Siliceous and Delicious

The sun is out, it’s forecast to be in the 70s today and up to 80 tomorrow. It’s the first day of spring. I’m sitting outside Darwin’s in a t-shrt, it feels wonderfully fresh and warm, and yet there’s something holding me back from really enjoying it. What, oh what could that be…

I feel totally paralyzed, still, by that question Zoe asked on Friday. What can you say about your results? I just don’t know. What are the two points do I want to make? What am I trying to say? What question is this morphospace project answering? Fuck.

Beau helped tremendously in DSA today. Somehow, talking it all through crystallized for me that there’s only one way out, and that’s through me. The help is going to come from nowhere, so I need to muscle my own way through it. Asking for help, being humble and self-critical and loyal to the truth is going to get me nowhere. I’ve had the best results in the past when I’ve been confident, self-assured, argued by advocacy and basically played the part of the blowhard. That’s just what I’ll have to do to get through this.

It’s been a long slump. And, though I somehow feel like I’ve said this often before, it feels like it’s been a real low point. But after a really great DSA yesterday, I feel much buoyed by my recognition of my own resilience, thanks to Beau’s really rather brilliant question (“if the wiser and capable self you know is in there could meet the you in the fog, what would you say to yourself to get yourself out of this funk?”). I haven’t yet formulated the pep-talk/positive inner monologue reprogramming incantation yet, but something about realizing that the power to get myself out of this mess lies within myself seems to have rattled something loose. Achingly, grindingly, things are starting to ease back into motion.

I tidied up the spreadsheet for the morphospace matrix to ready it for an influx of new (Cretaceous) taxa. I dug up the papers with Cretaceous occurrences. In the first one (Fourtanier, 1991), I chased down all of the references to other Cretaceous diatom occurrences that I hadn’t seen yet, and found they were all dead ends (well—the Barron, 1985 reference about the CESAR core from Alpha Ridge is published in an obscure book which I think I can’t be bothered to track down). Moved on to look at what genera are actually listed in the Cretaceous samples. The genera are Coscinodiscus, Eunotogramma, Gladius, Hemiaulus, Pterotheca, Pyxidicula, Rhizosolenia, Stephanopyxis, Triceratium, and Trinacria. Remarkably enough, only Eunotogramma, Gladius, Pyxidicula (though this seems to be similar to and perhaps synonymous with Stephanopyxis) are new. Phew. I think Pterotheca might be a resting stage, but I need to check when I’m back at the office.

Next, the second Cretaceous assemblage (Hajós and Stradner, 1975). This one lists a heaped metric assload of taxa. Including these ones not already in the morphospace: Acanthodiscus, Cerataulina, Creataulus, Epithelion, Goniothecium (isn’t that a resting stage, too?), Helminthopsis, Horodiscus, Incisoria, Kentrodiscus, Longinata, Odontropis (hmmm? sounds familiar), Poretzkia, Pseudopyxilla, Pteritheca, Pyrgodiscus, and Rattrayella. Holy shit. That’s fourteen new genera, at least. Yech. Si, se puede. Onwards! Oh. Missed a page. Tubularia, and Xanthiopyxis, which I’m pretty sure is a resting stage taxon.

And, the third assemblage, Gersonde and Harwood (1990). The most famous one. Here we have Amblypyrgus, Ancylopyrgus, Archepyrgus, Basilicostephanus, Bilingua, Gladiopsis, Kerkis, Kreagra, Microorbis, Praethalassiosiropsis, Rhynchopyxis, and Trochus. Yikes. That makes a total of 33 more genera to code up. Barf, barf, barf. Si, se puede.

Well, it ain’t pretty, and it ain’t much, but at least I’ve done something today. Better than the last few weeks. Things are moving upwards. Hey, ho, let’s go!

Monday was a pretty devastating day—better documented in DSA notes than I will here, but leaving me reeling on Tuesday. By the end of the day, I felt much better, having talked it through with Kati and Beau; I came to the point where the realization that I have a working identity, shaping and forming, and that it doesn’t include surrounding myself with people who think labor unions are an undesirable thing to be associated with.

I took most of Wednesday, too, to recover, getting some exercise in the morning (it turns out that having a strict schedule is the best way to accomplish this, and I’m glad to report that I’m back on one!) and going to see a couple of 1st-year talks in the afternoon, motivated by the last vestiges of collegiality left in this graduate student.

