Siliceous and Delicious

Progress report season… for the sixth time! Yay! Well, actually I’m not sure I even had a progress report the first two years, but whatever. I spent yesterday evening reading through the past year’s DSA notes (depressing), comparing them to the goals I set out at this time last year (actually, precisely to the day!). This morning, I sat down and wrote out the progress report and handed it to Andy. I was feeling pretty good about myself, particularly since I managed to convince him not to call a committee meeting (for the first time ever). But then he read over the report and came back to my office to request a change: I had described how, as per his recommendation, I was dropping the diatom diversity project and instead expanding the morphospace project to two chapters, he “reminded” me of the PlanktonTech book chapter we agreed to write and asked that I change the section in my progress report back to include a chapter on diatom diversity.

What?! I thought the diatom diversity chapter was dead. I thought I had explained to Andy that I didn’t think the SQ subsampling method was going to work on the Neptune data. I thought he had suggested I drop the chapter, “with an eye toward finishing sooner rather than later”. Well, that didn’t seem to matter much—I suppose he remembered that there was a book chapter due for the PlanktonTech people, and that it was supposed to be about diatom diversity, and that was it. Just add it to the dissertation, as another chapter.

I could freak out at this point. I could despair about how to goalposts keep shifting. I could sit down and try to realistically plan how I am going to go from two chapters worth of data and analysis and no chapters written to four chapters worth of data and analysis and four chapters written by September 15th (the deadline for dissertation submission for the November graduation date). But I think I’m just too exhausted to do that at this point. Andy wants a chapter on diversity? Fine. So I rewrite the progress report (here it is, by the way) to include a few sentences about how “the diatom diversity project will take on a smaller role and will be represented by a short review chapter for submission to the book resulting from the PlanktonTech research initiative”.

Whatever. I don’t have the energy to engage with stressing out about how long things are going to take, when I am going to be done, what the dissertation is going to look like. The best I can do right now is go from one day to the next. Today, I needed to get a progress report done and signed by my committee members. I did that—I got Andy, Jacques, and Dave to sign off on it (and without requiring a committee meeting!). Whatever happens tomorrow, or next month, or when the thesis is due, happens then. Who cares what the damn report says.

Had a meeting with Andy this morning—I had wanted to show him my disparity-diversity plots, particularly with the different story told by subsampling, and show him the interesting result from the SQS Good’s U values (being counterintuitively high through time, suggesting a major problem for the approach). The upshot was that Andy now definitely recommended splitting the paper into two parts (“everything you have plotted here should be a figure in a publication, but it’s too much to fit into one paper”), and—more importantly—that as two chapters, together with the radiolarian lineage project, would constitute a thesis.

I had to ask explicitly to confirm, though it was already clear by implication, whether this meant that I didn’t need to do the diversity project to graduate. “Yes, exactly,” he replied. Woot, woot, woot! One less project to do. Not necessarily the one I would have chosen to drop, but whatever. It’s one entire project less to do before I can leave this entire episode behind me. Hallelujah.

I spent a good while bathing in the glory of that news, and checking in with the new iPad being unveiled, then moved on to printing out thumbnails of my figures and pasting them onto index cards so I could work on how they would be arranged in these two new papers. It’s going to be a big challenge for me to figure out what the division between the two should be, and what the two narratives for the papers will be, but at least I now know that’s what I need to do.

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.

Began implementing the fantastically supportive structure that came recommended from DSA yesterday, and felt a marked improvement in productivity immediately. Well, almost immediately—stopped by the new Starbucks in Harvard Square on my way in with Kati, and, while I immediately hated myself for it, loved it. I will have to start working there, it is the perfect, quiet, focused spot with an excellently relaxing view, lots of power outlets, and their Clover coffee is actually surprisingly good, considering I usually very much dislike the “charbucks” approach to coffee making…

Anyway. The definitive highlight of the day was meeting with Andy—remarkably, on his instistence. I led off with an apologetic admission that I really hadn’t done anything since our committee meeting, but he was very understanding and gracefully waved it off with a platitude about how sometimes life takes priority over work. Thought this was very grand of him. We talked over and solidified plans to have the morphospace done and dusted by August 1st, and have a chapter in the bank by the time the new semester begins. This was reassuring, and he reiterated his belief that it was entirely realistic to aim to finish by next summer—and if not then, in time for graduation in January (2013, that would be). I want to shoot for May 2012, but it’s nice to have that parachute at the ready. Just in case.

