Friday, 26 September 2008

The evolution of an organizational system; or more information is better!

Right from the beginning of my PhD project I had a lot of reading to do to get up to speed on the project. Before I started this project I knew nothing about the geology of my new field area, and very little about metamorphic petrology. Sure, I knew that petrologists could come up with estimates on the temperature and pressure at which minerals grew, but I knew nothing of how they accomplished this feat. However, all of that reading I did during the first couple of years of my project was just that--reading. I didn't do much (any?) note-taking beyond the required "literature review" that I needed to turn in with my "preliminary plan" for the PhD project. Indeed, once I'd turned that in and proceeded with the data-collection phase of my project I found myself doing less and less reading of the geologic literature, and soon lost track of what I had and had not actually read (as opposed to simply obtaining a copy).

At least I had a good idea of what papers I had copies of, and in what format. I use EndNote to generate a list of papers cited within a document and keep my list of papers I’ve seen organized. I set up extra fields in EndNote just to keep track of my own filing system. One I call "label" into which I type a short description of the general topic (e.g. "geothermobarometry" or "crystallization"), which is also the name of the folder in which the paper is filed (if I have it in pdf format). Then, if I am looking for a paper on a specific topic, I can sort the full list in EndNote and look at the list of just the papers on that topic. This makes it much easier to find a specific paper than if I needed to look through the full list (344 references in the list so far!). I've also got a field named "format/where" in which I record if I have that particular paper in pdf, or I have a paper copy, or I checked it out from the library, or it is in the department thesis cabinet collection, or if I borrowed it from my advisor and have since returned it. This makes it simple to find papers or books again if I need them. However, I eventually found that knowing where to find a paper isn’t always good enough.

Two years into my project I was conversing with one of my friends about a 100-a-day skills challenge wherein the participants practice 100 repetitions of their chosen skill a day (usually physical skills, such as juggling, or dance steps, or whatever). The goal being to see how many days in a row one can manage, and see how much the skill improves whilst doing it. Thinking of that challenge I decided to apply a variant of it and challenged myself to read something from the geologic literature every day. 100 being too small a number where reading is concerned, I settled upon "1,000 words a day" (or roughly the equivalent of reading for abstracts) as my goal. And promptly set up a spreadsheet to track the days, what I read each day, and if I had any comments to make on the reading. Initially I only recorded the author name and year of publication, but after a bit of time I started also recording the title of the paper (or book) and the name of the journal in which it was published. However, other than those comments, I still wasn't really taking notes.

Sometime more recently one of my friends persuaded me to obtain a program designed to help one organize their "to-do" list. Realizing that I'd been downloading more papers "to read later" than I was actually reading, I begin a category in that program called "things to read" and started making a note there whenever I downloaded a new paper. Sure, that information was also in the spreadsheet recording my "1000 words a day", where the "comment" would say something like "downloaded a copy to read later", but I wasn’t actually looking back into the comments field of the spreadsheet. Creating a single list of everything I’ve obtained that I haven’t read yet made it easer to figure out what I should read next. Months elapsed before I realized that when I added a new paper to the list, I should also use the "notes" field to record *why* I'd downloaded it. Did I find it while doing a search for a specific subject? Was it referenced in another paper and I thought I should follow up on it? Did my advisor give it to me to read?

I'm now working on a part of my thesis wherein I need to talk about *why* I chose certain methods to do certain tasks. This means that I need to make reference to papers written by other geologists who chose similar methods, or to papers which used a different method and explain why their technique won't work for me. So now, I am actively taking notes as I look through the list of papers on the general topic, trying to find those which address the specific issue upon which I'm currently writing. As I find them, I type (or, when possible, copy-paste—how much easier a scholar’s life is in the modern age of papers published as searchable pdf files!) quotes into a file to sort out later, once I’ve finished the collection part of this minor literature search. However, in addition to putting these quotes into a single file, I am also copying them into that scheduling program in the “notes” section associated with the paper (most of which I can move to the “papers read” folder at this point), so that I still have them later, if I ever need to look such things up again.

All of these little techniques to keep track of what I’m reading has really paid off, and, so long as I manage to continue them throughout my career, will make the process of keeping current with the literature, and knowing what sources to cite when writing my own papers ever so much easier. I only wish I had thought of all of them sooner, so that I had better records from the first part of my project as well!

PS: for my 1000-words-a-day challenge, I keep track of the number of consecutive days I meet the goal and read 1000 words or more (often much more!) from the geologic literature. Occasionally I forget, and then I have to start my count over. In the past 455 days I have forgotten on eight separate occasions. My current count is 93 days in a row, which is my second-highest count yet (my record is 112 consecutive days, and my worst was only 7 days before I got distracted and forgot a day). How many of you would be able to beat my record? How many would want to thus challenge themselves?

Saturday, 13 September 2008

Now you see it, now you don't

When I first arrived in the Brooks Range to do my Master's Thesis field work my advisor, who was able to join me for only the first day or two of my summer mapping, commented to me that sometimes the lighting really matters--that some folds, like the ones just there, in the Kayak Shale on the ridge above my camp, will only show up when the light is perfect. Having said that, he promptly took out his camera and begin taking photos. Being a dutiful student, I too took photos of the ridge, and, at the time, I was quite certain I saw the minor parasitic folds we were recording for posterity.