This morning, however, anxiety levels surged again. There was an email from PlanktonTech informing members of the structure of the forthcoming Springer Verlag book associated with the project—including two (!) chapters written by me. Spoke briefly to Andy about this, who agreed to take the lead on one of the two, but wanted an outline by tomorrow, by which time the Germans had requested a first structural draft. Then, there was an email from Dave Lazarus, telling me about his wonderful new project that is essentially my diatom diversity project, except for radiolarians, though he appears to also plan to include diversity calculations for diatoms. He is presenting the results with his PhD student (I didn’t even know he had one) at the TMS (micropalaeo society) meeting in France next week. So, it seems I am scooped, again, in a way. Fantastico.

To add dung to the steaming pile, there was a reminder from OCS that the sign-up deadline for the job acceleration workgroup was tomorrow, so I had some thinking to do this morning. Do I take my visceral response from Monday at face value, and drop out of the on-campus recruitment experience altogether? I decided that I would take part after all, go to events and talk to people, eat some free food, but not apply for anything that isn’t 100% convincing. There are sure to be one or two companies that will interest me—notably Google—and it can’t hurt to get a bit more experience in the process. So I spent some time re-shaping my resumé to incorporate Laura’s feedback from Monday, and submitted it to Amy to sign up for the workgroup. Crucially, though, I didn’t change the RSMU section. I was president of an organization called “Royal School of Mines Union”, and I’m not going to lie about it. If I had worked at the Microsoft Corporation or the RAND Corporation I wouldn’t doctor my resumé and say I had been a member of the “Microsoft Collective” or the “RAND Organization” if I was applying for a left-leaning job. On the one hand, it just seems idiotic to lie in that way. On the other hand, keeping that line on my resumé is, I think, a good canary for my own happiness in the application process. If a company is going to take offense at the word “Union”, then they’re probably not a good fit for me. End of story.

Maybe this seems like a small and inconsequential thing, but it carries some symbolism for me—a commitment that I’m going to be true to my values, to my gut feelings, and to the pursuit of a kind of work that feels genuine. And I think as long as I keep that in the forefront of my mind, stay true and honest to myself, I’m OK to go ahead and milk the job-hunting/on-campus recruitment program for what it’s worth.

The non-work portion of my worries finally out of the immediate way, I settled down to trying to get some actual research done as well, in preparation for meeting with Andy tomorrow morning. Loaded the Neptune database up in R and created a new field, N$Genus, containing only the genus name (strsplit’d out from the N$Species field). Made adjustments in the dataset to reflect mistakes I discovered in the process of describing the genera:

• Bachmannocena is a silicoflagellate (leaving this in, it simply won’t be called in the plotting)
• Bacteriosira is Bacterosira misspelled
• Bruniopsis is a synonym of Neobrunia
• Calloneis is Caloneis misspelled (wow, holy shit… there are only two occurrences of this genus?! WTF?). Round also considers this to be the same as Pinnularia, but as I coded both taxa I wanted to check for consistency and keep both in there for the time being, perhaps expunge them at the end
• Charcotia is a synonym of Actinocyclus; again, left this one in the matrix to check for coding consistency, and left it in the Neptune database as well
• Denticulopsos is Denticulopsis misspelled
• Dicladia is a resting cell (leaving this in, it simply won’t be called in the plotting)
• Goniothecium is a resting cell (leaving this in, it simply won’t be called in the plotting)
• Huttonia is a synonym of Neohuttonia (again, only ONE occurrence… holy shit, that’s awful)
• Liradiscus is a resting cell (leaving this in, it simply won’t be called in the plotting)
• Liriogramma is a synonym of Asteromphalus, retained for comparison
• Lisitzinia is Lisitzina misspelled
• Macrora is incertae sedis or at best a silicoflagellate, not a diatom (leaving this in, it simply won’t be called in the plotting)
• Muelleriella and Muelleriopsis are resting cells (leaving them in, they simply won’t be called in the plotting)
• Naviculopsis is a silicoflagellate (leaving this in, it simply won’t be called in the plotting)
• Neodelphines is Neodelphineis misspelled
• Odontropis is a resting cell (leaving this in, it simply won’t be called in the plotting)
• Opephoneis is probably supposed to be Opephora
• Periptera is a resting cell (leaving this in, it simply won’t be called in the plotting)
• Pseudorocella is a synonym of Macrora and thereby not a diatom (leaving this in, it simply won’t be called in the plotting)
• Pseudostitodiscus is Pseudostictodiscus misspelled
• Pterotheca is a resting cell (leaving this in, it simply won’t be called in the plotting); Pterothecas its misspelling
  
• Raphidodiscus is Rhaphidodiscus misspelled (though Round et al. make the mistake, too)
• Screptroneis is Sceptroneis misspelled
• Simonsenella is Simonseniella misspelled
• Stephanophyxis and Stephonopyxis are Stephanopyxis misspelled
• Stichodiscus is Stictodiscus misspelled
• Thalassoithrix is Thalassiothrix misspelled

This done, I backtracked briefly to complete a plot I meant to make earlier, breaking down the morphospace into more groups. The result was pretty disappointing. Rather than showing more structure, the subgroups of the pennate and centric groups totally overlap and don’t at all occupy different areas of the space. So, that intuitive failsafe first test of the morphospace that Andy had suggested way back when,  as a response to my doubts about the project (“it has to be true, for example, that the invention of the raphe represents the invasion of a new area of morphospace”)… failed.

