texture short course, day one

Back at the beginning of the summer I saw an ad for a workshop on texture analysis to be held in Tromsø in October open to students and researchers. It sounded interesting, so I sent them a note asking if it was open to researchers who are between contracts, and they said that it was, and (more importantly given the "between contracts" part, the only course fee would be to cover the copying expenses. When I got the job offer for the position I will start on 1 Nov. I asked if he thought I should attend the workshop, or if my time would be better spent staying home and reading literature directly relevant to the project. After looking over the flyer for the course he said that he thought I should go.

It turns out that the most efficient way to get to Tromsø from Luleå is to drive—they have no train this far north, so one would have to switch to a bus part way there, and flights go south to Stockholm and then west to Oslo or Trondheim before heading back north again. Therefore I checked with a friend of mine who is a graduate student with a flexible schedule, and he thought a road trip sounded like a good idea (besides, going away for a week might actually get him to do some writing). We had a nice drive up on Sunday—left Luleå just after 08:00, and arrived at our B&B (located 15 minute walk from the Uni) just after 18:00. (I, of course, forgot to take out the camera once during the drive, since I was so busy gazing out the window at the lovely mountains once we got close to the Norwegian border).

The course is divided into two sections—the first two days we are learning how to use the programs they use here to convert a series of rotated photos of thin sections into data showing the orientation of the crystallographic axes. The technique works only on uniaxial minerals, such as quartz or calcite (or ice), but since these often occur in units which have been deformed it is a useful tool.

It was very enjoyable to be back in a classroom again after a longish break, though a bit of a challenge to keep up with the exercise—the program we are using runs only on MacOS, and I haven't really needed to use Apple computers since my class in programing Basic on an AppleIIe back in highschool. Apple products have changed a bit since then, and while there are similarities in the handling between Apple and PC there are just enough differences that I found myself pushing the wrong button more than once and then frantically trying to undo that and get back to where I was meant to be before the teacher had gotten so far ahead that I couldn't catch up. Sometimes I managed it, sometimes I was the voice saying "wait, what folder was that?".

Fortunately, she was very patient when we got lost, and would back up and explain the steps we hadn't caught so that we could go on to the next step. I think we all managed to convert the raw data into the correct formats and align the stacks of images properly. Tomorrow we get to actually process that data into the sorts of final images that wind up in publications…

A short course in Vienna

As I type (Saturday morning 4 Sept 2010) this I am sitting on a train, traveling from Vienna to Zurich, where I will change trains for my trip home from my latest adventures. The plan, when I scheduled the travel was to enjoy the mountain views out the window, but the clouds are low, so while I can tell that there are hills out there, I can’t tell if they rise up into mountains. However, as we passed Salzburg I did get glimpses of the peaks as the clouds parted, so the time spent on the train will have been worth it for that view, if no others come along. With luck I will get a chance to post this once I’m home, since I don’t expect to have any internet access at all next week.

After leaving Budapest and the IMA conference I traveled first to Salzburg, where I spent the weekend playing tourist and visiting the salt mine at Hallein (photos from that trip to follow in another post), and then doubled back to Vienna, where I attended a short-course on the Kinetics of Geologic Materials.

The course turned out to be as useful as I’d hoped. I signed up for it in large part because, having had such a long break between taking my last math course and enrolling in my PhD program, I’d found that when reading papers I had a tendency to skip over formulas and jump to the next descriptive part of the text. In an effort to overcome this habit I have checked out text books on the thermodynamics behind the chemical reactions which form minerals, and, to some extent, they helped. However, I still felt like I was missing something in my understanding of the math/formulas that one needs to describe what is happening during mineral-forming reactions, and so this course.

There were more than 25 of us who signed up for the course, traveling there from Italy, Germany, Hungary, the Czech Republic, and more. We range in experience from advance undergraduate geology students to post-doctoral researchers. At the end of our course we shared information on our current research in a poster session ( good percentage of us had attended the IMA conference in Budapest), and our specialties range from experimental studies to traditional petrology—from the crystallization of minerals from a melt, to zoning in metamorphic minerals and a number of points in between. One student is even studying the ability of rocks in Hungary to store man-made CO2.