Then, he very carefully enquired, it might worth starting to think about next steps, and wanted to know whether I had any thoughts about it. I answered quite honestly that I’d been both thinking about it for a while, and was entirely undecided. I went on to say that following the academic track was an option that I was considering, but if so it would be a teaching heavy job, since that was what I had enjoyed most. He nodded earnestly and added that I was also very good at it, which I thought was very nice of him to say. I also said I was considering options outside of academia—in business and industry—but that I was at the beginning of learning what my options were there, but that I was open to possibilities outside of science. I mentioned how Kati and I had been talking about locations, and how being on the East Coast was a prerequisite, and that we might well choose a city before we choose a job—rather than following a dream job into the wilds of, say, rural Indiana.

To my enormous relief, Andy nodded understandingly and  said he would of course support me as best he could in whatever decision I took. He also said that if I went off to do something outside of science but stayed in the Boston area that I would always be welcome in the lab, and that if I wanted to continue doing research on the side there would always be space in the Knoll lab for me. This, again, I felt was a very kind gesture—as unlikely as that outcome might be…

Been having a very hard time motivating. Finally got moving today and completed coding the first genus for the morphospace, Abas, although I’m going to need to make a trip to the Farlow library to look up a few characters in a reference about that taxon before it’s fully done. Yes, I’m going alphabetically. And yes, it’s going to have to progress a lot faster if I’m going to get through all 147 genera before the end of my PhD—I can’t take a week for each or I’ll be here till I’m forty.

Didn’t help things motivation-wise that I got the dreaded “annual progress report” email from the graduate studies committee, demanding I meet with my committee and get them to sign off on a written progress report by April 8th—or else agree not to meet if it isn’t necessary, and just sign the paperwork. I had hoped that perhaps I could convince Andy that it would be the best use of my committee if we put off meeting until I had some morphospace results to discuss, fearful as I am of a repeat performance of the last two annual progress reviews. No such luck—”all progress is good progress”, Andy said mystically, and insisted we meet, although his schedule is booked up and it’ll be closer to the end of April. Grrr.

Andy also wanted to know if I was happy with the composition of my committee. With a view to the defense, I pointed out, I’ll probably need to add someone from within EPS, since having just my advisor from the department probably wouldn’t satisfy EPS’ requirements. Andy suggested either Ann or Dave, both of whom I think would be fine (though I think that Dave might—might!—be a little easier, and I have a better personal rapport with him). In any case, that adjustment would happen after the progress review, so nothing to worry about right now.

Anyway. I tried to work some more and kept getting distracted. Couldn’t focus. Felt unbelievably tired. Motivation is definitely at a low. I think the anxiety over the radiolarian project is stifling any progress I could be making with the morphospace—not knowing whether I’ll even be able to get images, and not receiving any useful help from Andy about microscope objectives, and not knowing where to turn, and even if I’m able to make the imaging work against all odds not knowing whether the species I need are going to be on the slides—that is making me deeply anxious.

An unsatisfying day. At least I feel justified in having started late and ending early, since it was so frustrating. Spent most of the morning trying to get the damn camera to cooperate with microscope and Canon’s own software. Much of that turned out to be my own idiocy, since I was baffled as to why the software wasn’t allowing me to control the camera’s aperture. This lasted for a long time, until I realized (sound of penny dropping) that since the body was mounted to the phototube without a lens attached, there was no aperture assembly to control, hence no setting to make. Duh. Eventually I resolved the problem I was having with the live preview being much darker than the captured final image (setting with shutter speed priority at 1/125 seemed to mitigate the issue, goodness knows why). In the afternoon, however, the next frustration, this one less tractable—couldn’t get an image out of the 63x oil objective (the highest power on the scope). No matter how hard I tried, no image. Eventually caved and asked Andy for help, who at first demonstrated knowingly various condenser settings I hadn’t considered, but after futzing and trying for a good half an hour, and trying a couple of other lenses on his microscope and from his drawer, came to the conclusion that he couldn’t get an image either. He apologized, but didn’t really have any good suggestions for how to go on. He seemed to hint at some point that the 40x objective was also really good, but I made it absolutely clear that that wasn’t going to fly—I was using a 100x objective in Bristol and Berlin to make the shell thickness measurement, and I wasn’t going to settle for something that much crappier (it also just won’t work, full stop).

