Research

Alternative Visualizations

One of the primary challenges associated with my research is that another individual must visualize everything first. As a blind chemist, I require the assistance of readers for the greater part of my work. They represent the main conduit between research results and myself. Without creating a system for me to “look” at the results or data in a reasonable amount of time, research analysis can become a frustrating and time-consuming process. Here are three ways that I help myself “see” complex output and trends:

Mathematical Approaches

My graduate thesis focussed on HP urease, an enzyme with approximately 148,000 atoms. This massive system is difficult for a sighted person to analyze, let alone a blind individual. One of the techniques I used was detailing motion in terms of distance, deviations, and radial distributions between set residue pairs, as shown below in Figure 3. Mapping movement mathematically allowed me to ask the readers very concrete questions. It became a matter of accessing data mathematically, rather than in a complex visualization with lots of extraneous, distracting visual factors.

I would ask the readers to describe any general trends: for example, the green line has a steep upward climb from 100 to 200 ns. This is a mathematical approach to understanding molecular motion that avoided visual dependence and instead utilized a reader’s detailing of minima, maxima, plateaus and other features on a Cartesian plot. Mathematical approaches like this are often a good alternative for visually-impaired researchers, and can, as in the case of my project, lead to the discovery of patterns that sighted students pass over.

Figure 3

Play-Doh

Colored_Play_DoughWhile working on my graduate thesis project, I often had my reader use Play-Doh to build a basic pseudo-structure of the protein so that I could get an understanding of what was visually going on. By keeping Play-Doh on hand, I had a tactile model to explore and refine.

3D Printing

Screen Shot 2016-02-24 at 5.27.32 PMLooking to the future, I am very interested in the possibilities of 3D printing. A friend and fellow blind chemist, Henry Wedler, has spent time developing a method to print molecular models and modeling kits that include Braille labels for things like atom identity, bond lengths, and bond angles. I am hopeful models like these will become widespread in the education of blind students, and I am looking into the possibility of incorporating this technology into my own daily work.

Dr. Wedler has co-authored an article in the Journal of Computer-Aided Molecular Design  that demonstrates ways that 3D printing can aid a visually-impaired researcher. The article can be found at this link: http://link.springer.com/article/10.1007%2Fs10822-014-9782-7#/page-1.

He has also made a powerpoint detailing 3D printing strategies, which can be found here: https://acsdchas.files.wordpress.com/2014/08/tantillo-wedler-3dprinting.pdf

See Modeling Kits.

Learning to Ask the Right Questions

Researching with readers is more challenging than studying for classes because the correct answers are no longer written down on the page for readers to read. You are the brain responsible for analyzing information, and you depend on your readers to receive that information. When they have no idea what they are looking at, you need to learn how to ask them the right questions to get the information you need.

I start by asking my reader simply to describe to the best of their abilities what they see, beginning with the big picture. Based on their answer, I hone in on details with more specific questions. Then, I develop hypotheses in my mind about what might have occurred in the experiment, and use that as a starting point to ask precise questions that could supply information that would confirm, deny, or redirect my hypothesis.

The process of analyzing results through another person’s eyes is a challenging activity, to be sure. The only way to get better is with time. You will learn from your experiences as you go along.

Chunking

Being visually-impaired means you need to depend on your memory more than a sighted researcher. If you’re not sure about something, you can’t just glance over to check.  

Memorizing things like large protein structures can be very daunting. I approached this by dividing the protein into manageable chunks first, and then gradually adding more details. The protein that I studied for my thesis had twelve identical parts. Distinguishing the different sections by color with Visual Molecular Dynamics allowed me to gain a better understanding of how the pieces fit with one another. When I had a general idea of how this protein looked, I was able to slowly fill in finer detail. Using play-dough models, I was eventually able to become so familiar with the placement of different structures in the protein. In the end I had nearly the entire peptide sequence memorized so well that I could identify the location of almost any amino acid residue.