The lectures started with an introduction to thermodynamics—the study of the relationship to the energy of a system to the equilibrium thereof. The common physical example used to illustrate this point is to stand a rectangular block on its narrow end. So long as it is on a flat surface and nothing happens to it, it will happily stand there all day. However, being taller than it is wide, should anything bump into it the block will fall over and land on its broad side. We describe the block standing on its narrow end as “metastable”, because if energy is added (it gets pushed), it will transform to its more stable state of lying on its broad side. Chemical reactions are much the same. Minerals are each stable in a specific range of conditions (pressure, temperature, and composition of the rock itself), but some chemical reactions take more of a “push” to make them happen than others. In these cases the minerals will often exist in conditions during which they are not expected to exist, in which case, like the block standing on its narrow side, they are metastable.

From this simple example the course built up the mathematical framework of how to describe the energy used to “push” the reactions into happening, and how to use published values for that energy to determine for any conditions what minerals will be expected to be stable in an equilibrium situation. We touched on many related topics related to kinetics, including diffusion (how the elements within the minerals move from one location to another so that the chemical reactions will happen), nucleation (the earliest stages of the growth of a new crystal), and the boundaries between grains and/or phases. For most topics presented we also had exercises to work on during the lab hours—using MATLAB to perform calculations on these processes for model (simplified) systems.

All in all the week was a very valuable experience, but train has reached an area where the mountains are visible, so it is time to shut down the computer and enjoy the view.

Active reading techniques to improve understanding & retention

I spent this week taking a short course on Successful Scientific Writing: from Proposal to Publication taught by Dr. Sarah Shephard at the Center for Teaching and Learning at ETH Zürich. The course provided such a wealth of useful information I’ll try to do several posts about the things I’ve learned. Today’s post will be all from memory, as I left the notebook full of handouts at home when I came into the office this morning.

Today’s topic is reading. Reading is something at which I’ve always excelled—I can’t remember the time before I was able to read, and I’ve always been one to “fall into” books, getting totally immersed in the story and not noticing time elapsing in the real world. Unfortunately, reading articles in scientific journals does not have that same effect. Narrative stories are designed to flow smoothly and to engage the audience, but most science writing is designed to communicate results of a project and discuss the implications thereof. We read journal articles with the goal of learning, not entertainment (though, in some fortunate cases both are possible), and she recommends a very different approach to reading science literature than is taken when reading a novel.

She suggests first reading the literature when you are in the “deciding upon a project to do” stage—find out what is the state of the art on the topic(s) of interest, not only what is currently known, but how those facts have been interpreted thus far, and if there is more than one “school of thought” on the topic. Which author(s) do you agree or disagree with, and why? Keep these questions in mind when doing the initial reading of the literature.

When you sit down to read a new article, first glance over the entire article—make a note of the structure of the article—how much of it is devoted to the introduction, the methods used, the results, and the discussion/conclusions? What headings did they use for the various sections? What figures and tables were used to illustrate their points or provide supplementary data? Once you are comfortable with what information is going to be presented think of specific questions you expect to be answered in the article, and make a note of them. Now you are ready to begin the reading process.

The reading itself should be punctuated by writing on the part of the reader. Read one paragraph, and then jot down notes to yourself about what it said. Paraphrase their point in your own words—this is an important component of learning the subject matter—by taking an active role in the process and writing it down, you will better remember what it said. After you have paraphrased the paragraph ask yourself the following questions: Did it provide the answers to any of the questions on your list? Did it make you think of other questions you wish to find answers to within the course of the article? After you have completed all of these tasks read the next paragraph and repeat the process of writing a paraphrased summary and determining if it has answered any of your questions or posed new questions. Once you’ve done this process for a number of paragraphs (five is a good number, but there may be reasons within the structure of the article you are reading to include more or fewer) go back and look over all five paragraphs and your notes thereon and determine what combined information they relate—write down your own summary of the whole section. Ask yourself if this section answers any of the questions you have. Do you agree or disagree with what has been said thus far and why? Does this section of the paper agree or disagree with other papers you have read? Repeat this process through the entire paper, and at the end condense it all into a brief summary of what you feel the key points are relevant to the topic you are currently studying.

