November writing challenge update

Back at the end of October I put my hand up to participate in a science writing challenge for the month of November by finishing up two papers that really should have been written long since. On 1 November I started my new job, and didn’t write at all that first week as I focused on the 1001 tasks necessary to starting a new job, including moving into my office, rearranging the office furniture to suit my working needs, meeting my new colleagues, obtaining employee cards, library cards, etc.

Early in week two my office computer arrived, and another two potential writing days were lost installing programs and generally making the computer ready to use. However, on Thursday and Friday of that week I actually sat down and finished up the current draft of the paper based on my PhD research. The previous version I had done (while back in Australia in July) was good in terms of presenting the basic facts of what was done and what the results were, but I had been kind of sketchy in the discussion and conclusions section. (I think that is a common failing on my part that I should work on—I am totally comfortable reporting facts, and I am totally comfortable with editing a previously existing discussion/conclusion section, but actually confessing what *I* think is relevant or important about those facts? That is getting kind of personal.)

Be that as it may, since it was necessary to finish the paper I somehow found the necessary motivation/inspiration to just write it—I went back to my PhD thesis, looked at the points covered in that section there, and chose which ones to address here. Not only did I write it all down, in many cases the version in this paper is much clearer and more eloquent than what I had typed when finishing up the degree. Spending a couple of years thinking about other areas of geology actually helped give me some new insights on that project.

In this, my third week on my job I have continued to split my time between needful tasks for this project (doing background meeting, arranging a trip to the mining company with whom I will be working, obtaining a card to let me use the uni gym (free to employees during business hours), etc.) and finishing up previous papers. Since I had sent a copy of the PhD paper to my erstwhile advisor in Tasmania on Friday that meant I could focus on working on the paper from the experimental post doc position I finished last December.

This week I have managed to do some editing of the text and make major progress on a set of figures that should have been done long since: BSE images of every experiment, annotated to label the mineral phases present.

Why hadn’t I created such images previously? Because I documented each microprobe session in CorelDraw. My standard operating procedure was to look at the sample, determine a region to work on, take a picture, transfer it to my personal computer, open it in CorelDraw, and create a new layer for the day’s session in which I would make colour-coded circles superimposed over the picture at the locations for each analysis point. I would give each circle a name that matched the name recorded in the microprobe (such as RC1-NMg1 for the first garnet analysis on sample #RC1-NM). Repeat for each analysis, taking additional photos as needed.

This works very well for recording things, and one can easily go back and compare the results with the appearance of the phase analysed. However, the layers can get confusing for those samples with multiple microprobe sessions (due to the difficulties in getting good results for some phases).

The new, improved, pdf images I am creating for each sample make things much easier—they are all labelled with the pressure and temperature of the experiment, which bulk composition was used, and which phases are present. The phases are colour coded to indicate the quality of the data—if they are in bold print I had five or more good analyses of that phase for that sample which agree. If they are in normal print there were three to five good analyses, if they are in red there were two (or fewer) good analyses, and if the red text has a question mark next to it I know that the phase is present, but it was too small to get a clean analysis so I do not actually know the composition of the phase. Having this information right there with the photo of the sample is very helpful. It is also pretty easy to see why the red text is in red in most cases—those phases really are smaller or too amorphous to get good readings—one can see that in the photo, too.

There is still a week and a half left in November—I think I may be able to finish compiling these images today, so there is a chance that I will be able to complete all of the other tasks necessary for this project before the month ends. However, even if I do not complete this goal, I still thank Anne for having inspired me to set it—I am certain that I would have found plenty of tasks to keep me busy instead of writing these older papers if I had not stated publically that I would do it.

and the draft comes back

Any readers who have been paying attention for a while know that I have yet to actually publish the results from my PhD research. My first attempt at a paper draft, written during the first month or two after starting my first post-doc position got a "this reads too much like a thesis, you are putting in too much information" reply from my advisor. Somewhat discouraged I set that project aside and didn't make much more progress on it during the 1.5 years of that post-doc position—only really managing to take it out once in a while, dust it off, work on it for an hour or three, and set it back aside.

However, when I was back in Australia this July (applying for my visa to settle in Scandinavia with my partner), I met with my advisor. Together we determined what I needed to do with the paper, and I managed to leave him what felt to me like a very good draft before boarding the plane to return to the northlands. Today, at long last, he has returned that draft to me with comments. Not surprisingly, his main point now is that the paper has become too short—while culling stuff from the too long version I got over-enthusiastic. Fortunately, this time he has concrete suggestions as to what should go back in, and why. Therefore I now have a goal: try to get a new, improved, draft back to him before my job interview next week (since, if I get the job I will want to focus my energies on learning the new position, rather than finishing up overdue projects). With luck I will not only accomplish that goal, but it will land on his desk at a time when he is actually able to reply promptly, rather than having a month or more slip by before he can even look at it. Perhaps one day in the not too distant future I can change the status of that paper from "in progress" to "submitted"…

why you should publish before you finish your degree: a cautionary tale

When I completed writing my PhD thesis two years ago I boarded the plane the very next day to head off to my first post-doctoral position. Somehow, while I made a few attempts to write a paper based on that research during the 1.5 years of that post-doc contract, I didn't actually finish writing it—the first couple of drafts were still attempting to include too much information.

