Siliceous and Delicious

A day for miscellany. Started by tackling email, got a message from Dave reassuring me that I did not tread on any toes with my Neptune database request, but that it was not in fact openly available in full. Wrote most of my regular mini-progress-report for Andy, and spent the rest of the morning at the Farlow library getting my hands on the papers I needed. I got very nearly everything I needed, with the exception of one reference. Weighed down with two huge, bulging bags of books, I now have a monumental amount of photocopying (or scanning, I haven’t decided yet) to do this afternoon.

After lunch, finished writing up my report for Andy. Also found Wil and asked him about dry ice—I wasn’t sure where to get it, how long it would last, what kind of container it should go into, etc. and he was tremendously helpful. In about three minutes I learned everything I needed to know, which would have been impossible to find out any other way (of course, all of this is the sort of information everybody who does microbiology/enzyme extractions/DNA work knows how to do, but doesn’t bother to write down). I now have an appropriately sized cooler, instructions on where to buy dry ice, and how much, and what it will cost, and how long it’ll stay cold. Done!

Had my meeting with Andy at 2:30, which followed a now almost completely predictable format—I hand Andy my report, we go through it, he tells me things are looking good, and keep working. He didn’t have a whole lot in the way of feedback, although he did agree with me that Annika’s concern about the stratigraphic coverage of her Lophocyrtis was less of an issue than she suggested. He also asked a good question in my discussions of the various calculated preservation statistics I showed him (for the diatom diversity/e-o project), which made me realize it would be helpful to also plot diversity on those graphs, to see how—if at all—diversity can be explained by preservation. He also raised the point (though indirectly, and I’m not sure if it was intentional) that it’s ever so slightly sketchy to test explanations of Neptune diversity patterns by using statistics calculated from the same underlying diversity data.

After the meeting, and an extended trip to cookies with our new postdoc Walton as a reward, it was time to head down to the photocopiers and start working through the ginormous pile of literature I brought back from the Farlow this morning.

It’s not exactly the crack of dawn, but it’s an improvement—I’m reporting for duty on the second day of the second push a good half an hour earlier than yesterday. And raring to go (sort of). Throwing myself right back into the swing of it, I’m looking at Neobrunia, which Round states is a substitue name for Brunia, the same situation I encountered when I was covering Bruniopsis. Now, perhaps I’m really getting better at this: thought I’d just do a quick googlation before moving on to the next taxon, and found a paper with a reference to a description of Bruniopsis, which will be helpful for both that and this taxon. Slammer.

Next up is Neodenticula, for which Round refers to a DSDP report and claims synonymy with Denticula kamtschatica, at least for the type species. The DSDP report has an adequate generic description. After a brief intermission to print my study card, get it signed, and carry it across campus (to avoid a $40 fine for missing today’s deadline), I moved on to the next taxon.

Odontotropis was first described by Grunow in 1884, according to Round. That’ll hardly be a useful reference. Bolli has a paragraph about O. klavsenii. It looks suspiciously hyaline, which—from what I’ve read over the course of compiling this character list—suggests it might be a resting stage rather than a vegetative cell…? Indeed, a search throws up a reference to this paper title: Suto, I., M. Watanabe, and R. W. Jordan (2008b), Taxonomy of the fossil marine diatom resting spore genus Odontotropis Grunow, Diatom Res., in press. That’s evidence enough for me to let it be and press ahead.

Opephoneis is next. It doesn’t appear in the generic names index of Round at all (which is unusual!), and nowhere on the internet, except in the listing of taxa in one ODP hole. There, it’s O. martyii, which is also the type species of Opephora, which I’ve already covered. I interpret this as a misspelling/invalid name—Opephora martyii is probably what was meant. Moving on.

Peponia is a little harder. There’s a paper in the “International Journal on Algae”, which is not available—in print or online. There seems to be very little else out there, which is frustrating. The IJA paper is for purchase for $35, which I’m certainly not willing to shell out. Stupid oopid. Eventually sent an ILL request for the paper and decided to move on.

Periptera. Here, again, Round suggests the genus may be a resting stage of Chaetoceros, much as with Goniothecium.

Pseudodimerogramma. Again, DSDP comes to the rescue. Woot.

Pseudoeunotia. Round refers to an 1881 Van Heurck paper. Yich. There’s a paragraph in Bolli, which helps a bit. A DSDP report has some LM images, and a reference to a description by Hustedt, which appears to be in the Farlow libary, in an English translation, even. Check and move on.

Pseudopodosira. A Jousé reference from 1949 is what Round has to offer. Nowt in Bolli. Added to my to-get list a conference volume allegedly containing a paper entitled “Morphology of the Diatom Genus Pseudopodosira” by Olshtynskaja. Moving on.

