Second Day of Prep

I arrived at Dr. Farmer's Paleoceanography Lab at Hofstra this morning to start a second session of specimin prep. All went well enough. There were still a few samples that were either lost, or that seem to have too little material in them to be useable. I went back to the first day's worth of prep and collected the ones that also looked like problems. Between tomorrow and the next day I will finish the normal picks, and then also re-do the problem samples. With all that, I should have around 36 samples crushed and ready for the final day of preparation.

Thesis Proposal

Part of the process of doing a Master's Thesis is proposing the project. It is an odd requirement, since by the time you're presenting the propsal, you're already heavily invested in the project. That goes double for me, since I've proposed my project in the middle of the same semester that the thesis itself has to be completed.

The presentation went well, started at 4:30, with the process of doing a power point presentation and then a question and answer period lasting a little more than an hour. In the week prior I had written up the thesis proposal itself, which ended up being only 5 pages of actual text.

I presented to Dr.'s Christensen, Farmer, Coombs, and Russell, who together make-up my Thesis Committee. I'll have to defend the thesis before them at the end of the semester. Dr.'s Christensen and Farmer of course I am working with, and Dr.'s Coombs and Russell are professors from the department. They did seem genuinely curious about the project, which isn't to surprising. The details of my project are barely within the normal confines of biology, at least here. It seems like everyone else here is doing a genetics project, running PCRs, gels, etc. And then I come in with what looks like spoonfuls of sand 'but I assure you, they're fossils'. True enough, these professors have heard of Foraminifera, and surely are aware that they're marine protists that extend pseudopodia outwards to pick up food particles. But be damned if I've got to deal with actual living ones. These things are dead as dirt. Literally, they've accumulated as dirt. Most biologists tend to think of biology as involving things that were at least relatively recently living.
This idea actually seperates biology into two overly wide domains. Pale-ontology, and Ne-ontology. Everyone in the department here is a neontologist. If they haven't killed it themselves, or known the guy that did kill it, they don't want any part of it.

Fortunately they looked past any of that, I was genuinely concerned that there would be objections to it for being too much of an environmental studies programme sort of project. Dr. Christensen prepped me well for the presentation, I was at least able to prevent myself from trying to speculate too much and rather just admit that I don't know the answer to a question. Speculation, it seems, can be too easily received as bullshitting.

I suspect that the actual thesis defense will be a much more rigourous process. I don't expect to have the thesis accepted right off the bat; that's relatively rare. Equally rare is to have it completely rejected. What normally happens, or so I read, is that revisions are requested, and the degree is awarded sort of 'conditionally'.
One of Dr. Christensen's previous students, from another University, infact has been through many revisions. He defended his thesis before I was even in my Master's programme, and he's been going back and fort with revisions ever since. This is while already being accepted into a PhD programme.
I can't really even consider thinking about the revisions at this point, I just have to work on actually finishing the data collection and writting the initial, pre-defense, draft, first.

More forams

Met with my Professor today to go over what I need to get done before the semester starts. We're going to meet for another couple of days to review what I've gotten done. I need to reorganize my Thesis Proposal, so I can present it to a committee for approval. I also need to actually select who will be on my Thesis Committee too. Apparently I might be able to include Dr. Farmer on this, even though she is at Hofstra (and in a different department on top of that). That should be helpful, since she has direct experience with this kind of work. I will need to contact her soon to set up when to come to the lab and find out exactly how many specimens to pick for each level.
Thats the big task right now, picking the specimens. I started by trying to pick out G. bulloides from Jim's slides, I got through half of one section of the core and was barely able to find one. I think I might've picked too liberally when I was looking for Nq. pachyderma previously, and taken up all his G. bulloides. So I went back to my old slides and really started hitting a roadblock on just what defines which organism. I definitely picked a lot that weren't Nq. pachyderma, in the early slides at least. I was able to get some G. bulloides out of them too. But now I am not at all confident in my understanding of which characteristics define which. Yes, I have Kennet & Srinivasan right in front of me, but the descriptions just seem like they can go either way on so many individuals. I ended up spending a long time in the lab, but got nothing done with it.