It will come as no surprise to anyone to hear that I continued to not work on that paper during the six months I was in Scandinavia on a visitor's visa living with my new-found love. Now that I have returned to Australia to submit my application for a permanent resident visa so that he and I may continue living together I have begun again, at long last, to working on that paper. One advantage to waiting until now is that instead of discussing the paper and the proper aims and scope thereof with my erstwhile adviser over email I can stop into his office and get real time interaction and feedback.

Today we had our first face-to-face meeting in two years, and he cautioned me that he expected that, given how long it has been since I have worked on this project, that it would probably take a good three days just to re-familiarize myself with what I was doing so that I could move forward on the project. How I wish that he weren't correct in that.

I recall having, on more than one occasion, cursed previous researchers who studied these rocks for the information that they left out of their theses or publications. Today I am cursing myself for what, now, appears to be a fairly random organizational system which has made it difficult to find the spreadsheets I need.

An additional complication I have encountered is my computer upgrade. I purchased a much-need new computer last October, and while I was able to replace most of the programs on it, it was not possible to replace my copy of ArcMap. This is the program in which I recorded the positions of each and every analysis point from every microprobe session I ever did during my PhD research. It is a wonderful program which permits one to accurately align photographs with x-y coordinates such that one can see at a glance where on each crystal each analysis point is located.

In the course of my research I exported the images for many of the samples to CorelDraw in order to create figures to be used in the thesis. I now wish to create a new figure for the paper I am working on, but the exported version contains the location of the analysis points for three out of four of the minerals used in the calculations. This means that I need to open the ArcMap files. I should be able to do this when next I am at the university, by using one of their computers, but it will require a bit of effort to explain to the program the new location of all of the files required.

So now the researcher who I find myself cursing for incomplete information is none other than my past self! There is no one to blame but me, each time I chose to do something other than writing this paper while the information was all still fresh in my mind I was also choosing to make the eventual writing of the paper just that little bit more difficult. I freely admit that, at the time I made those choices, it seemed like a reasonable price to pay, but now the time is nigh, and, indeed, it looks like it just may be a good three days to get back up to speed on this project so that I can finish it.

Wish me luck—as one of my colleagues pointed out to me today "research which is not published is wasted effort", and I do not wish all of that effort to have been wasted.

dating one's research

I don't normally read on-line comics, since I tend to have too many things to read in the way of e-mail, friends posts to their facebook, livejournal and blogs. However, today one of my friends sent me this link from the PhD Comics, and I thought it worth sharing with others. Having done a thesis kind of recently I really understand what the author is saying. Yes, yes indeed, one really does get *that* close to one's research project...

Hey, I’m an international expert!

For the first time today I received a random e-mail from a stranger asking for help with a geologic question. I happened to check my hotmail address (for the first time in at least a month), and saw a very short note from a researcher in India, who asked me to assist him with creating “pseudosections” for his samples using THERMOCALC, and he attached a file of his data. I opted not to open the attachment, but instead sent a politely worded note letting him know that I don’t actually know how to use THERMOCALC, but that I had been taught to use PERPLE_X, which gives similar results (and added a citation to a paper which used both programs to compare them). I added that for prompt replies, he’d be better off using my uni e-mail address, as I only check the hotmail account about once a month. I did not provide said address, but it is available in a few places on line if you know my name.

Much to my surprise about a half an hour later there was a longer note from him in my uni in-box, explaining that he’d tried using PERPLE_X, but had encountered problems with a specific step in the process, and could I please help him create pseudosections; one of his papers was being held up in the review process because he hadn’t created a pseudosection for his data, and that he’d be happy to give me full credit for the assistance—but if I couldn’t, could I perhaps send him my build file so that he could figure out how to edit his so that it would work.

I happen to have a Word document which I call upon any time I need to use the “build” program in the PERPLE_X suite of programs, wherein I have all of the questions the program asks in black, and the answers I give it in blue. Any time I need to run a new sample, I edit that document first to contain the data for the new sample, and then run build and copy-paste the answers into the program. Therefore it was the work of perhaps three minutes to reply to his e-mail with a copy of that document and suggestions of how to use it and what to do afterwards, along with an apology stating that I wasn’t able to do the work for him, as I really need to finish the writing of my PhD, which is behind schedule. Aren’t they all?) This got me a very polite letter of thanks. I hope he is able to make the program work.

Somehow, being seen as enough of an “expert” in my field to get random letters from strangers asking for help with their own research feels pretty good. It has been an intense 3 ½ years working on this project, but the end is in sight, and I can tell from here that completing the degree isn’t really the end, but rather is just the very beginning. There is ever so much more that I can learn, to build upon the knowledge I have gained here. I am starting to see post-doc positions advertised in my areas of speciality, and am applying for them. Each one has its own appeal, and would draw upon different strengths and use different skills. I can’t yet tell where my path will take me next, but the glimpses I’m starting to see through the trees are very, very intriguing.

Always double check!

