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?

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.

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:

Andalusite

Apatite

Barite

Beryl

Biotite

Calcite

Chromite

Chrysotile

Copper (native)

Cordierite

Corundum

Diamond

Dolomite

Florencite

Galena

Garnet

Glaucophane

Gold (native)

Graphite

Gypsum

Halite

Hematite

Hornblende

Illite

Illmenite

Kaolinite

Kyanite

Lepidolite

Limonite

Magnetite

Molybdenite

Monazite

Muscovite

Nepheline

Olivine

Omphacite

Opal

Perovskite

Plagioclase

Pyrite

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

Rhodochrosite

Rutile

Sanidine

Sillimanite

Silver (native)

Sphalerite

Staurolite

Sulphur (native)

Talc

Tourmaline

Tremolite

Turquoise

Vermiculite

Willemite

Zeolite

Zircon

(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...)

Connecting Microscopic and Continental Scales

This month’s Accretionary Wedge is on the topic of “connections”, which is a terribly appropriate topic for geologists, since everything is interconnected in this universe, and we (generally) study that portion of the universe which we call “Earth”. The planet itself is a ball made of up a variety of layers some of which, over time, do a bit of mixing up. They call this mixing “plate tectonics”, which theory has been around in a changing, but reasonable stable form since I was a child, and existed in a much earlier form (as early as 1915) called “continental drift”. The theory of plate tectonics is a very inter-connecting, unifying theory which helps explain the current distribution of continents around the planet, which parts of the continents (and the ocean floor as well) are wrinkled into mountains (and how the relative motion between two “plates” causes that wrinkling, either in the form of very high mountains when two plates “crash” into one another (e.g. the Himalayas, where India is colliding with Asia) or in gentler mountains where they are sliding past one another (e.g. the San Andres Fault).

Plate tectonics is also useful when looking at rocks, like those I’ve been studying for my PhD project (see photo in my user pic!), which, while at the surface of the earth today, have evidence that they were once buried quite deeply. Every mineral has its “favourite” temperature and pressure—the conditions wherein it will grow, given enough time to do so. Many minerals have a range of compositions, and they will vary their composition based on the temperature and pressure under which they are growing. Garnets will swap in magnesium (Mg) and out iron (Fe) at the same conditions that biotite swaps in iron and swaps out magnesium. This exchange has been studied extensively, going back to the 1970’s with experiments involving putting a tiny amounts of biotite in with large amounts of garnet (and vice versa) with known amounts of Fe and Mg into tiny containers which they then squished (that’s a technical term) with lots of (a known quantity of) pressure and high heat for an extended period of time. Then they checked the mineral which was present in smaller quantity to see how its quantities of Fe and Mg had changed. Doing this a number of times at different conditions permitted them to work out how much iron and magnesium each mineral prefers at a variety of pressure-temperature combinations. As a result of such experiments and comparing them with the proportions of Mg and Fe in biotite and garnet in real rocks, we now have a method of working out just how hot and how squished (how much pressure) rocks must have been to grow the minerals they currently have. This helps us work out the details of the past configurations of the continents—it is known how deeply something must be buried to reach a given pressure, so from the composition of the minerals we can figure out how deep the rock used to be, and therefore what its prior plate tectonic setting would have been. It is all interconnected, from the microscopic level to the scale of an entire continent!

How I became a Geologist

Even as a small child, I never wanted to have a job. To me “work” was a terrible thing which caused people to reply: “No, sorry, I can’t, I have to work.” when asked: “will you be attending this super-fun-upcoming-activity-you-wouldn’t-want-to-miss?”. But I loved going to school—learning new things every day was fun! When not at school I generally had my nose in a book, unless I was outside admiring the beauty of the mountains, or exploring the woods near my home.

