Siliceous and Delicious

Back yesterday morning after a very welcome break in The Hague, Düsseldorf, and Amsterdam. Spent the morning catching up on e-mails, and booking my flight to DC for next week to go and pick up samples from the Smithsonian for the radiolarian by-lineage study. Though I started strong in the morning, jet lag soon caught up with me, and I wasted most of the afternoon away just trying to stay awake. It might have been more productive to stop work and go for a walk in the beautiful autumn sun.

I need to think about a strategy for the coming weeks. It’s going to be a fairly busy time, what with Maria coming to visit, and I am going to need to prioritize. A good time to review where I am with each of my projects (oh, how I wish I had Tony’s whiteboard back now!):

2A: Pre-Cenozoic Rads—Project sleeping. Can’t be a priority right now, because it’s essentially got a daft input:output ratio (way lots of work for dubious payoff).

2B: Rad lineages—Finally approaching start time on this one. Flying to DC next Wednesday to pick up samples for five of the six chosen lineages from the MRC at the Smithsonian based on the list I made over the summer. I am very hopeful the slides I picked will actually have the taxa I need in them. I could, of course, spend much longer at the MRC and actually check the slides before I select them (this would be the smart way to do it), but since I had assumed I’d be able to just request the slides and have them shipped to me, I had already started down the “pick samples and hope” path. Worst case scenario is that I find the samples don’t have what I need in them, and I go back for another day or two to get more. Not the end of the world, and probably more efficient than going through all the samples there only to go through them again once I get here.

The sixth lineage, Lophocyrtis, is still waiting to have samples selected. I hadn’t found it easily possible to get samples for these out of the MRC/Neptune combo, and decided to write Annika Sanfilippo for help. It turned out she has many samples from this lineage, which she described and defined over several decades. She has offered to send me whatever samples I want, but I haven’t been able to figure out exactly what samples she has, nor what taxa are found in them. The lineage is complicated and has lots of splits and branches in it. Annika also sent a stack of her notes on one of the descendant lineages of Lophocyrtis, Cyclampterium, by mail. I need to go through this and figure out which samples I want from her for a first-pass study of the lineage.

3: Diatom morphospace—this project is tantalizingly close, and I feel frustrated not to be making more progress on it, because the promise of getting it out the door is palpable. The next steps are quite clear, finish going through the stack of papers from the Farlow, then synthesize the morphological notes I’ve been taking into a master list of characters and associated character states. The challenge there is going to be to find a good way of describing the gross morphologies, e.g. valve outline shape, and dealing with the difference in sets of characters between raphid/pennates and centrics. Once that’s done, I can send it off to Wiebe Kooistra for review. Then, after making whatever adjustments I need from Wiebe’s comments, I can send it to Charles for review, and following further adjustments, plug and chug on coding the characters for each of the genera in Neptune.

4A: Extant diatom FIB—this project is essentially sleeping, too, since the diatoms I ordered from the CCMP came back all crappily silicified.

4B: Fossil diatom FIB—just sent an email to Nicholas to set up the next overnight FIB sessions. I’m not doing anymore unassisted sessions, since I’m sick of wasting my time doing runs that lead to nothing because there’s some technical glitch or another that I can’t fix myself.

5: Diatom sonication—got the diatoms, sonicated them, put them under the SEM, they are very lightly silicified and very zapped-to-bits. Next step is to try cleaning them again without destroying them as much (i.e. less sonication). Don’t know how to do this, so need talk to Jacques about it. That’s the next immediate step. The medium term decision is how to go ahead, whether it’s possible to work with this material, or to re-order more material, or to try to culture this myself (I’m not really interested in that option as much, it’d be a lot of work, although at least now there’s a cleaner lab without Dave’s meddling to work with). I suppose another option is to travel up to Canada again and do the culturing work with Zoe. Apart from her agreement, this would require a pretty substantial time investment in the cold dark depths of Canada, which I’m not excited about.

6: Diatom diversity/E-O—kind of unexcited about this project at the moment. I suppose the next step is to get the Alroy-style subsampling working, though I’m now hoping to implement in a slightly different way, because I think his way is too specific for PBDB, not necessarily appropriate for Neptune given what I’ve learned from reviewing Dave’s manuscript about the Neptune data. Ideally the right way to go about this will be to apply some Dave-style pacman/hats-for-rats type data filter, then a Neptune-appropriate subsampling based on % coverage (i.e. SQ subsampling). The next step here is to do a bit of thinking and planning, and probably ideally talking to Charles/writing up what I’ve learned from Dave’s paper and outlining my strategy. This is going to take some time and I’m hesitant to sink time into it when I’m so much closer to getting somewhere with other projects.

So much, then, for where I am. Where to go next, where to focus my energy, and how to do it, is the question. I went ahead and booked FIB time with Nicholas for the overnight slot from Monday-Tuesday. To be realistic, the time I have available before Maria gets here next Friday evening is just over four days. Friday afternoon is lab meeting at MIT, which will make for a short day. Monday afternoon I will be setting up the FIB overnight run, so that will be a short day. Wednesday I’ll fly out to DC at 6:30 am and won’t return until late at night. That leaves Thursday and Friday. So four days and a bit.

I really feel stuck deciding between these two. In a conversation with Jc I learned that she does most of her work in bigger chunks—rather than units of hours or days, she switches projects weeks at a time. This suddenly struck me as a very wise thing to do; a lot of my stress I think comes from trying to decide what to do next, and once I do, a lot of energy sinks into switching my brain back and forth from one project to another. As important as I think getting the samples ordered from Annika is, I think my primary need right now (for emotional reasons if nothing else) is to make progress, and the best promise for making progress is with the morphospace project. So as much as it pains me to leave the other projects aside for the moment, especially since they all feel pressing at the moment, to some degree or another, that’s where I think I should start focussing now.

Tomorrow.