Friday, 29 January 2010

starting the day right

Compared to the rest of my family, I am a morning person. I am able to wake up instantly, and without being grumpy about it. This trait has become enhanced in recent years as I have discovered that my morning series of sit ups, leg lifts, twists, etc. all conspire to get my blood flowing and brain functioning, even when I didn’t get as much sleep as I might have liked (because I am also a bit of a night-owl, with a tendency to stay up late working on projects, reading, or visiting with loved ones. However, despite my ability to function in the morning, I also prefer a slow start to my day, and I consistently choose to start my morning with the more passive entertainment of reading e-mail/blogs/facebook/livejournal while eating breakfast (and for some time after the food is done) rather than the active options of replying to any of the above or working.

Given that I’ve always been one to read while enjoying my breakfast (going all the way back to reading the cereal boxes when I was a child), the surprising thing is that it has taken me so long to hit upon the idea of combining my reading of 1000 words a day of the geological literature with my breakfast reading session. In the 2.6 years since I first set myself this goal I have mostly done my “1000” at the end of the day, before going to sleep. Occasionally, it would be done during the course of my working day as it became necessary to look something up for my own writing. As a result of the random time of day it has happened fairly often that I would occasionally forget and miss a day.

This month (after taking most of December off from reading my 1000 words a day while I was travelling and visiting family and friends in Alaska, Seattle, and California) it has finally occurred to me that the best possible transition from by breakfast social networking reading to work is to first check the geoblog sphere for interesting posts and then do my 1000 words a day. By the time I’m done with my 1000 I have made the mental transition from wondering what my on-line friends have been up to recently to thinking about geology and why I find it exciting. In turn this helps me get ready to actually do some work for the day. This time it has only been 23 days since I started my current count of reading 1000 words of geologic literature a day, but I am hopeful that this time I will break my previous record of 118 days in a row. I think it will be harder for me to “forget” to read over breakfast than at any other time of day.

Thursday, 28 January 2010

with understanding one becomes free to explore

I received a comment on one of my AGU highlight posts today which mentioned that “…there are as many as 6, perhaps 10 person in the world who do really understand a-X models”. Given how slowly my own understanding has been building on this topic since I was first exposed to the concept early on in my PhD project, I suspect that he’s probably fairly accurate in his count, despite having offered the number in jest.

Doing the sort of modelling metamorphic petrologists do can be compared to various skill levels in cooking. Some people “cook” by opening a box or a can and following the instructions printed on the label to heat the contents. Others “cook” by looking at a recipe and faithfully performing every step of the instructions in the sequence suggested, with no real understanding why the author of the cookbook wanted them to do step A before step B; but by correctly following the instructions they obtain a result which they are happy to eat. Still others of us decide what we are hungry for, rummage around in the pantry and throw together delicious food that brings us joy to eat, instinctively doing some tasks before others because we understand the manner in which the tasks coordinate to create a perfect dish. We do things differently every time, never fearing to improvise because we understand *why* things work in the kitchen and what things may be changed and what rules are iron-clad.

As a petrologist I’m slowly working my way from the one end of that spectrum towards the other. The first time I attempted to use Perple_X to calculate what phases should be present in my rocks I had no idea what I was doing, or why. My advisor had pointed out a recently published paper which used that tool for calculations on a similar rock type to my own, so I downloaded the supplemental data set, used the “in” file provided, and ran the program using the settings their paper reported them to have used. Low and behold, the program generated a diagram which looked just like the one they had published (open box, remove plastic from tray, put trya in oven at 350 F for 35 minutes).

Thus encouraged, I edited their in file to show the composition of my sample instead of theirs, and ran it again, getting a very different diagram. This marked my first baby step in moving away from heating packaged food to something about on the level of complexity of using a packaged cake mix (just add water, eggs, and oil). Some months passed while I used this technique for a variety of different samples. Then, one day I realized that I needed to generate a different type of diagram, so I began to learn what changes are necessary to do so. This required much reading of the tutorials accompany the program. Not unlike learning to follow a recipe (cream butter and sugar together, beat in eggs and vanilla, add flour mixture alternatively with milk…).

I find that the more papers I read on this topic, the more I understand about the many, many options for calculations available in programs such as this one (there are others out there I should like to try as well, if I can only make the time to do so). It is my hope that, eventually, I will join the ranks of those who understand a-X models and will be able to reach the same stage of confidence in using these as I enjoy each time I enter the kitchen to cook or bake myself something yummy.

Friday, 22 January 2010

Everyone should know a geologist

I just saw an article on a meteorite which fell into a doctor’s office in Virginia. The article said that “A receptionist working in the office is married to a geologist, who recognized the meteorite for what it was. The meteorite was then carried by courier to the museum for confirmation”. I wonder what they would have done had they not had a handy geologist to turn to?

Wednesday, 20 January 2010

“It Happens”

The lessons we learn in this life come with a cost—be it the time we spend reading books, or the consequences from the mistakes we make. Yesterday’s lesson has to do with polishing the capsules for my experiments. The cost: I need to re-do two weeks of work, and will have less data than I’d hoped to put into the conference abstract that is coming due soon.

