Siliceous and Delicious

I’m going to call the overnight run a partial success—in the spirit of my renewed attempt to be positive and enjoy my work. It did produce a very nicely cut and polished cross section of one diatom. However, when I arrived in the morning, I found the instrument stuck in an infinite loop of beginning the polishing operation (milling the last fraction of a micron slice of diatom with a very low-current beam), in which it was repeatedly stepping through the first thirty seconds or so of the polish, then performing drift correction, and then starting over. Having watched this merry-go-round for some twenty minutes, I aborted the process and shortly thereafter witnessed the FIB throw itself into some flurry of error messages that ended the day’s productive work on the machine.

This can probably all be corrected quite easily if I spend more care and time on setting appropriate milling times and parameters in the setup for the next run—this time, I spent a good two hours trying to get the beams focused, stigmated, aligned, and coincident… Setting drift correction to kick in every five or ten minutes (rather than every thirty seconds) will probably be more than sufficient.

Spent the rest of the day working on the “1-pager” summary of the diatom diversity project, which is rapidly ballooning to fill a second page, though in my defense it also contains three graphs so far. And, producing these graphs takes time—today, for example, I spent a good portion of the day calculating and plotting quality of preservation (as recorded qualitatively in the Neptune database in categories of Good, Medium, and Poor). It was kind of a big effort for something so simple, but it does show that the Oligocene dip in diversity also corresponds to a dip in preservation quality. So, there may be something beyond just biology going on!