Siliceous and Delicious

Wednesday

Not the most productive afternoon in history. After a lunchtime talk (about the promise of an anarchist archaeology) I received word that my mother had fallen and broken her jaw, which precipitated a flurry of phone calls, emails, and text messages. This was followed by a brief domestic with Kati, followed by an early afternoon shopping for her birthday presents, followed by an evening shopping for Halloween/birthday party costumes.

Thursday

Took my two Australian rock samples to the saw room, cut them, crushed them (in the process doing some not insubstantial damage to the floors—sorry Andy, I should have known hitting a rock with a sledgehammer will dent the lino underneath), and put them in acid. Spent some time reading about extraction techniques for getting siliceous fossils out of carbonates, which was not terribly inspiring. It seems that most folks work with much less indurated rocks. Mostly they appear to be able to get their fossils out with weak, dilute acids (acetic or carbonic acid, or at most 10-20% HCl), while I’ve been failing to get mine to dissolve with really quite strong HCl (50%). One paper described putting rocks in a bucket with a liter of pretty dilute HCl, then topping up the whole bucket with hot water! Maybe this is what I should be doing? But if it’s not dissolving in strong acid, I don’t see how diluting the acid, even in hot water, is going to help…

Tried to start putting together the list of pre-Cenozoic radiolarian sample sources. Realized I couldn’t do this properly without organizing my Papers library, because although Papers had imported all my papers, the metadata was not complete, so I wasn’t able to find out which papers I already had vs. ones I needed to download. This ate up a good chunk of the afternoon. Then had to proctor an exam for Andy’s class.

After a guilty spoonful from the procrastination honeypot (OK, two spoonfuls), I went through the sample R script Rabosky had written for me to show me how his analysis works. It made partial sense, though only in as far as how it calls the functions. I still need to go through each of the functions he calls and annotate them to understand what actually goes on under the hood, and compare this to what he writes in the paper, to see if the two match. In particular, I need to see what he means with the number of “stratigraphic sections”, since I’m not entirely sure what this represents, and he specifically mentioned in his script that he couldn’t remember what that meant, either.

Friday

After a late start (going to see a show on a weeknight does not for early mornings make), spent a good hour emergency-reviewing Phoebe’s Nature paper, which I now recall I also spent a good hour doing on Thursday as well. Then had to call my cousin Philip to ask if I could stay with him over Christmas. Then had to set up my account with “Manuscript Central” so I could check the status of the diatom review paper submission. It seems to be somewhere in the review process. The interface is not entirely idiot-proof, apparently.

In the afternoon, returned to the diatom diversity project. Investigated the first-order problem of Rabosky having a different-sized database to begin with. Downloaded the entire Neptune database from CHRONOS (only diatoms, only dated samples, do not include synonyms): 73,422 lines of data. Tried to download the entire Neptune database from PBDB, as I had done previously, but kept getting an error. The file I had from the summer has only 64,295 lines in it—but I don’t remember what I included/excluded. I’m going to start with the CHRONOS file, since that is the official source for Neptune, and also what Rabosky used. First step is to cull the data.

Monday

The best laid schemes o’ mice an’ men
Gang aft agley,
An’ lea’e us nought but grief an’ pain,
For promis’d joy!

A day of putting out non-academic fires, ixnaying the best-laid OmniPlans of this Mighty Mouse-wielding man. Irritating. The morning began with a personal financial emergency of the now-familiar kind (birthday-related, unchecked spending spree resulting in overdrawn account and sledgehammer-to-the-head bank charges), which segued seamlessly into a frenzied reading of the two chapters of Darwin’s “Origin”, which I was to have read by lunchtime but, as a result of the aforementioned birthday, had not. Immediately following lunch the OEB financial department generously presented me with a second financial emergency, regarding the whopping $2,800 rental car bill that overdrew my credit card last month. The reimbursement for this has itself turned into an epic kerfuffle. It’s now closing in on 3 pm and I have yet to start the day. This is a frustrating feeling to say the least.

Closed out the day with the scarcely redeeming achievements of OmniFocusenzing the current OmniPlan tasks for each of my three projects, searching for radiolarian papers (not many found), and looking through the DeWever book (“Radiolarians in the Sedimentary Record”) to see if there were any pictures of radiolarians with scale bars. There were none.

Tuesday

Finally crafted the email to respond to Zoe’s offer of samples, a mere eight days after receiving it. This, surprisingly, took up most of the morning. In the afternoon, went to a presentation about green cards, which—counting the travel time to and from Longwood—consumed most of the remaining hours of the day. However, I learned more during those two and a half hours than I have during this whole semester! Immigration law is a complicated thing, and getting an employment-based green card is damn hard. At the end of the day, met with Andy and presented my three project OmniPlans to him. Though his response was incomparably more subdued than it used to be during our meetings back in the heady days when my future seemed promising, he expressed both his gratitude for my showing him the plans, and his approval of their content. He said that he thought some of the projects might take longer than I have allowed for in the plan (stretching through the summer rather than wrapping up by the end of the academic year), but seemed satisfied with the prospect of my having three thesis chapters completed by the start of the next academic year.

In terms of more specific feedback, Andy suggested:

• That I address the issue of diatom diversity not equalling diatom abundance. One way to do this would be to quantify the abundance of radiolarian cherts and diatomites through time, perhaps using published ODP reports.
• In terms of the diatom morphospace project, he suggested that the two techniques I want to trial (FIB-SEM and CLSM) would yield very different, yet both important results, and that I should try to make both measurements. In terms of the question of authorship, he was happy to have Zoe be a co-author on any papers arising, and was happy to have thesis chapters result from collaborative work (“we all do it”, he said of collaboration—sounding a little bit as though it were a dirty secret).
• In terms of the pre-Cenozoic radiolarian samples I have been trying to dissolve without success, he suggested I have thin sections made, in case they are too silicified to be able to dissolve out microfossils.
• Dave Lazarus’ suggestion of weighing radiolarians rather than measuring dimensions under a microscope was well-received. With modern high-accuracy balances, he suggested it might be possible to make these measurements without having to isolate thousands of radiolarian specimens, as was done in the original study of radiolarian silicification in the 1960s.

In conclusion, Andy reviewed the past year as having been a useful exploration, even though it might feel like lost time to me (which it does)—it helped me develop good foci, realistic projects. As he put it, “these things will work.”