Pseudopyxilla. Found the original paper online, but in Italian. A more helpful (but incomplete) description in a Gersonde & Harwood paper. The original has a description in Latin:

Frustula libera, singula (vel bina, apiculis, ut videtur, inter se conjuncta aut conjugenda) plus minusve longe cylidrica, hyalina, vel, in margine tantum valvae exterioris, subtiliter granulata, apicem versus semper hyalina; valvae inaequales, exterior plerumque interiorem omnino amplectens; valva exterior in apiculum varier instructum plerumque abiens, sed etiam cupulata (ut in P. Tempereana); interior vice plerumque faciem opercularem delicatissimam, aegre conspicuam praebens, nunc superficiem subplanam, nunc leniter convexam ostendens.

Now, what does that mean? An online translation tool helpfully suggests the following:

To break to pieces free , alone ( or bina apiculis , when videtur , among himself to unite either conjugenda ) much little far cylidrica hyalina , or , upon margine only valvae exterioris , precision granulata , writing towards always hyalina valvae inaequales , foreign for the most part interiorem altogether to embrace valva foreign upon apiculum variety versed in for the most part to send away , but as yet cupulata ( when upon P. Tempereana ); to slay events for the most part the making opercularem delicatissimam , with displeasure striking to offer , now surface subplanam , now gently to shatter show.

Wow. That’s actually harder to understand than the Latin by itself. Remarkable. I guess I’m going to use what I can extract from the Gersonde & Harwood paper. And move on.

Pseudorocella. Not in Round. Turns out it’s a synonym of Macrora, and as I found out yesterday, thus not a diatom at all. Boom.

Pseudorutilaria. Diatom wiki has the relevant snippet from the original reference (of 1886) that says it’s basically the same as Rutilaria, but missing the central clasping apparatus. Easy.

Pseudostictodiscus. Tricky bastard. Various lone images in DSDP/ODP reports, but nothing in the way of a decent description anywhere. Ended up adding the original reference to the list of papers to get at the Farlow, and moved on.

Pterotheca. Round refers again to that ghastly Italian paper. Yech. There are some hints in snippets that this is also a resting stage… A passing remark in a paper by Suto is enough for me—it’s a resting stage, and I’m ignoring it. Moving on.

Pyrgupyxis. Round mentions this genus is very similar to Pyxilla and is seemingly agnostic as to whether it is truly separate or not, and also mentions the possibility of it being a resting stage (but does not support this idea strongly at all). Downloaded the original citation referred to in Round, which I eventually found (after much hunting) in the biodiversity heritage library as a PDF.

Rhaphidodiscus. Something in Bolli, but no picture or details. Original reference ancient and unlikely to be helpful. Found reference from 1988 in a book that’s in the Farlow that promises to be more helpful. It’s on the list, and on to the next taxon.

Riedelia. Round refers to Russian paper from 1971. That’s a no-good-thanks for me. I’ll stick with the Schrader & Fenner description of the only species in Neptune, R. claviger, which is in a language I can understand and a publication I can access. Rad. Moving on.

Rossiella. The original reference in Round is to an Indian paper from 1948. Found a way awesomer paper that describes the genus in excruciating detail (Yanagisawa 1995). Next!

Rouxia. Round helpfully points to a DSDP initial report with a relatively up-to-date (at the time of its publication!) description of R. californica, but unfortunately it’s not quite clear how generally applicable to the rest of the genus this description would be. I went with it anyway, and was satisfied—and thus decided to stop here for the day, it being 8:30pm, things going well, and being within 10 genera of the end of my list (at first pass, of course). If all goes well, I’ll blaze through those 10 genera tomorrow morning, and make my first trip to the Farlow library to get those references.

I think I’m doing pretty well.

Spent the morning unboxing my possessions and moving back into my office, now sporting a sexy new carpet and fetching off-white walls. And a whitewashed ceiling now lacking chipping paint and mold. After having essentially taken Friday and Monday off, combined with an intensive weekend, I found myself feeling quite disconnected from work and tempted to wile the time away without getting back into it.

Fortunately, there’s a memory left of the great momentum I was able to build up over the Great Leap Forward last week. I’m a little skeptical of returning to my previous model of one-project-a-day, now that I’ve seen how much I can get done if I really let myself delve deeply into a project for a three-day push.

Alas, there was no work to get done today—just as I had finished unpacking, taking care of emails, and had a bite to eat, my visiting friend showed up and that was the end of the working day for me.

Moved Beau and Mo to Julie’s, and a portion of my stuff back into the office.