She cautions that this process takes longer than simply reading each word on the page in order one time through. However, she also insists that it is worth the extra effort on your part because these techniques greatly enhance one’s ability to understand and remember what one has just read. She also says that not only should one read everything one can find that is relevant to the topic at the start of the project before doing the new research, one should also go back and review all of those papers (and any new ones published subsequently) after obtaining one’s results and before actually writing the paper to publish the results. That second reading should go much faster, as you will have your old notes on the paper to look at, in addition to the paper itself. However, having done the research you may find that you now have different questions or feel that different aspects of each paper is now more important than the parts you had initially recorded.

Because this reading method is more intensive than simply “falling into a good book” she recommends that it be done in small segments—read for 10 minutes at a time, then take a short break. Someone who is experienced in this technique might be able to read (and do the writing/thinking about what has been read) for 30 minutes at a time before needing a break. However, remember to make the break short and return to the process!

Traveling, again

I took a train across the Alps today, and was reminded, yet again, how much happier I am when surrounded by mountains. While I love my current job, I really do hope that whatever I find to do when this contract ends in December is located in a mountainous area. There is just something about topography which makes me happy. When the topography comes complete with glacially-sculpted valleys, craggy peaks and clearly visible fold and fault structures it is even better. Even though today was a cloudy day, and the southern Alps were barely visible through the lower parts of the clouds, still I spent most of the trip looking out the window (save for the times we were in tunnels, of course—they don’t light those up enough to see the rock-walls, and, I suspect we were going too fast to get a good look at the tunnel-walls even had they been lit up.) The clouds over the northern Alps were nice and high, so my views were clear. The central portion, where there is still snow on the ground was, by far, my favorite part. I so love snow, and miss living places where it stays on the ground after falling.
I am now settled into a hotel room in Zurich, where I will live for the next four days while I attend a scientific writing workshop. It is designed to assist us with every step of the process, from creating a proposal to publication. I am really looking forward to it. While I’m comfortable with the skills required to craft a sentence that says what I meant for it to say, I’m not so comfortable with the process of deciding what parts of an accumulated data set are worth sharing with a general audience—how much is too much, or enough, or not enough? When one knows the flaws in the data, is it still ok to draw some conclusions from it? These are the issues I hope they address this week. However, other students will likely have different needs. It will be interesting to see how it all comes together.

the geology at Chiesa di San Remigio

One of the highlights of spending a week in Verbania for the Short Course is the short walks I’ve done during our breaks between lectures. So far my favorite attraction is the Chiesa di San Remigio, a beautiful 11^th Century church on the ridge above the school/hotel where the course is taking place. As one wanders up the hill towards the church one reaches a place where the stone wall along the side of the road changes from a blocky, quarried, igneous rock sitting upon the road bed to a place where the wall rests upon outcrop of some nicely folded schist, and the wall is comprised of primarily very local stone—both round river rocks, and platy bits of the local schist.

On my first walk up the hill the outcrop got my attention, and my feet led me ever up, wondering what would be next.

I was truly delighted when I reached the top of the road and discovered the little stone church.

Like the stone fence above, is also built directly in contact with the folds of the schist.

Since discovering this delightful location on Monday, I have made a point of returning each day, and each time I discover new interesting rocks amongst the building stone. Today a small group of us went up, and we crawled all over the foundations looking at the rocks (as you do in such locations).

One particularly cute rock is so garnet-rich it is nearly pink. However, while I have searched carefully, I have yet to find any others of that sort, so suspect that the river and/or glacier (the lake is clearly a filled glacier valley) which carried it here brought it from quite a long way away.

The only other rock with visible garnets in it that I saw was this one with the lovely stretched quartz.

However, I did find a good-sized garnet in the mortar

I like the way the different stones were used as embellishment.

As were some spare bricks they had lying around.

I have often said that I’d like to live in a castle, but would settle for an old stone church. However, until this trip, I’d never actually met an old stone church in a location in which I’d want to live. This place, despite the density of houses in the village, is one in which I would be happy to live. The view from the church is just as amazing as the rocks of which and upon which it was built.

day two of the short course

I really enjoyed today’s lectures. The morning was a talk on the Dissolution-Reprecipitation During Melt-Rock Interaction in Partially Molten Silicates. It was very well organized and presented, and included movies showing the changes in composition of the crystals and melt during the reactions between them. It is amazing how much easier the topic is to follow when there are movies involved—the last time I would have had classes on melt-crystal interactions of any sort would have been in the early 1990’s when diagrams were still drawn on the board by hand during lectures. It worked (and gave us time to copy them in our notes), but seeing them change (and having a copy of the powerpoint presentation and movies to refer to later) is ever so much better.

During the short coffee break between lectures I went for a walk up the hill, and was delighted to see the lovely stone church at the end of the road. It is built out of an igneous (dolerite by the look of it, though I didn’t actually check proportions of various minerals to confirm or deny that identification) on an out crop of nicely folded schist. In a few places there are layers of the schist incorporated into the building, the thin stones stacked at an angle to the main blocky building stones, in a very nice effect. As soon as I’m home and once again have the cable for my camera I’ll share photos.

The second talk of the morning was on Microstructural Modeling with ELLE—Introduction and Applications. It was also well organized and presented—starting with the answer to the question “Why do numerical modeling at all?” (Because geologic processes operate on way too many scales, ranging from fractions of a μm to 1000’s of km, and from fractions of a second to many million years, and models can handle all of these scales, but experiments are limited in how much time is available and how large of a sample they can operate on, and field work isn’t always enough to show how the rocks achieved their current configuration.)
After lunch we spent some time playing with our own copies of Yan’s movies, and then we started learning how to use ELLE. We were only able to brush the surface of what is possible with this, but with the tools he’s given us, and access to their forum, anyone who is keen should be able to take this information and run with it.

off to a short course

I am currently spending the week in Verbania, Italy, attending a short course on Microstructures and Physico-Chemical Properties of Earth and Planetary Materials. I am pleased to be here for a number of reasons. Not only is the topic of the course interesting, but the location is beautiful. The town is nestled between a large lake and some mountains. The views across the lake are lovely, and the view of the town against the hills as seen on the approach is very nice. I arrived on Sunday afternoon, taking the hotel shuttle the 7 km from the train station with a group of other attendees. Most of the people in our carload had travelled here from overseas—several from Brazil, and one from the US.

This is a very international group. While the majority of attendees are from Italy, the list includes Lithuania, Germany, France, Belgium, Switzerland, Ireland, Norway, Brazil, Mexico, USA, and Korea. As a result of the mix, despite being held in Italy, the lectures are all in English, for which I, as one of those people who still suffers from mono-linguistics, am grateful.

This morning started with lectures on the Microstructural Evolution in Materials Science, taught by someone in the Materials Science field. As a metamorphic petrologist, it was interesting to see him talking in terms of phase diagrams wherein one changes from a single phase to a double phase field due to *cooling*, rather than in response to heating. He is also accustomed to not considering effects due to pressure, since materials science tends to focus on processes which happen at surface temperature and pressure. Nonetheless, most of the information he provided us apply to geological systems as well.

After morning coffee break the next lecture was on the topic of Estimation of Anisotropic Physical Properties of Aggregates with Preferred Crystal Orientation with Applications to Seismic Anisotropy. This lecture was very, very heavy in math and formula, but it was supplemented by the occasional photograph of real samples, both in thin section, and in images made by TIM.

We then had a break for the very elaborate lunch served by the hotel, followed by an afternoon devoted to practical sessions on both morning topics (plus supplementary lectures). I've had to leave the room to go download a program I didn't know I needed, which is why I've got a moment to post this, which was written during an earlier break.