To close, some country song lyrics that sum up my feelings about graduate school quite nicely (via the VPhD forums):

Well, you filled up my head with so many lies.
You twisted my heart till somethin’ snapped inside.
I’d like to give it one more try,
But my give-a-damn’s busted.

Slightly delayed, but much more optimistic start to the day. Beau has made some excellent headway in laying out a path ahead for the DSA book, which has me very excited about a project completely outside the realm of academic work, but still about academic work. Unfortunately, my MacBook has run completely out of storage space, to the point where DropBox is now complaining and will no longer sync… This is problematic. Especially as I am working from the new Starbucks in Harvard Square this morning, which is a very conducive atmosphere indeed. I priced out the cheapest bailout I could find (short of replacing the SSD in the laptop with a spinning platter hard drive, which I’m unwilling to do—I think the slowdown would drive me insane), which is to replace the optical drive with another SSD and put the optical drive in an external enclosure. That, unfortunately, comes out at $200, which is a bit of a hefty price after the financial burden of the wedding…

Hmmm. The world is conspiring against my will to work… or, maybe the world is conspiring with me against work? I don’t know. In any case, Kati got a very disturbing phone call this morning about her cousin, who was just diagnosed with progressed cancer, news that delayed the morning by a good few hours.

No progress the rest of the day… A downer. But then a very good DSA with Beau, with excellent news on his end, a concrete plan for action, and hope rekindled.

…but the beginning of a new project—DSA: The Book.

In spite of the bittersweet “last ever” backdrop of the meeting, it was very helpful—as summarized in Beau’s own words:

Andy had a look at 1 pager and responded as per expectations. Andy review was very positive, lots of good vibes. After successful previous three day push, still aware of temptation to stop and procrastinate. Continueth previous approach: make a note on the blog and then move on… Important to maintain positive and energized thinking over these periods. Also potential arrangement with Kati joining to work in evening removes possible familial stress on the three day efforts.

Ben reported not using Omniplan at all. Focusing more on getting things done. Realized he sinks too much time into making these plans, and doesn’t really use them. Nature of research is so different from what he envisaged it to be. Much less systematic and plannable than he expected. Rapid development of ideas and experiments is in principle much more suitable, although in practice not always possible. Applicable to some projects more than others. Omniplan channels a certain kind of thinking, sets up false expectations. Implies he can easily switch projects and just needs to put in the hours and be done. Not coincidental with the way he works, much more curiosity driven. Charles was trying to say this all along. However both OP and OF were useful in helping with back of the envelope calculations to check basic feasibility.

It’s clear that what is most important is motivation, not a framework. Motivation comes from success in achieving things and getting good feedback. Getting things on paper is even better – provides concrete feedback. This is why regular checking in with Andy and the 1 pagers has been so useful. Also recently snagged a big whiteboard and now has it next to desk with immediate status on every project.

In general, Ben reported feeling optimistic right now, much like back in January. Will know that things are going well and going differently when first set of results are in hand, and Andy approves and starts talking about how to write it up. At that point, can think about graduating. Don’t want to jinx anything at this point!

Ben is also thinking about getting a paper out of the confocal laser project – can he find a simple application and write at up? Andy kind of dismissive, but Ben should push on regardless. Potential collaborators in Germany? At some point in the future need to set aside some brainspace to sort out pitch to German folks.

Found myself drifting a little again, unsure about what to work on. Now that I’ve abandoned the strict 1-project-a-day schedule (which was itself a great improvement over the 3-projects-a-day schedule it replaced), and have my motivational sights set on the next three-day push, the rest of this week feels like it’s in a bit of a vacuum. Or, it would be, if it weren’t for the ever-useful deliverables set in the meeting this morning. I caught myself on the verge of slipping into the abyss of procrastination again, not knowing exactly where to start, so I turned to my gmail checklist of DSA tasks, and forged ahead…

The first task on the list was to compute the % coverage of genera in Neptune provided by those genera described in the Round et al., 1991 book. This, as a reminder, was in order to try to figure out whether I needed to code all of the Neptune genera for my morphospace analysis, or whether it would be sufficient just to consider the subset represented by those described in Round. The results are, well, sort of what I expected, though I’m not exactly sure how to interpret them.