I feebly suggested that Dave might have an idea of what’s going on. The best suggestion I got out of him was that, since insufficient working distance might be the problem, there might be a better objective out there for the job, and if so, that we could buy it. I’ll send Dave an email tomorrow—I promised him a report of  how my research is going anyhow—but today I’m done and heading out for wedding planning chores galore.

Put together a report for Andy late last night for our meeting today. It was an interesting exercise—made me realize a) just how much I’d actually done in the last three months, b) what a good call it was, motivation-wise, to stop working on the outline morphospace Sébastien when I did, before things spiraled out of control, and c) how incredibly useful it is to keep this journal of what I’m doing. There’s no way I’d have been able to give a full accounting of what I’d done since November without the help of this blog; in fact, when I sat down to start writing, I had no clue what I would write—I couldn’t remember really having done much at all. How wrong I was.

Before our 10:30 meeting (which went on for almost an hour and a half), I quickly set up my laptop and rushed to fix all the little things (application settings, macro installations, working directories, path names for file references) that would allow the RadData interface to run in the microscope room so I could demo it to Andy. Got it working just in time, though I realized in the process that there’s another couple of features I need to add to the interface. Inserting a slide with the “New slide” menu option is required before the first measurements are recorded in order to set the current_slide variable, but the resulting SQL INSERT fails (as it should) if the slide entered already exists. Two things thus need to happen:

1. The exception thrown by inserting an already-existing slide to the slides table needs to be handled so the program doesn’t crash in that case.
2. The user needs to be presented with an additional menu option in order to choose a slide already existing in the database.

Andy’s feedback was mostly of the usual kind—looks great, I agree with you, do what you say you’re going to do, you’re on the right track, etc. He did have a fair few things to say about the mathematical morphospace, most of which I found elicited a “you really have no idea” type of frustration. He was quite keen that I continue on with that line of inquiry—eventually, at least, since he agreed that it was smarter to focus my energies on completing the morphospace first—and “not make it too complex”. He pointed out that the genius of Dave Raup’s groundbreaking work on the morphospace of coiled shells was that he was able to think about it simply, identify the smallest number of parameters that were likely to be functionally consequential, and ignore the rest of the complications. This, of course, is easily said, and is exactly what I set out to do initially when I first started thinking about this problem (over three years ago!), but I’ve come to realize that it’s naïve to think that this sort of solution is possible for all sets of biological shapes, just because it’s possible for coiled shells. I wouldn’t for a second suggest that Raup is anything short 0f utterly brilliant, but he also chose the right problem to work on. It’s just the case that coiled shells can almost all—in a general and imprecise way—be represented by a simple three-parameter geometric model. It’s my belief after wrestling with diatoms for the last three years that the same is just not possible for diatoms. There’s an underlying developmental process in how coiled shells are produced biologically, regardless of whether they’re clams or snails, and that process is easily captured by a model that describes a generating curve rotating through space. The developmental processes that lead to diatom frustules are fundamentally different, for starters occurring at the cellular level, mediated by the cytoskeleton, which moves cell compartments into a much harder to define array of different structures.

I voiced my concerns about the potential functional meaning of looking at just one cross-section of a complex 3D structure (i.e. the outline shape), but Andy dismissed my concerns with the argument that most of the shapes are really just flat-topped or domed, and that “the silly shapes really don’t make up much of the morphospace”. Well, I just don’t know if that’s true. Sure, many of the most abundant forms are simple in their topography, but isn’t the point of a morphospace to look at the realization of successful morphologies in a broader space of shape possibilities? Anyway. I smiled and nodded and thought to myself, “well, let’s see if I get to it, but I think I’ve tried this, and I’m probably going to leave it up to someone more genius than me to solve this problem”.

