Erick Peirson Developing Computational Humanities

I'm a software architect with an historian's mindset Here's what I've been up to lately.

New research in BioEssays about organism choice in biomedical science
By Erick Peirson
Apr 6, 2017

The diversity of experimental organisms in biomedical research may be influenced by biomedical funding. BioEssays, March 2017. 10.1002/bies.201600258

How and why biologists choose to work with the organisms that they do has intrigued me since before I started graduate school. I remember being exposed to behavioral neuroscience research in an undergraduate special topics course offered by one of my favorite professors at Puget Sound. I was puzzled by what seemed to be huge analogical (quasi-anthropomorphic) leaps from what mice do in an arena or a maze to explanations of complex human psychological phenomena. Of course, I understood that analogical reasoning can be important for getting experimental traction on complex problems, and that quite a bit of careful thought likely goes into that process. Nevertheless, the question of what makes one family of analogies better than another, particularly when it comes to developing model systems like mouse and rat models, has always nagged at me. As I learned more about the history of biology as a graduate student, it became clearer that the answer to that question would depend on understanding more than pure epistemology: past choices, economics, disciplinary norms, happenstance, and a variety of other path-dependent factors may all play a role.

I finally got a chance to spend some time on questions about model organisms when I was approached by a fellow graduate student about automating a classification task in literature review focused on neuroscience. Unfortunately that project died out as the people running it moved on to other things, but it gave me a chance to develop a fairly reliable workflow for identifying organisms in scientific literature using Named Entity Recognition. With a little more time on my hands as a post-doc, I revisited this work, and was surprised to find that despite considerable philosophical and historical scholarship on model organisms, there was very little data about large-scale trends in organism choice in the life sciences.

So I decided to inject some data into the conversation. The work that we describe in the BioEssays paper (link to full-text above) provides a high-level view of the organisms that scientists have been using in the biomedical sciences since 1975. One of the surprising results ā€“ contrary to the lamentations of many philosophers about hyper-reductionism and myopism in biology ā€” was that the overall diversity of study organisms has been on the rise. But there is an intriguing slow-down in that diversification in the 1990s, possibly due to changes in the funding landscape.

This short paper is only the beginning of what has become a fairly substantial area of research for me: developing a quantitative understanding of organism choice in scientific fields. Iā€™m looking forward to posting updates here as I prepare subsequent research for publication.