Spring 2005

It's just a little more than a week since I submitted the renewal for my NSF Arabidopsis 2010 grant via Fastlane. The grant renewal was my primary focus between end of the Fall semester in mid-December and its submission. Because much of the important work (our in planta ESE assay and the characterization of SR protein genes) is not yet published, I focused on documenting our progress. It was great to work with people in the lab to bring it together, and I'm very pleased with what we have accomplished. On the other hand, I wish that I had spent more time (and more of the 15 page limit) elaborating my future plans, particularly the global alternative splicing microarray. I fear that I let my enthusiasm for timely and similar work by Pan et al. obscure the fact that I had been thinking hard about these experiments for some time.

Prior to that, the Fall semester was especially challenging because I was teaching two full courses simultaneously (BSCI410 and MOCB630). Thus, the past week has presented a kind of freedom that I haven't felt in several months. It has been a pleasure to do whatever task was a hand at an appropriate pace, free from the influence of an impending lecture or grant deadline.

Of course, there is a lot to do. My immediate priority is with the NIH panel (coming up in less than three weeks), and with the ESE paper I hope to submit by the end of March. There is also the 2010 web site, CBCB web sites, several searches for faculty in my field and the paper with Jason Edmonds on SR protein knockouts. Other goals for the Spring semester include getting the undergraduate Bioinformatics program approved by the PCC and writing a grant proposal for the June NIH deadline. I'd also plan to make it a habit to post here more regularly. My hope is that the time spent will be justified by frequent practice at putting my words out where they are subject to public scrutiny.

Names for things that are only sometimes exons

I am grateful to Myles Axton for introducing the readers of Nature Genetics to his term for coding segments that are less than an entire exon, which is CROE (Touching Base, Jan. 2005). This word is an acronym for "Coding Region of an Exon" and can be pronounced as in "crow." I do indeed feel that such a term is necessary, and it was my appeal at the Drosophila ENCODE meeting (Dec. 5) that got Myles' attention. Soon after my Arabidopsis 2010 grant is submitted to NSF (Jan. 21) I will post here in more detail, explaining why this term should apply as well to coding regions that are coincident with an exon (so that one can say something like "the ORF is broken into seven croes").

I will also be throwing out a second request. We need a term for segments that appear as indels when two alternatively spliced mRNAs (or cDNAs) are compared. The latter can be a complete exon, part of an exon or an intron, and need not be coding.

Update on science and the tsunami

The New York Times published another article on Dec. 31, "How Scientists and Victims Watched Helplessly", which explored the various ways it might have been possible to get word to tsunami victims in time and how it was that none succeeded. Reading it through, I'm a bit less bewildered and outraged, although the sense that opportunities to save lives were somehow missed remains.