Siliceous and Delicious

After a restorative run and morning squash game with Mark, I spent the morning preparing a second set of SEM stubs of the diatoms I had sonicated and cleaned yesterday afternoon (the batch I’d made yesterday seemed a little too dense, having left behind a thick chalky white dot where the water dried up). I booked the next available SEM slot, which—miraculously—was at 1pm today, raced to get the stubs sputter coated, and checked them out.

The results are not far off what I expected to see—a lot of flimsy, warped diatoms—and also indicated that even the little sonicating I did yesterday (one blast of about 30 seconds or so, then three more short blasts of <5 seconds) was too much for these weakly silicified things, turning most of the material into rubble.

Here a selection of what I saw.

Each sample had a sharp edge where the water droplet was—with a lot of indiscriminate goop (organic matter?)/fine-grained debris over most of the surface, except at the edge, where some coarser material was visible:

There were some moderately intact valves amidst the debris:

Many of those looked like they were so flimsy they were essentially warping or folding; some had very large-pored/flimsy “skirts”:

The second set of samples I made were a little less crowded, but still far too dense:

Even the best-preserved specimens didn’t look like much:

For comparison, this is what the species I’m looking at here —Lithodesmium undulatum—is actually supposed to look like (courtesy of this website):

Finally had my training to use the sonicator this morning; it went quite well, there doesn’t seem to be too much to it, though I will need to buy some little Eppendorf tubes in which to do the sonicating, and figure out a way to rig up the tube and its ice bath so that it is held up under the probe. I came back to the office and grabbed lunch, but then didn’t find there to be quite enough time before I had to be back for lab meeting, so I tied up a few loose ends, and took a first look at some of the diatoms from the frozen vials I got earlier in the week under the microscope. I was not dazzled by what I saw—now, I’m no expert, but it struck me that the frustules on these things looked extremely thin and fragile, and they didn’t look none too large, either. Of course our microscope has no measurement system, or even calibrated graticules, so I don’t really know, but it seems to me a distinct possibility that the cells (at least the ones I looked at) were harvested right at the brink of the stationary phase, where silica was depleted and so the frustules are thin. That, of course, would suck ass for what I’m trying to do. In any case, the cells looked so flimsy to me that I couldn’t even tell whether the frustules were intact or not—there were no pores or striations to be seen, or any cellular structure really beyond the brownish blobs I took to be the plastids.

Bumbled in rather closer to lunchtime than the morning today, but found that my harvested culture had finally arrived from the CCMP. I set to work immediately and spent the remainder of the morning bustling around—finding somewhere to store the frozen samples (Dave’s lab has a new freezer in which they found a home), finding a way to dispose of the dry ice (Ann’s lab found a use for it), and so forth. In the afternoon, set out on a mission to start using the sonicator—a mission, like all grad school missions it seems, that was far more odyssean than I could have imagined. Not only did I clean out a nook in one of their back rooms to have a space to use the sonicator, then move the hulk of a machine from the lab to that space; not only did I subsequently move the machine back to the lab after a grad student complained that the thing would be too noisy in the room next to her office (understandably enough of course), but I also had to settle on Friday morning as the first available time to be trained to use it. So, it looks like this project’s on hold for the rest of the week.

Of course, I’d have to wait anyway, since (as I found out) there isn’t any of the particular detergent (“RBS-35”) mentioned in the Crawford paper whose methods I am trying to follow available around these parts. And since this means putting in a VWR order with Diane (which I promptly did, after searching around in the Knoll and Pearson labs), it may be weeks before I see the stuff.

I had to cut the day short to answer one call for departmental community service I couldn’t turn down—Tom had asked me to come to his quals practice talk, feedback which I recall appreciating tremendously, so I had to return the favor (karmically speaking).

So, I didn’t get to writing the comments for Dave’s manuscript—and I don’t hold out too much hope for it tonight either. It feels like crap not having done it, but on the other hand, I really, really don’t feel like doing it. I know it’s awful, but I just can’t seem to help myself!

Arrived at work just in time for a meeting with Jacques about the diatom sonication project and what next steps to take, now that the culture is harvested and seems finally to be close to departing for Boston. Jacques agreed with my plans for cleaning, then sonicating the frustules at various intensities, though he made the very helpful suggestions to a) look at them under the light microscope to check initially how well the sonication has worked, and b) rather than sonicating different samples at different intensities, and then examining the results (which is what I had in mind), sonicate for a couple of seconds, examine a little bit, then sonicate some more, etc. This seems like a much more sample-efficient way to deal with the problem of finding the right sonication intensity/time.

The rest of the day just wouldn’t take. Read the papers for lab meeting this afternoon, but found them to be utterly uninteresting, even though they’re closer up my street (research-wise) than anything else we’ve read for lab meeting in months. Then sat in front of Dave’s paper, agonizing over what I should write in response. “Thanks for the vision of doom, Dave, that’s great. We can’t do macroevolutionary studies on microfossils”.

The abstract is good. The introduction is fine, outlines what’s been done with microfossil data and what Neptune is. The section on “The pelagic realm” is clumsily written, but makes the point that lots of the known protist groups are in the plankton, and that they’re quite widespread in oceanic provinces. Their populations are large. The “Preservation of pelagic marine plankton…” section makes the good point that only a few of the groups of planktonic protists actually have a fossil record at all, five out of twenty-six protist groups, as compared to 10 (20 including Lagerstätten) out of 30 metazoan phyla in the marine shelf record.

“Preservation at the species level” starts with the distinction in importance of species between micropaleontology and animal paleontology—with the assertion that species don’t matter much to most paleontologists, but are crucial to microfossil workers. I’m not 100% sure I agree with this. Aren’t the exact same sort of morphospecies just as important in ammonites, for example?