is nearly optimal for maintaining existing functional proteins and that codes with a higher MS(0) than the standard code.

Our studies focus on the role of the genetic code in a different "evolutionary task": evolving functional proteins from noncoding DNA sequences.

These functional proteins are folded on a 2-dimensional square lattice. Fitness depends on the stability of the protein and it's binding affinity in three different simulations:

  1. Making Polymers. Evolving proteins that can stick together in long lines, like a stack of identical lego bricks (or, in biology, actin or tubulin polymers). This requires the proteins to have two 'phobic faces so they can plug together, along with some 'philic ones to set up the correct orientation. For example, the protein below binds to another copy of itself in the same orientation - so it forms polymers:
  2.         k-a v-h
            | | | |
    K-A V-H y i m i
    | | | | |     |
    Y I M I l l-i g
    |     | | | | |
    L L-I G t f h-h
    | | | | | |    
    T F H-H t-d    
    | |            
    T-D            

  3. Making Dimers.  Evolving proteins that can stick together in pairs - face-to-face.  This requires proteins to have only one 'phobic face to stick to their partner, along with some 'philic ones to set up the correct orientation. For example, the protein below binds to another copy of itself in mirror-image orientation, so it forms dimers:
  4. S-R D-L-S      
    | | |   |      
    M W M I-V r-p-s
      |   |   |   |
    P-M F-V v-f m-p
    |   |   |   |  
    S-P-R v-i m w m
          |   | | |
          s-l-d r-s

  5. Binding to a particular ligand. Evolving proteins that can bind to an arbitrary small protein "ligand" with a defined shape.  This requires a specific 'philic surface as well as a shape to bind the ligand.  For example, the protein below binds to the ligand (lower case letters):
  6. K-A a-k-g
    | |     |
    L M-L-E k
    |     | |
    D-I F-R e
      | |   |
      P M d-g
          |  
          h  

Preliminary results suggest that simulated organisms using codes with high MS(0) values evolve these model proteins more rapidly than organisms using codes with low MS(0) values (including the standard code).