Writing: Chemistry

Warren Beck is an Associate Professor of Chemistry at Michigan State, where his research group is working in the general areas of biophysical chemistry and molecular biophysics. One area of current work involves time-resolved laser spectroscopic studies of protein dynamics associated with protein unfolding and misfolding, as is involved in the amyloidoses (Alzheimer's and Parkinson's diseases). He is also working on the nature of protein reorganizational dynamics associated with electron transfer, as in photosynthesis and in redox proteins, using time-resolved fluorescence and femtosecond vibrational coherence techniques.

Here is a view of his entire screen in the middle of one working day.


In a single application, Tinderbox allows me to define an easily customizable notetaking system, an outlining system, and a smart reference database. In my setup, prototype notes are defined with attributes that keep track of the bibliographic information, the web URL, and link to a local pdf for each literature reference. Another set of prototypes define links to my experimental data files and to plots and tables prepared from them. The notes based on the prototypes for each source often include snapshot images obtained from the original pdf documents. Aliases to these notes can then be arbitrarily organized in an ordered list that forms the basis for a section of a manuscript. The links back to the prototypes allow the notes for each source to be viewed in a separate list.

Agents provide a constantly updated list of notes that correspond to stored queries, so it is easy to find the sources that pertain to a given issue. Maps provide yet another way to visualize and order the relationships between concepts, sources, and notes.

This system uses the basic features of Tinderbox in an elemntary way, yet it provides a dynamic view of my ideas and sources that is uniquely powerful. It removes the main obstacle that I have faced many times: what is the first step that must be accomplished in order to get a project off the ground? Using this system, I find that the first step is just to write down a single idea in a single note in Tinderbox, and the energy required to do that is minimal and the time required short. But the progress accomplished with the writing of that note is permanent; it can be used now, for the intended purpose, and it might emerge in a later project when pulled out of the corpus by an agent. It is the accumulation of notes in a Tinderbox document that provides the driving force towards finishing the project.

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