I collected most of my samples for my PhD project in March of 2006, consequently their field numbers start 06___. Those samples all came from the northern fault block of the Collingwood River Metamorphic Complex. In November of 2007 my advisor and I did one additional trip, to the southern fault block of the Collingwood River, in search of the long-lost Tasmanian whiteschist. We found it, and collected a number of other samples from the area as well. Whilst we were out, we also stopped by the northern block and picked up another couple of oriented samples, just for good measure.

In October of 2008 we decided that there was just enough funding left to do some detrital zircon dating for two samples from the Collingwood River. I was told to select "sandy" samples as being most likely to contain zircons. So I picked out half a dozen from both the northern and southern blocks of the Collingwood River which were sandier than the others, though not necessarily sandy enough, and brought them along to my lesson on rock crushing. My teacher du jour narrowed it down to three likely candidates, two with 06___ numbers, and one with a 07___ number. So we, thinking that there might be value in having one from each fault block, chose one of each and we commenced crushing.

Since then I've been thinking in terms of having crushed one from each fault block, so was not too surprised when their detrital zircon patterns were somewhat different from one another. Today, at long last, I decided to make the figure showing the location these two samples were collected from. Yup, you guessed it. They are both from the north block! They were collected from locations not more than 250 meters apart from one another along the highway.

However, since the other 07___ samples were all rejected as not being sandy enough to bother, I can't really complain that I don't have one from each block. There is just that lingering embarrassment that one gets when one realizes that the assumption under which one has been operating doesn’t actually apply. The best cure for that? Admit the mistake publicly—then it won’t ever be repeated!

And always consult the map...

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!

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…

Anyone know of an interesting post-doc and/or teaching position for which I might apply?

It is an exciting thing to be nearing the end of a PhD project. However, it can also be somewhat overwhelming. So many tasks yet to be completed before the project will be “done” and I can submit the thesis. In tandem with completing these myriad tasks, I am also contemplating “what comes next”. There are so many different directions which sound appealing at the moment. I have very much enjoyed this project, therefore a post-doc position which involves research on metamorphic rocks sounds interesting. I very much enjoyed my Master’s thesis project, therefore a project involving structural geology sounds like fun. I also am terribly fascinated with the art of the Migration period, the Viking Age, and the early Middle Ages; therefore I might enjoy making the transition into “geo-archeology” to see what can be learned about trade routes based upon the sources of the materials used, as determined from their chemical compositions. I also like the idea of teaching, and have been working on a “statement of teaching philosophy” to go with an application for a position that has been advertised at school that has an educational philosophy that very much mirrors my own.
I wonder if it would be any easier if I had only *one* direction in which I wished to go? Is it better to spend my precious time allotted for “job search” looking for one, specific, thing, or to send out many e-mails of inquiry in a variety of fields? I have no idea where on the planet I shall be next year, nor what I will be doing, but, given how very many things sound like fun, I suspect that I will enjoy it, whatever, wherever it may be!

But I hope that it is in mountainous area…

Such a simple time-saver, why didn’t I think of it ages ago?

I have been using the program suite Perplex to do “garnet isopleth thermobarometery” as part of my PhD project. This program uses the command prompt as the user-interface into which one enters answers to questions before it does the calculations. I have been using this program on a very regular basis, for a couple of years now. Very early on I figured out that one does not have to wait for it to actually ask the next question before answering it, and for those calculations which I perform over and over for a variety of different samples I soon memorized the sequence of questions/answers so that I could save time by simply typing in the sequence of key strokes needed and thereby get to the part where it does the calculations sooner. However, there were occasions wherein I’d hit an incorrect key, and then I’d have to start the sequence over again. Now, that my project is nearing the end, and I’m meant to be only writing up the thesis (but, of course, I keep doing an occasional bit of calculations too; I just can’t help myself!) I have finally stumbled upon A Better Way (TM). Instead of answering the questions each time I do the calculations, I’ve set up a Word document into which I’ve typed all the key strokes needed for each of the tasks I do, starting with typing the name of the program. Now, instead of typing:

werami

in

2

8

Gt(HP)

1

2 1

4

2 1 5 1 7 1 8 1

n

n

100 100

N

0

pscontor

cpl

n

n

y

every time I wish for it to calculate the isopleths for the pyrope end-member of garnet, I simply click on the heading “X_Prp” in the word document, copy, and paste the lot of it into the command prompt. I then enter only the three numbers needed to answer the final question (and which will be different for every sample) and I’m ready to import the graph into CorelDraw and see how it looks. I have these set up for all four garnet end-members, and an additional sequence for just the “pscontor” portion of the process, because I create two graphs for each end member—one showing all of the isopleths in the range of the graph using a 0.01 contour interval, and one showing only the one corresponding to the composition I measured in my garnet core.

It is truly amazing how much easier this process is since it occurred to me to set up this time-saving device! The wonder is that it took me so long of doing this before I came up with the idea. How many of you stumbled upon a brilliant way to save yourself much time/energy/frustration for a task you have performed 1000’s of times before? Or does everyone else think of these things within the first half a dozen times they repeat the task?

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?

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!