However, after he left I spent two more months in the field, tromping around my field area working on my map, and each evening, when I returned to camp, I'd look up at the ridge above my camp at the patch of shale, scratch my head, and wonder what we'd taken photos of--all I could see were a few sheep trails and no sign of any folds.

It wasn't until my very last week in the field that the sun was at the exact correct angle once again, and I looked up at my ever-present ridge and lo and behold, there were the folds, clearly visible! Needless to say, I hurried to grab my camera and once again took photos, to be certain that I had a record of them--they were so clear and easy to see.

The next day I looked back up the hill, and was not in the least surprised when I could not see the folds. My advisor was correct, sometimes the light does have to be at exactly the correct angle.

Wednesday, 10 September 2008

I spend my days making graphs

There are a variety of techniques used to determine the temperature and pressure at which a group of metamorphic minerals grew. All of them have been built up over the decades by dedicated scientists who combine information from the study of thermodynamics and various experiments wherein real minerals have been made to grow in laboratory conditions. The one I have been using involves a suite of computer programs, which, if given the composition of the rock sample, will plot a diagram showing all of the possible combinations of minerals which grow from those ingredients at any given temperature and pressure. If all of the minerals present have uniform compositions, then it is a simple matter of comparing the list of minerals that are present with the list of minerals which should be present and thereby get a good guess as to the temperature and pressure at which they grew (how good will depend on if the "field" for that particular set of minerals is a large or small one).

However, if there are minerals which are "zoned" (their composition changes from the center to the rim), it complicates things. You see, for this technique to work, all of the minerals have to be in “equilibrium”, which means that the chemical reactions which make them have to have “gone to completion”. An entire zoned mineral, by definition, can’t all be in equilibrium with everything else present, but it is possible for the outermost bit of it to be in equilibrium with everything else present, and the inner portion to be “frozen” and no longer participating in the chemical reactions which are taking place outside of it. When this happens, the “bulk composition” of the wherein the chemical reactions are happening is constantly changing as some of the ingredients get “frozen” in the center of the zoned crystal. In such a case if you know the composition of the entire rock sample these diagrams only tell you what minerals could have been present way back when that zoned mineral first started growing, which list may or may not bear any relationship to the ones which are present now.

So, how can you read the diagram when there are zoned minerals present? You can’t tell what minerals were there at the time your zoned mineral first started growing, because as that mineral grew it subtracted some of ingredients from the surrounding rock, and “froze” them into its “core”. This process caused the remaining list of ingredients present to be sufficiently changed that the list of possible minerals present at any given temperature and pressure also changes. This is not unlike comparing the list of what you might be able to make for dinner on any given evening without going grocery shopping. They day you first stock the house up with food the list of meals you might make from the ingredients on hand will be much larger than it will be a week or two later (if you don’t go food shopping in between) and have been using up some of your ingredients in the meanwhile.

So the “trick” I use is to consider my zoned mineral (in this case, garnet) as being made up of proportions of four specific ingredients. Just as different cake recipes might call for differing amounts of flour, butter, eggs, and sugar, and still be a cake, so a garnet will have differing amounts of iron (Fe), magnesium (Mg), calcium (Ca), and manganese (Mn). (These elements, being of similar size, all manage to fit into the same slot in the crystal structure.) How much of each is incorporated into the growing garnet at any given time will depend both upon the ingredients available and the temperature and pressure at which the garnet is growing. Therefore if we make a diagram which shows the expected changes in quantity of each of those four ingredients in garnet (at different temperatures and pressures) it is possible to find the spot on the diagram which corresponds to the garnet being studied.

I do this by measuring the composition of my garnet using an electron microprobe and making a note of how much of each of those four ingredients (Fe, Mg, Ca, and Mn) is present in the center of the garnet. I then highlight the lines in the graph corresponding to each of those numbers, and where the four lines intersect marks the temperature and pressure of the first growth of garnet. Often this works, and there is much rejoicing. Sometimes it doesn’t.

There can be any number of reasons why it doesn’t work—perhaps I’ve not actually measured the center of the garnets. Perhaps the composition I started with for the whole rock doesn’t actually match the composition that was present when the garnet started growing. Perhaps the composition of the rock has changed with time as fluids carried in new ingredients and carried away old ones.

Creating these diagrams, they joys of having them work, and the frustrations when they don’t are a normal part of my life as a graduate student. Biologists get to play with plants or animals, chemists get to work in a laboratory, I spend my days entering lists of numbers into a file, setting the program calculating based upon those numbers, and, when it is done (it can take quite a while—these calculations are actually quite complex, which is why we delegate them to a computer), opening images in a drawing program to see the results in a graphical format. Once I’ve got results the fun part begins—where I think about what the numbers mean, and how my rocks could have been buried deeply enough to grow these minerals in the first place, and how they managed to get back up to the surface so that I could collect them in the second.

50+ minerals meme

I've used the adaptations
to this meme suggested by Kim

Use bold to indicate minerals you’ve seen in the wild. Italics is for those seen in laboratories, museums, stores, or other non field locations. And Underline for those you’ve analysed with a microprobe.

50+ minerals everyone should see:









Copper (native)









Gold (native)























Quartz (oops, that wasn’t what I meant to probe!)





Silver (native)



Sulphur (native)









(by my count that is five without a formatting change, and then only because I didn't look them up to see if I should have recognized the name...)