Private Kotrc, slogging in to report for… yawn. It’s a little later today—9:05—on account of a very, very wet and cold run this morning, and in spite of popping out of bed at 5:30. Anywho, I’ve got no time to lose, and I’ve got a project to press ahead with. Still on Stichocorys, for which I eventually found 3 samples last night before I was kicked out of Darwin’s at 9pm. Today I’m starting the day at Kati’s office, where I have been generously offered some desk space in Nicole’s place, although I will most likely move at some point during the afternoon when Kati leaves to hang out with her mother.

Ran into problems fairly soon with Stichocorys. I had started out choosing samples from the Pacific, but couldn’t find MRC samples from the Pacific as time went on. My options are to go back and see if I have better luck with the Atlantic, or say fuck it and mix Atlantic and Pacific samples—although I fear this will undermine the credibility of anything I come up with to a potentially devastating degree (it could then easily be argued that any trends I see are just biogeographic bias). So, time to go back to square one and see what the sample distribution looks like for the different ocean basins. Another exercise in wrangling R’s plotting tools.

Well, it took almost an hour, and all it did was to confirm what my initial hunch was—the Pacific is my best bet (by far)… I suppose I just have to muscle through with the samples I have in the MRC, and skip those intervals where there’s nothing or nothing good.

Site 64 (of leg 7) seems to harbor a lot of these occurrences, but there are only a few samples in the MRC database from that site, and they haven’t got associated depth or age determinations—so I have to make those manually myself, consulting the original DSDP publications for what depths those core and section numbers represent. Yech. To make matters worse, this proved to be extremely confusing, because protocol seems to have changed over time in how holes at sites are numbered—the report refers to holes 64.0 and 64.1, while Neptune refers to holes 64 and 64A, which I can only assume are the same things…

A surge of panic struck as I noticed that some of the samples I’ve been selecting from the MRC database don’t carry the designation “finished” in the “status comment” field. This could, of course, be a simple matter of curatorial laziness/inconsistency, or it could mean that these are samples that exist at the MRC as residues or unprocessed samples only—not as made slides. What I’ve been doing since I noticed this is to also add, wherever possible, a sample that does include the reassuring “finished” comment, just to be sure—it’s easier to order a sample and not end up using it than not to have a sample you need. I’ll make the call at the end of this three-day work binge as to whether I’ll go back and seek out alternates for those non-“finished”-bearing samples that I chose prior to recognizing this fearsome possibility.

The next frightful fit of frustration came when I realized I’d made a foolish choice in only looking at Neptune occurrences designated with “C” (for “common”) abundance, something I’d done in an attempt to pick samples containing many of the target species rather than just one or two. Only, I realized that there are other abundance codes that I should consider, too—specifically, “D” (for “dominant”) and “A” (for “abundant”)… now I wonder if I should go back (again) and start over… ack!

Found that I can get a fair amount of coverage (at least as far as Neptune is concerned—no idea whether this reflects made samples actually available in the MRC collection, there’s the rub) from sites 16:158 and 138:844B, for the interval from about 15 Ma onwards. So, I’m going to go back to 15 Ma and see if I can find samples from those sites. Of course, it just so turns out that the MRC database is missing sample depths for 16:158, so I have to go through the exercise (again!) of digging up the DSDP report, finding the core logs, and calculating each sample depth myself… What a drag.

Unbelievably, at just before 4 pm, it seems I finished selecting samples for Stichocorys! Shit a brick. In other exciting news, I got an email from Annika Sanfilippo, whom I had emailed to ask about samples for Lophocyrtis, who sounded excited and very helpful—she has most of the samples (anything that doesn’t contain holotypes) for the study in her collection at Scripps, and she seemed to be willing to supply some (at least that’s what I read between the lines).

So! Now it’s the half way mark—three lineages down, three to go… and with one (possibly? or more?) on the way from Annika, the outlook, for once, is positive. It’ll take some time—she’s out of the office for another week or so—but hopefully it’ll make things easier. For now, on to Centrobotrys, but this time, I’m going to start where I should have started in R last time: with a more thorough search for a single site or, failing that, a couple of sites that will provide coverage of the whole range. Better to have only a part of the range covered, but have samples from a single site, I think, than to cover the whole range but have a patchwork of sites.