Before all that I had to clear up an issue with financial aid. They had cut a refund check for me early in the semester, but when the TAing tuition waiving came through, they shut off the financial aid. That meant that the check that the school had cut for the refund wasn't being covered by my Financial Aide, so now I owed them for it. Luckily, all that needed to be done was to have a stop put on the check.
After that, I gave the biology office my probable schedule for Spring. Hopefully, I will be able to get another TA position. The professor in charge of doling out the positions had only picked up the student schedules earlier this morning, so they shouldn't've assigned anything to anyone yet. On top of that, one student that was a TA last semester isn't doing it again, so that should mean I am pretty certain to get a position.

Procedural Corrections

After picking around 300 individuals of G. bulloides from my six sample sets, I was able to successfully clean them over at the Hofstra Lab. Dr. Farmer was very helpful during this process.
I only had the two seives that she had created, but I don't think I would've used more than that to clean them at once.
Procedure:
I brushed the samples into the seive, then marked down which seive correlated to which sample.
I placed the seives into a regular beaker that had enough methanol to fill to the half-mark of the seives.
I placed the beaker into the sonicator, and sonicated for 3 minutes.
After sonication, I removed the beaker and then the seives from the beaker quickly and placed them on a paper towel to dry. This took a few minutes.
I then carefully tapped out the seives onto fresh weighing paper.
I curled or folded the weighing paper and poured the forams into a numered jar, which was underlain by another peice of weighing paper in case of any spillage.
I then marked down which jar had which sample.
There were some problems. The first two samples I sonicated for 5 minutes, but that turned out to be too long, they became broken up. This made it difficult to remove them from the seive or get them off the weighing paper and into the jar. I had to use a brush to do this. I used a different brush for each one, but the first brush was the brush I had used to get them into the seives previous to cleaning. It seemed like some of the sample was lost because of the breakage. After those first two, I switched, upon the advice of Dr. Farmer, to a 3 minute sonication, and no more breakage occured. The samples easily fell out of the seives and poured off the weighing paper.
Breaking in itself shouldn't be a problem, the samples are going to be crushed, vapourized, and then, to further abuse them, that vapour gets scorched into soot and that soot is analyzed for the actual dating.
At one point, I neglected to record which sample was in what seive until after sonication had started. I am nearly certain that I remembered which was which, but there is a chance that, say, sample 3 is marked as "4". This should be corrected by the carbon 14 dating.

Technical Difficulties

Technically, today was a disaster in the lab. For the past week I've been 'picking forams' for analysis. We are going to have the carbon-dated. I needed to pick out around 300 individuals of one species, Globigerina bulloides. That was expected to give me around the 10 miligrams of sample that were needed. Six sets, each from a different depth of the ocean drilling project core, were selected, those were the points that we wanted dates for.

So I pulled the specimins, and brought them over to the Hofstra lab, there is a professor/researcher there who has the lab materials and has similar research interests and was kindly enough to permit me to clean the samples there. This is a necessary preparation step before they are sent away to be C14 dated.

I had to put the specimins into a small seive that she had created (six seives, one for each set of 300). These were then split up into two large beakers, which were filled with methanol to about the middle of the seives, which were now partly submerged. These beakers were then put into a sonicator, a device that has a water bath and that vibrates, the vibration will travel through the water to the methanol and mix the methanol with any dirt, clay, sediment, and other carbon bearing materials that need to be eleminated. The non-foram carbon will screw the analysis.

After sonicating for about five minutes, I remove the beakers and take out the seives to let them dry. They dry quickly, because the methanol just evaporates away. I started brushing one of the samples out of its seive, but noticed that a glue used to hold the tiny cloth-like seive screen to the seive had become very soft. The forams were sticking to it.

Crap!

Thats not good! Forams bound up with glue! Thats allways bad no?

