Siliceous and Delicious

Had a meeting with Andy in the morning, which went well. He was very impressed with the quality of the plots, which pleased me, and how I had “really sweated the small stuff”, as he put it. He was, as ever, relatively thin on the detailed advice, though, in his defense, it would be very difficult for him to do so at this point, since it’s impossible for him to have the sort of insight he’d need to be able to make constructive remarks at the operational level with the limited involvement he’s had (for which I am also in part responsible, not having gone to him for several weeks now). He did have some helpful observations of the data that, being stuck in the operational details and coming at everything from a pretty pessimistic point of view, I hadn’t noticed—that Figures 2.4b & c divide the morphospace into quadrants, that Figure 2.6 shows that those quadrants aren’t sensitive to the choice of ordination, and some interesting observations about the location of sister groups relative to clades in the morphospace (though I had to demolish the validity of that observation based on the difference between the phylogeny supplied to me by Sörhannus and the topology of published phylogenies, including his).

He did suggest that I might include the original big grid plot (PCO axes vs. characters) with the more severe, original cull, because the methodological argument of how selecting data affects the outcome of the morphospace is actually quite interesting, he thought. With that extended discussion of methodology in mind, he also suggested that it might make sense to split the project into two papers (=chapters), since having two major take-away points (the method and the biological story, which has yet to emerge) might be too much for one paper, and the whole thing might get too long to fit in a digestible paper. This sounds fine to me, especially considering the parenthetical comment Andy included in that context, that this decision might also make sense “with a view to finishing sooner rather than later”, which I took to mean that this chapter splitting might mean I could give one of the other chapters the boot. That would be nice. Very nice. At least I think that’s what he meant—I didn’t ask him to clarify that comment directly, though maybe I should have… In any case it depends on how long the paper ends up being—he did suggest I keep writing it as one paper for now and then split it up if it gets too long.

Anyway, that was the morning, and I spent a bit of time reading and preparing for the afternoon’s “geobiology” group meeting which I co-led with Justin (and help from Tinker), and with the meeting itself (which went pretty well, as far as these things go) that accounted for the rest of the day. By the time I got home I was exhausted by the week and decided to treat myself to the night off.

For the first part of the week, the new pep-talk motivation strategy was working quite well. I finally started down the list of Cretaceous taxa to add to the morphospace, and though it was slow, I was making progress, and that felt pretty good.

On Wednesday, however, Andy asked me to lead the discussion for the dreaded Pearson-Johnston-Knoll joint lab group meeting on Friday, on a paper of my choice. I was in no position to decline, given that I haven’t presented anything at lab meetings for several years, and have in fact abdicated from even attending them, as they are completely unproductive for me: it always ends up as a discussion among faculty (or between them, if it’s only two) witnessed by a large group of 10-30 silent graduate students and post-docs.

So I sank the better part of three days into catching up on three years of silica/diatom literature, choosing two papers, trying to read and understand them, pull together a few slides, and come up with discussion points. Predictably enough, the meeting went exactly as described above (Andy, Radcliffe visitor Paul Falkowski, and Zoe where literally the only other people to speak during the entire ninety minute meeting).

Strangely, though, it was a decent discussion, besides being utterly weird because it was 4 people talking in a room of about 25. I felt that it was oddly worthwhile to throw myself deeply into thinking about a couple of complicated problems for a while, and oddly engaging to lock antlers with Paul, who is terrifyingly sharp and very knowledgeable. His engagement in the material (versus the 21 others in the room who were completely still for the entire time) somewhat made up for his dickish “you must be in your 3rd year” remark the other week.

Perhaps the most vindicating part of the interaction was after we had finished and were walking out of HUCE we got into a discussion about the greater linkage between the silica cycle and the carbon cycle through silicate weathering. Paul brought it up and I was staggered, because this notion that accounting for silica in quantifying past changes in the global carbon cycle (through exercises like Berner’s “geocarb”/”geocarbsulf” models) was something that had struck me very early on in my time at Harvard. I had tried to sell both Andy and Dan on the idea, both of whom were very dismissive of it. Dan to the extent of falling asleep during my presentation on the matter in his class.

But Paul seemed to be quite excited about it, and seemed to understand exactly how this was important—and suggested that we get together and draw up some equations to describe it all… That was quite rewarding, and vindicating. I’m not such an idiot for thinking about these things after all. Fuck them all. Perhaps the biggest idiot I’ve ever been is in listening to others’ advice or waiting for “senior” scientists’ approval of my ideas. (How ironic, then, that this vindication has to come through a senior scientists’ approval…)

In other news, Mateo offered for me to join a dissertation writing group—so far just him and one other student. My first response was “I’m not ready”, but in further discussion and upon reflection I realized that it’s not too early to start, and it would probably be extremely helpful for me to start to think and write about the big-picture background of what I’m doing, rather than just sinking deeper into the morass of the ground-level mechanical exercise of the research grunt work itself. I haven’t yet gotten myself to the point of accepting his invitation yet, though, since I’ve also felt extremely overwhelmed during the past week, and the thought of adding another commitment makes me a little queasy. Something to think on a little more.

Spent the morning on the FIB with the engineer in charge, Nicholas Antoniou. He was very helpful and trained me in how to stigmate, focus, and align apertures on the various ion probes in the FIB. It’s a monumentally finicky process, but I think I get the basic picture of what needs to be done now. However, once we’d gone through this exercise, it became clear in a) a couple of trial milling operations we carried out using the now perfectly-tuned ion beams, and b) the conversation we had throughout, that using the higher-current beams (which would reduce the milling time from many—as many as dozens of—hours per specimen to a slightly more reasonable hour or so) is simply not an option. No matter how well adjusted the beams, the 23 and 45 nA probes produce an ion beam that is simply not sharp enough to cut open the frustule cleanly—the result is an unevenly cut frustule caked in ‘curtaining’, step-shaped deposits, and other milling artifacts.

This, needless to say, was a heavy blow. The probe sizes which gave halfway decent results (delivering 6.5 and 13 nA of current) will take countless hours (on the order of a day or two) to cut through the larger frustules I’m currently working with (the Cretaceous sample I’m looking at at the moment, for example, has frustules in the 100 µm length range). It’s simply beyond the size range of what the FIB is designed to efficiently handle (it’s really set up to work with nm- to few-µm size features on electronic chip circuits).

There was some moderately good news, though it was hard for me to really get excited about it. Nicholas talked at the end about the possibility of setting up automated milling operations overnight. This approach would involve milling registration marks (“X marks the spot”!) next to frustules to be milled, which are then sequentially found using pattern recognition in the course of a night’s automated milling. The FIB locates the desired feature on the stub and aligns it using the registration marks, then carries out a pre-set milling operation, then moves on to the next registration mark, and so on. Theoretically this would make very long milling operations (at least on the order of several hours) more feasible.

The amount of time this implies, though, is still staggering. Assuming I can mill 2 or 3 specimens overnight, this will still require on the order of 100 nights of milling to generate measurements for the 50% taxonomic coverage case I suggested in my thesis proposal. This is patently ridiculous, in spite of being a probably wildly over-optimistic assessment of how much time it’s actually going to take to make these measurements.

I’m distraught and demotivated. Nothing seems to want to work at the moment. For better or worse, we have an early lab meeting this afternoon—a dull paper about some early Proterozoic pyrite concretions that are suggested to be biological, maybe even multicellular and (heresy!) eukaryotic in origin. In any case, daft and dreary as it may be, I’m going to have to spend the remainder of the day reading the assigned papers, so I don’t look like any more of a fool in front of my advisor. Yech.