Over the course of a couple of summers I watched a small stream change its course as a bend in the waterway around a peninsula met itself, causing the peninsula to became an island, and then the island was abandoned as the water chose the shorter, straighter course in preference to the longer loop around it. Years later, in my first Earth Science class, when the teacher reached the part about how rivers meander and change their course I was excited to realize that this was something I already knew—my own observations had already revealed it to me. I think that this may have been the first time I realized that what I learned on my own, through my own observations, was every bit as valid as the “official stuff” that was presented to me via my teachers at school, and indeed, the things taught in school were all based upon *someone’s* observations! Science is really, naught more than the collected and organized observations of thousands of people. Observations made at every scale imaginable—from the tiniest microscopic investigations to seeing patterns in the outlines of the continents. It all meshes together to create a wondrous whole, if one knows how to look for it.

So once I completed high school I choose to, in part because of my above mentioned quest to “avoid working”, enrol in a University, intending that I would “be a student forever”, and just spend my life taking classes. Somehow, although I had heard the phrase “PhD”, I didn’t really realize that classes were only the beginning of University in general and Science in particular. So I took classes. Lots of classes! In many topics—introductory courses like Chemistry, Eastern Philosophy, Algebra, Computer Programming, Mountaineering, Norwegian, Modern Dance—more advanced courses like Medieval Literature, Chaucer, Old English. Years slipped by while I was having fun. Due to a variety of personal reasons I moved a couple of times, so my credits piled up at a several different schools, yet still I persisted in the dream of “being a student forever”—taking classes was what I knew and what I loved to do.

Sometimes people hearing this odd goal of mine would say things like “if you love school so much, you should be a teacher”, but I would shake my head and point out that it is much easier to write one essay than it is to grade 25 of them. Throughout this period, since I had no intentions of ever “graduating”, I paid no attention to what the requirements for graduation were, and never looked into truly advanced study in any one field. Even the “advanced” courses (designation based upon the course numbers assigned to the classes) I took were things I could easily take without worrying about things like “prerequisites”.

Then one day, one of my friends with whom I’d attended high school was wondering which of the graduate schools *offering him money* he was going to accept. Now *that* got my attention! You mean they are going to *pay* you to go to school?! How wonderful! At that point I was a live-in housekeeper to earn my room and board, and earned my tuition by working registration at the University each semester. I was getting by, but only just. Suddenly, I had a new goal. Rather than “never graduating” and “being a student forever”, I could “graduate”, and then “get paid to be a student”. But studying what? The problem with the whole “graduate school” concept is that they expect you to “declare a major”, a field of speciality. There were so very many interesting things available to study! How would I ever choose between them? So I consulted the course catalogue of the University at which I was then enrolled, and looked at the classes required for graduation in each field. As it turned out, *every* major available at my University required at least one class which sounded interesting, but also required at least one class which did *not* sound interesting! Hmm. This complicates things—I didn’t wish to be “forced” to take a class which didn’t interest me.

Around about that same time I was enrolled in a class called “Elements of Physical Geography”, taught by a Geologist. The teacher was a good one, who maintained class interest by frequently telling us stories which began “Geologists are stupid, we do things like…” and then he would tell us how close he got to Mt. St. Helens before it erupted while he was working with the machines which monitored the mountain’s current conditions, or he would tell us about other adventures, in the name of science, that people he knew had undertaken. Yes, he did say “stupid”, but I heard “fun”—without exception every story he told held my interest, I could picture myself doing things like that—having fun, risking (minimal) danger, and learning things in the name of science!

Back to the course catalogue I went—look, Geology wasn’t even an available major at my University! Undaunted, my research continued; clearly it was time to go look at other course catalogues from other universities. Hey—look! *Every* class that this University requires for their Geology Majors sounds like fun! Check another University—yup, every single class that they require of *their* Geology Majors sounds like fun too! Six years of being a full-time University student, and I’d finally found the course I wished to study! Very little time elapsed from that moment until I’d applied and transferred to another University, in another state, and became a Geology Major. The classes I took there were, in fact, as much fun as they sounded like they would be from their descriptions, but that will have to be a post for another time…