I hoped it was just because they weren't completely dry, so I put it down and gave them more time to dry. But it was no good, the glue dried, but at least half of the sample was bound up within it. I brushed out what I could. The Hofstra professor was completely shocked and I could tell that she was mortified and very concerned. She had created the seives herself, and had used them for the same purpose, and nothing like that happened. She speculated that perhaps the glue she used had aged and changed to become unstable somehow. We tried sonicating two seives again, hoping to loosen it completely and set the forams free. I set the sonicator timer for 10 minutes, and it did soften and loosen up, but the foram material was just immpossible to seperate. I though maybe it would be possible to dissolve the glue somehow, or flush it with methanol from a squeeze bottle, to get them out, and then perhaps boil it down on a steam bath, leaving just the forams and vapourizing the dissolved glue, but the glue wasn't necessarily dissolving, just softening.

Fortunately, the professor was able to find a different glue. We pulled one screen off its seive-ring, it had been loosened that much by the sonication, and used this other glue to hold it on. The rings for the seives are some type of acrylic, and the glue was methylene chloride, a glue for acrylics. We were worried that the seive screen itself wouldn't bind, but it turned out to work nicely once she assembled one under a hood. I was concerned that the methylene chloride would react badly with the methanol once we put it to use, so we threw in some sand and tested one out. It worked perfectly, the stuff held together, and the sand grains, a decent enough proxy for forams, didn't stick at all.

So I lost the samples for the most part, and basically have to pick them all again. I only say that it was 'technically' a disaster because I just wasn't too upset over it. Something allways goes wrong, something that forces you to start all over, and usually it happens a few times. Hopefully this is the only time it happens with this C-14 dating project, but who knows.

Contacts and Projects

I am currently continuing to work on setting up a project that can be used as my Masters Thesis. Fortunately, one of my professors knows a few people, not terribly well but well enough to hopefully get my foot in the door. We've sent emails to one worker at the AMNH, who does research in vertebrate paleontology. I revently sent another first contact email to someone at Lamont Dorety who also does paleontological work, although he doesn't just work on fossil specimins. In fact, his research might be said to be more on the geological side of paleontology, using research on magnetostratigraphy and structural geology to unravel some important events in, most excitedly, dinosaur history. Apparently his insitution only has a Doctoral programme, but its possible that he might have a project that isn't big enough for a doctoral thesis, and thus might be something that he's not had a chance to work on but would like to. If I am extremely lucky, he will permit me to work on any such project. Both the AMNH and Lamont Dorety contacts are long-stretched gambits that might not work out at all. In all likelyhood, I won't even hear back from either researcher. That is why I am also extremely fortunate that the same professor I worked on the foram project with has another project that could serve as a Masters Thesis basis. It would be looking at the morphometrics of forams. Not dinosaur paleontology, but still firmly within paleontology and something more than climate reconstruction. Climate reconstruction has proven insteresting, I can see myself doing more work in it, but its simply not my first choice.

On that, the material prepared for the poster presentation is of suffiecient size that it might be workable as a paper. I would have to look at some other ODP core sites in nearby regions, and try to relate the data from them to my site, in order to make it into a paper. That is definitly worth doing, and it should be exciting to get a chance to publish a paper no matter what the subject.

Publishing papers is, from my outsider's impression, a bit of an arcane and complex subject or art. There are many things that can go wrong with it, and even the choice of which journal to publish in can have huge effects, positive or negative. Choose one journal, and perhaps its readership just isn't interested in the subject at the time. Hopefully I'll be able to publish this in some place where it will get attention and be of some use to other researchers in the field. Thats a rather odd thing to think about, because, even if I don't do anything else with forams and climate, I will have, technically and unspectacularly, made an 'imprint' on that field. I've already gotten an email request for information on my poster, which is pretty darned neat; someone is actually interested in the work.

Presenting at a conference

The reserach has been turned into a poster, and the presentation of it has gone fairly well. Attendance at the meeting is lower than expected, but I've still been able to get a few people who have shown some interest in the research. Interstingly, a professor of one of my co-authors strolled by and talked with me about the research. That was intruiging. Lots of people have had some good comments and what to follow up with and the like.