The crowning glory of the meeting was a demonstration of the RadData interface, in its first sorta-kinda working form. I was astounded by how little Andy understood of the system as I demoed it… There was a giant chasm of understanding, actually, and it made me both very proud and a little bit sad. He was clearly quite impressed, but also didn’t really know what to make of it, I think. He was nodding attentively as I explained how it worked, and I thought he was on board, but as I was demoing the live preview on the Canon camera control app he asked whether the computer knew which of the specimens on the screen it was supposed to measure, I realized just how much more basic my explanation would have to be to get through… But that’s way more than could be fit into a one and a half hour meeting.

Started the day with a characteristically cathartic and constructive DSA meeting, followed by a lengthy lunchtime hiatus in honor of Tais’ last day at work. In the afternoon I met with Andy, going a long way towards resolving some of the issues and anxieties discussed with Beau in the morning. Some concrete outcomes of the meeting:

1. As regards the morphospace, Andy thinks my approach of linking morphometric data to Neptune is “spectacular” (his words), and thus worth the effort, even if this means putting in a fair amount of work tracking down obscure descriptions of fossil genera.
2. After hearing my complaints about the difficulties of the FIB work, Andy stated that he believed the morphospace, diversity/e-o, and radiolarian projects would make “three valuable chapters”, which I understood to mean ‘sufficient for a thesis’, and that I may decide at the end of the summer that the FIB project would be something I’d save for a post-doc.
3. Andy was very engaged by my re-telling of Alroy’s SQ algorithm and continues to think that the E-O project will make an “interesting and important” thesis chapter.

Knowing that the FIB project is not a requirement for graduation immediately transformed my perception. Suddenly—without the pressure of feeling that I have to do it—the FIB project seems infinitely less depressing and daunting, and much more like a challenging adventure. It’s funny how the mind works. All in all, a great day of meetings… and that’s not something you hear often!

Was struck this morning how it might be helpful to write out in a short report what I’ve been doing in each project for my quasi-weekly meeting with Andy. Found this quite good for me, as I read out what I’d been working on in our meeting, although I’m not sure Andy was much impressed. It was a characteristic meeting—mostly approving nods and noises from Andy, with little in the way of criticism or advice. Andy wanted to know what the radiolarian diversity data look like across the E/O, suggested I look at Wolfgang Kiessling’s thesis work (on Jurassic radolarians) for the pre-Cenozoic project, and suggested I browse through the initial reports from the earliest DSDP legs for help in where to find those elusive radiolarian lineage samples. That was about it! Andy appears to be satisfied with the rate of progress, and that’s good enough for me.

Although I do intend to step it up. Quite a bit in fact. And the “stay focused!” advisory, perched atop my computer screen, has worked well to keep me on track today—with more than a little bit of help from SelfControl, possibly my new favorite application.

After my meeting with Andy, I turned my attention to the diatom diversity project, as called for by the schedule. Step one is to read and, more importantly, understand Alroy’s paper—he finally emailed back (having discovered my emails in his lesser-used Macquarie account, rather than the NCEAS address I should have used) with not only a preprint of his forthcoming SQ paper in Palaeontology, but also a copy of the Perl script for carrying this out on PBDB output files. The Perl part could be a problem for me, never having worked in that language before (here we go again, another language!), but perhaps re-coding it in R wouldn’t be too hard to do. Plus, there’s also the option of just taking it at face value and, if I can make it work, just using the code without doing anything to it. That would be the easy way.

The SQ paper is a little hard to understand upon first reading. What I think I have understood, sort of, is the motivation behind it, or the shortcoming in the other methods that it tries to address. That shortcoming seems to be the following: all of the subsampling methods used so far (from rarefaction up through OxW) try to standardize sampling intensity to the same value, whether it’s measured in collections/lists, occurrences, or inferred specimen counts. So, visualizing the process of fossil collection metaphorically as pulling numbered ping pong balls from a large bag, the aim is to look at the same number of ping pong balls from each bag (at its simplest). While this seems “fair”, a problem crops up when the number of balls is very different from one bag to another. If, for example, one bag has one hundred balls (numbered 0-99), and another bag has only ten balls (numbered 0-9), things might go awry if we take five balls from each bag: the probability of picking the ball bearing the number zero is 5/10 or 50% in the second case, but only 5/100 or 5% in the second case! By this sort of reasoning it should become clear that all of these methods will severely underestimate relative diversity in time intervals where the true diversity was much greater than at other times.