What’s clear is that coverage does vary through time, and it does so systematically in the predicted way (i.e. the Round book more completely describes younger assemblages). Whether this bias is enough to mess up the results, I am not certain. My instict is it would: only about 50% of the genera in the database would be showing up in the morphospace in the Oligocene, but about 70% would be showing up in the Pleistocene—this could make the Pleistocene look more morphologically diverse (the sciencey way to say it would be, “characterized by greater morphological disparity”)… Anyhow, it took all afternoon, but it’s a satisfying plot! And it’s one thing checked off my list for this week already.

A really helpful DSA session this morning. Beau hits the nail on the head—what’s really holding me back, at the end of the day, is my own perfectionism. Yes, there have been, are, and will be external barriers, but everyone experiences those at some point and to some extent. The problem is that I’ve developed a totally dysfunctional relationship with my thesis—one where my monumental perfectionism leads me to distance myself from a project that I do not feel is up to the (unreasonably) high standards I expect from myself. As a result, I engage in the work at much less than my full capacity, and as a result, progress on projects slips further and further from what I expect for myself. This, in turn, alienates me further from my work, and thus the vicious cycle turns.

What to do about this? Identifying that this is going on is surely a step in the right direction, and Beau’s recognition of these emotions is worth much more than a suggestion for a fix from someone who doesn’t. I’m not sure I know what to do either, but I’m taking on board Beau’s idea of designating a few days of intensive effort, at the sort of level I know I’m capable of, and I know would me make me proud of myself. There’s always the threat of failure, and of further obstacles—in fact, that’s more of an inevitability than a threat. But at least this offers the hope of kick-starting a reversal of this nasty pattern into an opposite one of working hard, making progress, and feeling good about my project—allowing me to motivate to keep going. And finish.

So, the bottom line is: Tuesday through Thursday next week will be WorkFest I, in which I suspend, completely and consciously, my disgust for my projects, swallow my “I’m better than this” pride, and really get into it. With enthusiasm. I’ve got a few days to get myself psyched up to do it, and I’m hopeful that I’ll be able to pull it off—no matter what the outcome is research-wise. In any case, the goal is to get all of the samples for the radiolarian lineage project chosen, ready to send off to ODP for a sample request.

The other thing I realized in talking to Beau is that I’m disconnecting from Andy and the rest of my committee again, and that’s a cause of much anxiety. It’s been almost four months since my progress review meeting, and over three weeks since I met with Andy. I simply need to schedule that meeting—psychological trick or not, it makes me feel better to check in with Andy and report on what I’ve been doing, whether it’s led to great advances or not. And sending off the report I type up for him each time to my other committee members would do a lot to ease the feeling I have that they are slipping away from me again, forgetting that they are on my committee at all.

Decided to flee the heat of the office, and so decamped with Beau to Bloc 11 Café after our weekly DSA session at Darwin’s. The calendar called for diatom morphospace, but I thought I felt more like working on the E/O diversity project, so I started trying to download the Neptune database again—this time a full report including all four microfossil groups—in order to see what the qualitative preservation values looked like for the samples. Alas, the Chronos interface gave me the usual barrage of Apache server errors, and no matter how often I tried, denied me access to the database. Ah well. Back to the morphospace, then!

Started with Brunia (allegedly a synonym of Bruniopsis, which is in Neptune), described in the van Heurck book I downloaded the other day. Very hard to extract useful information from the verbal description given, on account of the rather different language used to describe the morphology. What on earth is meant by ‘a delicate cellular structure’ in the description of the frustule—surely the thing is unicellular! Perhaps this describes an areolate pore pattern? Or describes the funny lobed ornamentation at the valve edge? Anyhow, I did the best I could in translating the description of the taxon into the terms used in my character list, and moved on.

Next up was Ceratoneis, for which I’ll need to visit the Farlow. Cestodiscus was a bitch to track down. Though I eventually found a paper by Fenner (1984) describing two species of the genus, this did not help that much with a generic description. The official generic description is quoted on the Diatom Wiki—but is almost totally useless. It doesn’t really say anything specific other than that the frustule is circular or oval, and that it has ‘radiating granules or cellules’ (the latter of which I don’t understand), and a ‘submarginal circle of obtuse processes’, which I take to mean spines originating on the valve face inward of the margin.

Charcotia was next and needed a reference from Farlow. Chasea has a description in the original paper defining the genus, but the photographs are lousy and I don’t quite understand the description—it talks about the form resembling Chaetoceros, but with an ‘endocyst’: what on earth is that supposed to be? Some sort of resting stage/spore? Totally confusing. Well, as far as I can tell from the pictures and the description, other than the inner layer of silica forming some sort of central dome, it otherwise does look like Chaetoceros or some other bipolar form. Moving swiftly along…

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!