At the moment I am typing out this entry from one of the free access computers at the conference, mostly everyone has left the poster session. Whats absolutely hysterical is that right now there seems to be some other meeting at the conference center. I had thought that someoen was just singing in the hallway next to me, not realizing that they could be heard. But now they've worked up to a crescendo, seems to be a preacher of some sort. Every other sentence is 'in the name of jesus'.

Downward Spiral

After much work, my (small) Nq. pachydermaproject has been completed. The data has been tabulated, many graphs and comparisons were made, and the poster was prepared. Thanks, in no small part to my Professor whom I've been working on this with, I know have a rather professional looking poster to present. The last few days of the project were, perhaps understandably, the most hectic. And nerve wracking. At one point we thought that the entire way we were looking at the data was completely wrong, that we had defined a parameter in a way that it wasn't being used in most of the literature. Fortunately, it wasn't, there was just some initial confusion over the terms.
I have to say, its been a humbling experience, which is what I had hoped for and anticipated. Even in the simple write up for the poster I had a good deal of trouble. Often I was making 'wild assed speculations', and it was difficult to determine exactly what the data was permitting one to say about it and the situation. I have noticed before though that the best scientific papers are the ones where, when you read their results and conlcusions, you almost feel like the person is an idiot for stating things that are so completely obvious from their data. Similarly I have noticed that some of the best writting in general is the sort that states things that are pretty basic and that perhaps wouldn't be noticable in day to day life. I have yet to present the poster, so I might be quite a bit more humbled after that!
I am expecting that the people it is being presented to will have lots of questions, and that I will be caught completely flat footed at times. I haven't had any experience with forams or this region before this project, and there is such a huge amount of literature on those subjects, that there is simply no way that I won't be stammering in many responses. I can only hope that I at least manage to not make a fool of myself.
At the same time, I can relax a little because there are going to be a lot of other posters presented, and a lot of other papers being presented, so I at least won't feel too much in the spotlight.
I had previously presented some very preliminary results in a research conference at my University, and the people I had to talk to at that were mostly faculty and a hefty dose of people who weren't geolgy students or paleontology professionals, so it should turn out to be quite a different experience. At the same time, I expect that there will be some similarities. I know that when I have been at other poster presentations, I try to very quickly figure out what the whole presentation is about, why its important, and how good the evidence and interpreations match one another. People at the University research conference were, similarly, not interested in long drawn out explanations of things that they aren't familiar with, and at least one person actually interupted my initial blatherings to say, in effect, 'what were your conclusions'. That was good, because for the rest of the University conference I had to really excise out all the uncritical stuff. If there was anything anyone wasn't clear on, and they were interseted, they would ask.
So I expect that that aspect will be similar when I do present as this professional research conference. I will be presenting for two days also, and for a much longer period of time than at the University research conference. That should make a difference also.

Sinister Coils

As previously noted, Nq. pachyderma is composed of chambers that are added in succession. The chambers form a 'trochospiral' coil. This coil can be sinistral or dextral, left or right coiling. The sinistral forms dominate in polar waters, and are a proxy for such water masses. Right now, I am counting the relative abundances of sinistral and dextral forms throughout the core. This is proceeding much faster than the previous work of picking out Nq. pachyderma from the slide sample.

I've also been thinking of what to do in the future, as in over the summer and for a thesis starting next semester. Fortunately, I might be able to do some paleontological research at a few places, such as at another local university or possibly at a museum within a paleo-department. That would be exciting. However I am also concerned about focusing too narrowly on paleontology; it'd be nice to actually have a job after getting the 'peice of paper' that is a graduate degree. There isn't much call for paleontologists out there in the market.

Bah, that's the market's loss!

Update

My access to this blog was down for a while. I had given up on it, but I see that I have access again. Thats nice.

The foraminiferal project has been interesting. I have prepared a small poster on it, and will be doing a prresentation on it in the near future. I will say one thing though, I noted below that they can move around a little bit within the water column, thats what most of the literature says about them.

However, I have discoved an entirely new form of foraminiferal locomotion, saltation!