Except before I do that, of course, I need to see what’s out there in terms of literature, what species are in the lineage, and whether there’s a site or sites described which I could use as a go-to for getting samples… Sanfilippo and Riedel (1973, DSDP IR Leg 10) describe C. gravida as the ancestor, C. petrushevskayae as the intermediate, and C. thermophila as the descendant. The Nigrini and Sanfilippo ODP technical note agrees. The Bolli volume has much the same story, illustrated thus:

Interestingly, in the 91 samples I found in the sites that seem the best candidate for localized coverage (89:586B, 30:289, 7:64, and 7:64A), the order is not quite right… the oldest samples contain C. thermophila! Maybe they’re reworked, maybe they were misidentified, whatever. I’m not going to let it stop me, I’m cracking on with sample selection. Boom! Slam! Alas, 7:64 is out (no samples in MRC), and there are only a handful of 7:64A samples. There are some 30:289 samples, and even some 89:586Bs, too. So maybe I’m in luck after all.

And at 9:27 pm, I finished (I think!) selecting samples of Centrobotrys. Celebration! How valuable the half hour feels I now have to myself before it’s time to pass out in bed… I’ve worked hard and achieved a lot today. I don’t want to judge the Big Three Day Push before it’s completed, but so far it feels good to make headway. Really good.

Private Kotrc, reporting for duty. It’s 8:31, I’m installed at Darwin’s with a cup of coffee and another one already pre-paid, four swift miles under my belt and two cookies seeking to join them in the course of the morning. I am amped and ready to go—the radiolarian lineage project had better prepare to meet its maker.

Step one is to look over the two Sanfilippo papers I found last week, which may harbor some useful information on the Lophocyrtis lineage, and where I might find samples from which to study it. The Sanfilippo and Caulet (1998) paper, which I recall was one of the two, is of limited use, because it’s focused on the Lophocyrtis lineage at high latitudes. Since my master’s work (along with Dave’s undergraduate student) demonstrated that most of the change in silicification occurs at low latitudes, and that the high latitudes see very little change in silicification (if any), I want to be looking at tropical samples for this study.

For some unfortunate reason, I don’t seem to have saved the second reference I discovered—so it’s back to google scholar. Aha. There it is. Well, upon a first reading, it doesn’t necessarily make my life easier… One point of some concern is that she says the 150µm size fraction was the most useful for these forms—but the prepared slides in the MRC are (almost all, as far as I know) sieved at 63µm. So, the material I need may be missing. Also, her paper describes a whole host of descendant lineages from the ancestral Lophocyrtis, and it would of course make most sense to quantify silicification through the ranges of all of them. This seems like an unreasonable amount of work. If I am to choose, though, how to choose which one(s) to study?

I wonder if Sanfilippo has the samples used in that paper in her personal collection. Should I just email her to ask? I drafted up a quick email, but decided to move on to the next lineage quickly before losing too much momentum, as I could feel my motivation starting to flag a little.

The next lineage down the list is Artophormis. Let’s see if that’s any easier to get a handle on. Another search on google scholar confirms there are no useful references on this lineage beyond the entry in the Bolli volume (which was the reference I cited in my “game plan” document). There is a description of both species, A. barbadensis (the ancestor) and A. gracilis (the descendant), in the ODP Technical Note #27 (“Cenozoic Radiolarian Stratigraphy for Low and Middle Latitudes”, Nigrini and Sanfilippo, 2001), and it supports their evolutionary relationship, though it gives no additional information. In a sense, this makes things easier—I am looking for 15 samples that contain either species, over their stratigraphic range. So, into R I delve…

The most promising single-site candidate for this lineage is leg 41, holes 366 and 366A. They cover most of the range of the taxon… but the occurrences appear to be mostly A. gracilis, with only 5/61 being A. barbadensis. This might be a problem. Let me see how much A. barbadensis there is in Neptune at all. Hmm… again, the data in Neptune suggest that things aren’t as clear-cut as the literature would suggest: A. barbadensis (blue in the image below) doesn’t just change into A. gracilis (red squares) at the E/O, but they seem to coexist, and the ancestor seems to persist well into the Oligocene, and at least one sample suggests it’s still around in the earliest Miocene (although, this could of course be due to any sort of error, too).

In any case, I’ll go ahead and select samples adequately covering the ranges of both species according to the view afforded by Neptune, since it’s what I’ve got to go by.

Continued working on this after lunch, for which I had to return to the office (for use of the microwave), but found that progress slowed immeasurably once I was back in the windowless, fluorescent-lit hole I’m relegated to now that my office is being “refurbished” (these quotation marks justified by the complete absence of any workers since Thursday). Alas, I’m stuck here for the afternoon, as it’s not worth moving since I have to back here at 4 pm for lab meeting, which I don’t have the balls to miss—Andy was so excited, and seemed to really want me to be there. It doesn’t seem smart to snub your advisor when the aim is to graduate, and he’s the man who will make that happen.

Anyhow. My brilliant hunch to use site 366 for all my Artophormis needs fell flat on its face: the MRC collection does not have slides made at the relevant intervals. This is a bit of ginormous bummer, because I’m now going to have to scrounge around other sites and patch something together, probably from various ocean basins. It all goes to show that the Oligocene is a bit of a shithole when it comes to microfossils. It’s surprising that it would be so hard, given the great cloud of Oligocene points in the Neptune database, to find made slides that might contain Artophormis…

So, on I pressed… Had to stop for lab meeting, which was—unsurprisingly—pretty uninspiring. Andy announced that lab meetings would rotate among various levels of inclusivity this year, from once-monthly meetings of just the Knoll group, to those including the Knoll, Johnston, and Pearson group, to those including the whole geobiology group (including MIT). A heinous approach, if you ask me—lab meetings are barely ever productive as it is, and the bigger the groups get beyond that, the worse it is… Fortunately, a bigger group also means it’s less likely I’ll be missed if I don’t show up… which I imagine will be a frequent happenstance in the months to come.

At just before 7pm, I finished sample selection for Artophormis, the first completed task of the day. Not terribly motivating—at one lineage per day, it’ll take me another four days to finish sample selection (rather than the two days I have set myself as a target)… But, this is the Great Three Day Push, and thus not the time for doubt or dalliance, but as in other sorts of labor, the time for sharp, fast exhalations and pushing hard.

I resisted the monumental urge to reward myself with some procrastination I felt I had earned, and instead pressed ahead to the next lineage, Stichocorys. Not tremendous amounts of literature immediately apparent, so far as I can tell. According to the Bolli volume, and Sanfilippo & Riedel 1970, and the ODP technical note, S. delmontense is ancestral to/evolves into S. peregrina. S. wolffii is considered ‘probably not a good biological species’, so I’m best off disregarding it, I think. I can’t find anything about the phylogenetic relationships of S. johnsoni, and the other species of Stichocorys in Neptune (diploconus, armata, seriata, and biconica) don’t seem to have much in the way of mention in the literature at all (certainly not in the ODP technical note). I’m going to disregard them all for now; fortunately S. delmontense and S. peregrina make up three quarters of the of the Stichocorys occurrences in Neptune, so I should be OK.

I’m going to call the overnight run a partial success—in the spirit of my renewed attempt to be positive and enjoy my work. It did produce a very nicely cut and polished cross section of one diatom. However, when I arrived in the morning, I found the instrument stuck in an infinite loop of beginning the polishing operation (milling the last fraction of a micron slice of diatom with a very low-current beam), in which it was repeatedly stepping through the first thirty seconds or so of the polish, then performing drift correction, and then starting over. Having watched this merry-go-round for some twenty minutes, I aborted the process and shortly thereafter witnessed the FIB throw itself into some flurry of error messages that ended the day’s productive work on the machine.

This can probably all be corrected quite easily if I spend more care and time on setting appropriate milling times and parameters in the setup for the next run—this time, I spent a good two hours trying to get the beams focused, stigmated, aligned, and coincident… Setting drift correction to kick in every five or ten minutes (rather than every thirty seconds) will probably be more than sufficient.

Spent the rest of the day working on the “1-pager” summary of the diatom diversity project, which is rapidly ballooning to fill a second page, though in my defense it also contains three graphs so far. And, producing these graphs takes time—today, for example, I spent a good portion of the day calculating and plotting quality of preservation (as recorded qualitatively in the Neptune database in categories of Good, Medium, and Poor). It was kind of a big effort for something so simple, but it does show that the Oligocene dip in diversity also corresponds to a dip in preservation quality. So, there may be something beyond just biology going on!

Finished selecting samples for Didymocyrtis—Diartus lineage. Moved on to Lophocyrtis and was lost as to which species to use. Then found two very useful Sanfilippo papers for the latter, which will no doubt make sample selection much easier.

The morning somehow, magically, disappeared into a long run and a proof-read of Ben Gill’s Toarcian OAE paper. Once I got myself into work, had lunch, and worked my way through the administrative chores (emails, setting up a FIB overnighter for next week, etc), I was into a good part of the afternoon.

The plan for today called for diatom FIB, but as I’m de-emphasizing this project after my last conversation with Andy, and am waiting for the first overnight session next week (as well as waiting for the diatom culture to be harvested by the CCMP), I thought I’d return to the sample selection exercise I’d been making such good progress on yesterday.

Was interrupted by the arrival of our new postdoc, Erik, who asked for some help bringing his filing cabinet up to the office. An offhand remark of his threw me off and served a bit of a major motivational blow for the rest of the afternoon.