Category: Family

I received my topic for my oral exam. First I shall explain what this means. There are several requirements for the PhD:

1) B grade or better in 60 credits of classwork (I have completed this)
2) Complete 12 credits of ‘survey courses’ (I have not done this)
3) Pass 5 of 6 Comprehensive Exams (I passed 6 of 6)
4) Pass an oral exam
5) Write and defend a dissertation (also called Doctoral Thesis)

After completing steps 1-4 I will become what is called a ‘candidate’ while I complete step 5 (which may take up to 4 more years). I should have step 2 completed during this semester, but my goal is to get the oral exam done early this semester.

This exam takes the form of a 45 minute presentation to mostly faculty, during which I will be rigourously quizzed on all aspects of the topic. I expect to take 4-6 weeks to prepare.

My topic is how to determine protein stucture by reverse analysis of protein diffraction patterns. If this is something I find interesting then it may become the focus of my PhD research as well.

And what does it mean exactly? Think of it this way: when you pass x-rays through a protein crystal (such as solidified egg white) the x-ray image will contain a striking display of rings and arcs. Working out the atomic structure of the protein crystal by reverse engineering the pattern is akin to working out what a is blocking a bright light just by looking at it’s shadow.

< A protein diffraction pattern

Unfortunately it’s also not possible to work out complex protein structures via diffraction (or any other means for that matter). This is a holy grail of modern science, and my research will likely explore only a tiny portion of the many methods currently being investigated.

So, before I went and hurt my back muscle, we (Joyce & I) spent a lot of time doing a bunch of different yardwork in her backyard. In addition to the greenery and ponds, her yard is full of wildlife. Please enjoy these shots of frogs and chipmunks I took earlier this week…

< Large frog (about 8cm) living in Joyce’s patio pond

< Smaller frog (about 4cm). A baby perhaps?

There are currently a total of four of the adult sized frogs, and two babies. The adults seem to split their time between the backyard pond and the patio pond. Last Saturday we spent most of the day working in and around the patio, clearing off the debris of winter and early spring. We unearthed many worms during this work, and fed them to the appreciative frogs. Joyce even managed to get one to eat a worm out of her hand!

< Chipmunk on the wood pile

< Chipmunk at the big pond

The chipmunks are cute. Very skittery though; always on the look out for danger. The one in the top photo has a habit of sitting on the top of the woodpile and chirping for minutes on end (a high pitched squeaking sound). We have some of these at our place, but the ones here at Jim & Joyce’s house are either more active during the day, or less afraid of people. Or perhaps there is just more and better hiding places they can quickly duck into when they feel threatened.