Siliceous and Delicious

It’s been good to be away for two weeks, a break from thinking about the thesis. And time to regroup before the big, final push. Which starts today. Beau sent me, among other wonderfully thoughtful tools for facing the next months, a book on mindfulness meditation, which I started reading yesterday. It’s almost staggeringly apropos, and I think I already got a chance to practice what it preaches this morning. I walked in to the office, something I thought I might do over the next weeks to make sure I get some fresh air, but realized when I got here that I had forgotten to extract my Harvard ID from my travel documents. Being 8 in the morning on a holiday, the building was deserted, and I could feel the first waves of disappointment and despair lapping at the carefully constructed enthusiasm and optimism for this first day of unbound effort. But somehow I managed to recognize what was happening, acknowledge those emotions, and decide (having toured the whole building in search for any doors that might be errantly open) that I could just go and have a cup of tea at Darwin’s and return when the museum opened at 9. So I set off, proud of my first (emotional) achievement of the day, and thinking how perhaps this was a fortunate reminder that in spite of all hopes there will continue to be obstacles over the course of the coming months, no matter how close I am to approaching an end, when I spotted an anthropology grad student striding towards the building, and asked her if she would let me in. Win.

This first obstacle overcome, I found it challenging to get settled. It’s not surprising, being the first day back after two weeks away (and a reminder why it’s going to be important to stay focused over the months ahead), but it was definitely both overwhelming and frustrating. While I have a list of general tasks to fulfill, I found myself unsure where or how to start. The first item on the list is finding the PCO-equivalent of “loadings” of characters on the PCO axes. But since this was a sticking point before I left, I thought it better to start elsewhere. (In the meantime, reading Mike Foote’s 1999 paper on the crinoid radiation, I found that he describes a way of doing it, but the description is oblique and it sounds difficult).

So I moved on to deciding which the “important” characters are manually, and scanned through my big “everything” plot. But beyond making a list of which characters seem to cluster in well-defined areas, and another list of egregiously dispersed characters, I got stuck on what to do. Should I just make two dozen plots with these characters? Surely, something like the above (“loadings”), would be preferable. Maybe I need to come back to this and just do it if I can’t get something like loadings to work.

Next on the list is “pairwise distance”. This is, from my reading of Foote, his primary measure of “disparity”. This should be relatively easy to program, so I start here. I was eventually able to set down and do this, and the results are somewhat surprising. Basically, the disparity is flat through time, except that the Early Cretaceous time bin is a shade lower.

The very low value of the Early Cretaceous is probably because the things are all the same—and this could well be biased by the facts that 1) it’s only one single assemblage, and 2) that none of the pennate-ish taxa reported in that assemblage are coded, because there were no decent descriptions for them.

This task carried me through lunch. Then, a tough moment—to write? I had promised myself I would spend part of each day writing. Needless to say, there is something of a mental block to doing this, so I was definitely afraid of sitting down and beginning to write, feeling like I am not ready yet. I tried to get my mind to start focusing in on the “big picture” view of things by rereading both my thesis proposal and a term paper I’d written (back in 2008) about the function and purpose of the diatom frustule, which was a shockingly good read (did I really write that?). Anyhow, it mostly resulted in tiredness. At least no immediate clarity on how to frame the paper—in terms of questions about diatom evolution, or in terms of morphospaces?

These are of course oversized questions for the first day back. Obviously. Smarter to work a little bit on the methods section, which I did.

All in all, not the most productive day in history, but given my goals, a good one. By the time the sun went down, I could feel the two-week onslaught of european virobacterial attack on my respiratory system, so I decided to call it in and head home. I worked hard. I did not procrastinate. This has been a good start to the end. A worthy start for the big push.