Because every time I'd try to move one of the things around with the brush, *SPRING*, they'd jump all over the place!

I am also now looking into doing some more research. I have a few possibilities right now, some biogeochemical research might be possible, or some paleontological studies might also open up. I probably won't be doing any more work with forams in the near future. They're actualy really interesting little creatures, but it seems like that sort of research won't take me in the directions I am looking to go right now.

Foraminiferal Project

I'll be starting a new project now. Investigating paleo-ocean currents around the antarctic via studying foraminifera obtained from an ocean drilling project core.

Foraminifera are intruiging. They are animals, both planktonic and benthic forms exist, that, for the most part, have a 'shell' that is formed from calcarous minerals, called a test. Thus they are fora-minifera, mineral animals. This is shortened to "forams", which unfortunately looses and obscures the meaning of the latin.

An organism can be said to be planktonic if it resides in the water column and has no ability to swim against the ocean currents. However, a plankton, such as many forams, are infact active swimmers, its just that they swim to different positions up and down the water column, while at the same time being pushed along horizontally (and of course vertically at times) by the ocean currents.

I'll be specifically looking at a planktonic species called Neogloboquadrina pachyderma. This intersting creature's tests grow as a series of increasing ovate to spherical chambers that form a sworl. They tend to inhabit the higher lattitudes. If the organism grows in relatively cold water, the chambers form a left-handed sworl, in warmer waters, they form a right-handed sworl. Thus, by counting the percentage of right and left handed forms present, one can say something about the temperature of the surface water that they inhabit.

When alive, planktonic foraminifera can have all sorts of pseudo-podia and cytoplasmic projections stemming off of them, these things help them to stay afloat. They can also have pockets of gas or globs of fat inside of them that help them stay afloat also. They live out their lives and either die naturally or are ingested by other organisms, likesay, fish. Upon death, they slowly sink to the bottom of the ocean, where they collect on the floor as a portion of the ocean sediment. This sinking is aided by 'flocculation'. When the foram is ingested by a fish, it gets mixed with other materials and is eventually excreted. This mass then settles quickly, 'flocculating' other dead sinking forams and other organisms along the way. Thus, there is a "fish poop" express shuttle that gets them to the ocean bottom.

This is the overall process that has generated the sediments that make up the drilling core that I will be getting my forams from.

Because of the basic uniformitarian principle of superpositioning, the core sections further down are older and those closer to the top of the core are younger. Thus there is a time series. By examining the proportions of left and right coiling N. pachyderma at different sections of this series, I should be able to say something about the changing surface water conditions for that region, and thus can say something about the ocean currents that used to exist there.

The section was drilled from off of the coast of southern Africa. Thus it represents a region where there is movement of water from the Indian ocean and into the Atlantic, passing between the Antarctic and the Cape of Good Hope. Ultimately, this project will be looking at the formation of what is called the Circum-Polar current, which is the movement of water in a tight and uninterupted circle around Antarctica. Because this movement is unobstructed, it can get very stormy. Indeed, the tip of South Africa is euphemistically named the Cape of "Good Hope", because its an incredibly dangerous and stormy passage that sailors hope to get through.

The core isn't from off the cape itself however, its more north-east wards and is thoroughly a part of the Atlantic Ocean. In addition to the spin off of this circum-polar current, there is an input of water from the north. This is, infact, water that has made the global journey from the Carribean /Gulf of Mexico, up along the Atlantic Coast, over to the British Isles (where it represents an influx of heat and thus makes Britian warmer than Nova Scotia, which is at the same lattitude), and then travels down along the west coast of Africa to the region in which the core was sampled from. Along this long route, the water is giving up its heat and sinking, thus by the time it gets to the study region, it is Cold Deep Water. From there is moves back across the Atlantic and into the Gulf/Carribean region, to continue cycling.

It should be an interseting project.

Neogloboquadrina pachyderma fossil, left-coiling variety. The Bar represents a length of 1 mm:

Neogloboquadrina pachyderma fossil, right-coiling variety: