Thursday, November 27, 2008

Being Kind to Your Future Self

One of my unofficial mottos in life is to try to always be kind to my future self. This can be expressed in so many ways. Simple things, like washing the dishes promptly after eating, when the food residue is all still easily rinsed away, rather than leaving them to pile up and become a daunting and difficult task, or remembering to always put things where they belong, so that you can find them quickly and easily when needed. The latter one was an oft repeated bit of advice by my undergraduate field geology teacher, who insisted that we *always* put our compasses and rock hammers back into their holsters if we needed our hands free, even if it was only going to be “for a second”, because distractions happen, and it is easy to put that all important tool down on a convenient rock, get interrupted and called away, and not notice it is gone till you reach for the holster hours or miles away from where you left the hammer or compass.

Another way we can be kind to our future self is to distribute our work evenly, and not procrastinate until facing a hard deadline with too much work still needing to be done. This one can take years of practice to get right. When first starting out in graduate school it can be very tempting to translate the freedom of setting one’s own schedule into “I can take any time off that I want to take”, but students who take this approach often regret it later in their project, as their scholarships are running out, and the work isn’t yet done. I know that I tried to make the effort early in my project to work steadily, so that I’d have the same level of work-load throughout, but I’m not certain I managed as well as I might have, if I had only known more then about what I would need to have done by now. The end is in sight, but the effort being put forth does, at times, seem to have been exponential in its increase. Fortunately, even when one wasn’t perfect in distributing the work-level across the entire project, still projects are finite in duration, and the effort I’m putting in now will make life easier for my future self.

Wednesday, November 19, 2008

I'm taking this one from Silver Fox, who tagged these five categories of people: 1. Any geologist, 2. Anyone who has driven the Alcan, in either direction, 3. Anyone who has lived north of the Arctic Circle, 4. Anyone who hates moving, 5. Anyone who considers themselves an artist. I wasn’t going to do this, but I happen to fall in four of the five categories (I love moving!), so I took it as a sign that I should participate.

5 things I was doing 10 years ago:

(Let's see, 10 years ago was 1998.)

1. Completing my Master’s Degree.

2. Deciding to move to Kotzebue, Alaska (north of the Arctic Circle).

3. Lost my father to cancer.

4. Frequent Contra Dancing.

5. Reading lots of science fiction/fantasy novels (but this one applies to nearly every decade I’ve been alive)

5 things on my to-do list today:

1. work on my thesis

2. do some laundry

3. work on my thesis

4. eat some food

5. work on my thesis

and did I mention that I need to be finishing up my thesis?



5 snacks I love:

1. Fresh bread, straight out of the oven, with real butter.

2. Fresh raspberries (only one more month till they are in season!)

3. Mild cheese, esp. ricotta.

4. Salad made with fresh spinach, cucumber, avocado, grated carrot, tomato, sunflower seeds, flax seeds, sprouts, and a sprinkle of “tasty nutritional yeast”.

5. Home-made cake batter or cookie dough made with real butter, fresh eggs, and less sugar than most recipes call for (yah, kind of weird for a metamorphic petrologist to not want to ruin a perfectly good cookie by putting it in the oven, but there you go)

5 things I would do if I was a millionaire:

1. Build myself a small stone “castle” (probably only a tower keep), using six different pretty metamorphic rock types, spiralling them up the tower to give a barber-pole like effect with the change in rock types from one section to another.

2. Travel more.

3. Fund a scholarship for students interested in studying geology who otherwise wouldn’t be able to afford to go to Uni.

4. Learn to parasail—just think all the fun of climbing the mountain, without the wear and tear on the knees for the hike back down.

5. Fund my own research instead of needing to apply for grants.

More than 5 places I've lived:

1. Japan.

2. Germany.

3. Crete.

4. Several of the “lower 48” states.

5. Alaska.

6. British Columbia.

7. Tasmania.

5 jobs I've had

1. Baker.

2. Teaching geo labs.

3. Book Store clerk.

4. Massage therapist.

5. Graduate Research.

5 rocks I love:

(For geologists or any others who also want to add rocks.)

1. Garnet phoroblast schists.

2. Anything with nice large, pretty, igneous or metamorphic crystals

3. Rocks displaying crenulation cleavage

4. Rocks displaying flow banding

5. Mylonites

5 categories of people I'll tag (because I hit only four of Silver Fox’s five, I thought I’d pick five that apply to me, just to see if any of you manage them all, but only one is sufficient to play…):

1. Anyone who has lived in more than one country.

2. Anyone who likes deformed rocks.

3. Anyone with a love of mountains.

4. Anyone who loves moving.

5. Anyone who appreciates the art/beauty in science.

Monday, November 17, 2008

The Beauty Secrets of a Geologist

I recently encountered one of those surveys which wend their way around the internet and seem to serve little purpose, save offering us diversion from whatever it is that we are meant to be doing, and, betimes, giving us some insight into the manner in which we are similar to or different from those of our friends who have also answered the questions. This particular survey was on the topic of “fashion”. I, like many other geologists, am not terribly “fashion conscious”, preferring “comfort” over style, and I made the decision as a very young person that, unless I happened to be on stage for some reason, to never wear makeup. Therefore I found it appalling to read the answers some of my friends gave to the question inquiring as to their “beauty routine”. What is it that causes some people to equate “beauty” with slathering their faces with expensive goos? I nearly avoided the entire survey as a result of my reaction.

However, I then thought about it a bit more asking myself, do I, a sensible geologist with a “natural” look, have a “beauty routine”? It turns out that I do, so I thought I would share my secrets with you, so you can all be as beautiful as I.

* Maintain a positive attitude/outlook on life

* Smile often

* Refrain from gossip

* Stay out of the direct sunlight as a general rule (wear hats in the field!)

* Get plenty of exercise; do more than 20 minutes of yoga every day.

* Eat a healthy diet in moderate quantities; eat fresh vegetables, fruit and a variety of grains, nuts & seeds

*Whenever possible, eat only home-made items; avoid processed and commercially manufactured "foods".

* Shower regularly.

* Keep hair long, clean and tangle-free (braids are useful here!)

Given the level of shock one of my fellow PhD students expressed when she discovered my age the other day (I’m nearly twice her age); I think my routine is working.

Thursday, November 13, 2008

Monday, November 10, 2008

Sometimes, it is worth trying “one more time”

A major component of my PhD project, if one measures by time invested in working on it, is the modeling of my samples using Perple_X. With this program one enters in the whole-rock composition of the sample, sets the list of which elements are being considered, and which minerals they can be combined to form, and what range of pressures and temperatures to use, and it goes through and calculates which combination of minerals, and what specific composition of each, should be stable at every combination of pressure and temperature within the range. Needless to say, most folk use a simplified data set—rather than considering every possible element and mineral in the world they limit the ingredient list to one which covers all of the major minerals in their sample. The list I, and many others using this technique, prefer is Na2O, MgO, Al2O3, K2O, CaO, TiO2, MnO, FeO, SiO2, and H2O. This is enough to predict most of the major minerals in “pelitic” schists (metamorphic rocks which used to be ordinary mud).

If one happens to be working with a rock wherein all of the minerals are homogeneous the use of this program to work out temperature and pressure at which it probably formed is very straight forward. Simply enter in the composition of the rock, let it do the calculations, look at the resultant graph, and find the place on the graph wherein the list of minerals predicted matches those actually present. However, it is rarely this easy. Many minerals, particularly garnet, are zoned. This means that their composition changes over time, becoming richer in some elements and poorer in others. In these cases what one reads off of the chart from the calculations is the combination of minerals present at that point in time when the first zoned mineral started to grow, and further calculations are needed to determine what the changes to the whole-rock composition will be as a result of the garnet growth locking some of the ingredients away in the center of the crystal.

One of the samples I’ve been working on has been a major source of frustration for me. It happens to come from the highest-grade metamorphic region in the state, and as a result some of the garnets present are up to 2 cm in diameter. Because of the sheer size of these grains and the significance of the location it was one of the first samples upon which I attempted the Perple_X calculations. Alas, it also turns out to be one of the most difficult samples to model, with a variety of different complications interacting to prevent me from getting good results.

When I mentioned above using the whole-rock composition of the sample for the calculations, I neglected to mention that there are some corrections one needs to make to the measured composition before using the numbers. One of these is to convert the reported Fe2O3 into FeO, since FeO is the form that is used for the calculations. The whole-rock analysis doesn’t actually have a way to distinguish between the two valence states of iron, so one has to make an educated guess as to how much is really Fe2+ and how much Fe3+. For my samples the “standard” correction was to assume that 90% of the iron measured was FeO. However, with this specific sample when the calculations were complete it turned out that given the starting ingredients the program thinks that it simply isn’t possible to form garnet with as much iron in the core as this sample has.

Another correction is to account for the element phosphorous, which is measured when doing the whole-rock analysis, but is not on the above list of ingredients the program considers. One of the most common minerals to contain phosphorous is apatite, which occurs in very tiny amounts in most pelitic schists. One of its other major ingredients is calcium. If one assumes that all of the phosphorous in the rock happens to be in the apatite, that would also mean that a proportional amount of calcium was tied up in the apatite and so unavailable for use in other minerals. Therefore another “standard” correction I’ve been doing is to subtract enough CaO from the whole rock-composition to account for the measured P2O5 being locked up in apatite. Alas, this sample is low enough in CaO that doing this correction results in problems with predicting the calcium content of the garnet.

Another factor with this sample which may be quite significant is that this sample contains tourmaline. Tourmaline is not one of the minerals normally included in the solution set used with Perple_X, in part because it is a very complex mineral in terms of its crystalline structure, and in part because it is one of the few "commonly" occurring minerals to contain the element boron, which is not normally included in the list of ingredients used in the calculations, since it isn’t included in very many minerals. However, reasonable early on in my project, when I was first encountering difficulties with modelling this sample, I stumbled upon a paper wherein they expanded the list of solution models for Perple_X to include B2O3 and the various end-members of tourmaline. So I e-mailed the authors, got a copy of their expanded solution set and gave it a try.

After many attempts doing various calculations for this sample, trying various combinations of “standard correction” for iron, trying again with the assumption that *all* of the iron measured was FeO, rather than just 90% of it, the “standard” correction for CaO, and again assuming that only 90% of the Ca needed to account for the phosphorous in apatite was present, and trying all of the above with and without the tourmaline present in the solution set I finally found a combination (more FeO and CaO than “standard” and consider tourmaline) that came the closest to predicting the composition of the core of this garnet. Not a perfect match, since it *still* thought that my sample has more iron in the core than is possible, but it was the best I could manage, and I’d already spent too much time trying to make this sample “work”. So I gave up and called it “good enough”, and attempted to do the next step with the calculations for garnet fractionation.

Alas, no mater what changes to pressure and temperature I set for the calculations, in every attempt the program decided that there wasn’t enough CaO—each time it would run out of that ingredient and crash long before predicting garnet with as much calcium as mine has in the rims (all of my garnets start out with only a little calcium in the cores, and increase towards the rims—sometimes it is as high as five times as much calcium in the rims than I the cores).

While it is, in theory, possible to work around that crash by starting the calculations over at the point just before it crashed, but removing CaO from the list of ingredients considered, attempts at this work-around didn’t succeed in predicting garnet which matches the other ingredients measured in my sample. Eventually I wrote a number of paragraphs explaining the manner in which this sample wasn’t working and moved on to other samples.

However, it always nagged on me that this particular sample, of all of them, didn’t “work”. During the past few weeks I’ve been doing repeat modelling for other samples which did “work” in that they predicted a reasonable match to the composition of garnet, but, unfortunately, also predicted the presence of paragonite, a mineral which does not actually occur in my samples. Since paragonite is a mica, and micas contain a component of H2O, one change which can be made to the calculations is to limit the amount of H2O available to the calculations. Doing this turned out to not only convince the program to quit suggesting paragonite; it also caused the “reasonable match” to the garnet composition to turn into an even closer match, which made me happier with the results I am getting.

Now that I’ve got so many different attempts for each sample, I decided to create a spreadsheet which chronicles for each sample which settings were used for each attempt, what temperature and pressure was predicted, what level of accuracy was achieved in matching the garnet composition, and how much of which other minerals are predicted to be present at those conditions. Looking at these results organized into a table in this manner showed me patterns in the results for different initial settings, which in turn helped me to decide which samples might also benefit from additional calculations, and which settings to use for those attempts.

Finally, this week, I got down to the point wherein I had usable results for everything, save for that one, high-grade sample with the large garnets. Remembering the frustrations I had trying to make this sample work back when I was just learning to use the program, I almost left it be. Did I *really* want to revisit that sample and court the same levels of annoyance when it didn’t work? However, I realized that if I *didn’t* try, I would always regret it—I had changed everything else with this sample, but never tried modifying the amount of H2O. In the interest of being complete, I had to make the time. Never mind that I was actually meant to “complete the thermodynamic modelling” stage of my project months ago, it had to be done.

So I sat down, opened the file, made the adjustments and set the program going. Whilst it did the calculations I prepared and named the new folders needed to keep the results organized and separate from all of the other calculations done for this sample, and got my drawing program set up to display the results. The calculations finished, and with some trepidation I begun the process of creating the various graphs to see the results. Lo and behold, for the first time ever, the program predicted that *is* possible to create garnet with that much iron in it! And, better yet, there is a point wherein the garnet is a near-perfect match for that measured in my garnet core. There was much rejoicing as I collected the data and added it to the appropriate spreadsheets. Yet, there was still a component of dread. Yes, I’ve managed to model the garnet core, but what about the garnet fraction calculations? Do I really want to try them and watch the program crash again when it runs out of CaO?

I must admit that I did wimp out the first evening—rather than trying the calculations straight away once everything was done for the core calculations, I called it a night, did my yoga and went to bed. It wasn’t until the next morning that I managed work up the courage needed to try the fractionation calculations. You can only imagine my joy when the first attempt not only didn’t run out of CaO, but actually got somewhat close to a decent match for my garnet rims. It took only two other attempts, one at a slightly steeper slope, and one in between the two, to come up with a good match. For the first time in the two years since I first obtained this program and started trying to model this sample, I finally have results for it! Better yet, this was the last sample to be complete for this region; I can now devote all of my energies into writing up the thesis, rather than doing calculations which should have been complete ages ago!

Saturday, November 8, 2008

animals in the field, or to be more specific, birds


Others are sharing photos of animals they've seen in the field, so I thought I'd play too. This eagle came in to land on this tree near the top of Mt. Wellington, Tasmania, during a recent hike of mine. Much to my surprise, though our path went fairly near by (25 meters?), it didn't fly off. The crow, just visible on the back branch, came and went a couple of times as we worked our way long the ridge line past their perch, but the eagle was content to sit there showing off its beauty.

Sunday, November 2, 2008

Because I like it

Thanks to modern social networking web pages I have recently gotten back into contact with old friends from high school with whom I’d lost touch due to frequent moves in a pre-internet era. During our obligatory “what have you been up to for the past couple of decades” exchange of notes I’d described myself as “enjoying life as a PhD student”. This caused one of them to enquire if I had been under the influence when I wrote that, because by the time she’d reached the final write-up for her PhD she was so sick of the project that she was considering something more pleasant, like tearing out her eyes. This exchange brought to mind the advice I’ve heard often for people considering doing a PhD “pick something you love, because you are going to hate it by the end of the project”.

Why? What is it about our system of “higher education” which makes people think that we should hate it? I’ve met some people whose approach to life is to choose to do only things they enjoy; others of us choose to enjoy whatever we do. To my mind, there is no better thing I could be doing with my life than learning and/or sharing knowledge. Why am I enjoying life as a PhD student? In part because my schedule is my own—there is no employer standing over my shoulder saying “you must be at work between the hours of 9 and 5”. If I happen to feel like working at midnight, I do. If I happen to feel like working at 07:00, I do. I am free to set my own schedule, and to make it as random, or as consistent as inspiration makes it. This is a wonderful feeling. I may have a lot to do, but I am the one to decide when to do it.

I am also very much enjoying the project itself. My rocks, particularly as seen through the microscope in thin section, are pretty. They are pretty because of the changes to the mineralogy as a result of their metamorphism. My project seeks to understand those changes by using the chemical composition of the minerals to determine the pressure and temperature at which they must have formed, and then to use that pressure and temperature to tell a story—what happened to that mud to bring about its current beauty?

To do this I get to play with spreadsheets and graphs. I get to run computer models which take input and convert it to data from which I can make more spreadsheets and graphs. And you know what? I like playing with spreadsheets and graphs! It is actually fun to compare sets of data in a graphical format and see how they are the same, or how they are different, and to seek out patterns. I enjoy this so much that one of my biggest distractions from my project is keeping track of my personal data. To help keep me on track with the uni work I track how many hours a day I spend on various activities, so when I’m not playing with my uni data making graphs and looking for answers to questions, I often play with personal data, making graphs and looking for answers to questions. How many hours a week do I spend exercising? Doing e-mail/blogs/social networking? Can I make the graph change in the direction I want it to by changing my activities?

Enjoying the processes and day-to-day tasks required of my project helps keep me enthused. However, as I explained to my friend, one of the biggest reasons I’m still enjoying my PhD project is that there simply hasn’t been enough time elapsed for me to be sick of it yet. Because my goal when I first enrolled in University all those years ago was “to be a student forever” an entire decade elapsed while I was an undergraduate taking classes full-time in anything and everything which sounded interesting. When I did my Master’s degree four years slipped by between enrolling in the first class and handing in the thesis. But here in Australia the university system seems to think that a PhD is a short term project. They give students 3 years in which to complete their projects (note: no classes are taken—this is three years of pure research), and if you can show good progress (and demonstrate that any delays are due to circumstances beyond your control) it is possible to apply for an extension for an additional six months. After that your funding is cut off and you are on your own. So, here I am in that final, extra, six months of my project, not sick of it yet, still enjoying the work, and content to be working away. Speaking of which, time to get back to it…