What happened? Well, with my experiments the first step is to seal powder with a composition similar to that of natural rocks into tiny gold capsules (2 mm outside diameter, ~5-6 mm long). These capsules get placed into a nest of MgO (which looks just like normal chalk-board chalk, but contains Mg instead of Ca), which goes into a graphite tube; the tube goes into a cylinder made of salt, and that cylinder and its contents goes into a large steel container, which is hooked up to a piston-cylinder apparatus with thermocouple in such a way that it is possible to inflict quite high pressures and temperatures upon those little gold capsules. We run these experiments for two to four weeks, and once that time has elapsed the second step is to remove the capsules from their nest, clean off any of the MgO-graphite-salt that has become stuck to the outside of the capsule, mount them into epoxy and then carefully polish the resultant disk until the capsule is at the surface, with the inside of the capsule exposed.

During the experiments the powder within the capsule undergoes chemical reactions and minerals grow (just as happens in real rocks when they are metamorphosed by enduring such pressures and temperatures in the real world). Because we start with powder the minerals within the capsule are often not as well interlocked with one another as is the case with real rocks. Therefore our normal procedure is to polish just until the uppermost surface of the gold has been removed, and then add additional epoxy, which soaks into the powder and holds it all together, letting that dry before doing the final polish in preparation for analysis with the electron microprobe. Yesterday that isn’t quite how it worked.

Before I left for AGU we “uploaded” my fourth experiment into the piston cylinder machine. That “run” completed its two weeks of mineral growth at high pressure and temperature (650° C, 22 kbars) during my absence, and my boss “downloaded” it, and left the package of salt-graphite-MgO-gold capsules-contents in my experimental drawer for me to deal with upon my return. Last week, after my return from my post-AGU holidays, I removed most of the salt-graphite-MgO layers from the now somewhat deformed gold capsules (it would be odd if they didn’t deform under that much pressure), but a small amount of it remained suck to the outside of the capsules—small crystallized bits with one edge wedged between wrinkles in the capsules surface, or merely adhered to the outside. This is normal, and our standard policy is to just ignore such small contaminants on the outside of the capsule, since our analytical methods are able to focus upon individual mineral grains within the capsule, so long as they are 1 μm or larger (remember that there are 1000 μm in every millimeter).

Therefore I dropped them off to be mounted into epoxy on Friday, and picked them up on Monday morning. I did a bit of polishing on Monday, just enough to remove the surface epoxy, revealing the tiniest bit of gold at the surface of the disks (one per capsule). Then I decided that I was really too sleepy to be engaging in such work (not only had I not yet completely adjusted back to this time zone after my flight from the US the week before, I’d also, foolishly, stayed up quite late both nights of the weekend) and I set the project aside for the day, and returned to it Tuesday evening.

In retrospect, I now believe that my brain was still not functioning at full capacity on Tuesday (no doubt do to once again, foolishly staying up late on Monday night). Why do I think that my brain wasn’t working properly? Because when I looked at the disks to be polished I could clearly see a bit of the “stuff” adhering to the outside of the capsules, so when I started polishing I told myself that I needed to polish past that “stuff” to get to the capsule itself and its contents. Therefore, each time I paused in my work to look at the capsules under the microscope I was convinced that the non-gold “stuff” I was looking at was naught more than the external contamination from the salt-graphite-MgO casing that had been around the capsules during the experiment. It never looked like the dark, powdery stuff that I’d found within the capsules of my earlier experiments, and, so, thinking I’d not yet polished deep enough to expose that powder, I kept polishing. And polishing. And polishing. Eventually, I suddenly had a gap in the gold between the top and the bottom ends of the capsule for one of them, and looking at it from the side view, saw that there wasn’t much left to the capsules at all. Confused, but undaunted (a *huge* clue that my brain wasn’t working properly), I then picked up the other capsule (I’d been switching between them as I worked, to keep them at more or less the same point in the polishing process) and proceeded to polish it, too, down past the middle of the capsule, with only the very ends remaining in the epoxy disk. Then I began to panic as I realized that if I hadn’t yet found the top of the contents, then, perhaps, what I had been thinking of as “outside contamination” was really the contents I’d been seeking. Oops. Major oops.

How was it possible to thus mistake it? Well, part of it is probably the difference in quality between this run and my earlier runs. The first couple of times I attempted to weld shut the capsules my seal was not, quite, perfect for all of them, which resulted in the water (which we put inside of the capsules along with the powder) to boil out of the capsules. Without that bit of fluid present the chemical reactions are inhibited and the minerals don’t grow as large as they do when the fluid is present. Therefore the resultant product is darker and more powdery than one obtains when the capsules are properly sealed and the fluid remains inside to participate in the chemical reaction. The hard “white stuff” I had been so carefully removing because it wasn’t the black powder I was expecting was, in fact, exactly what I wanted to see. Some combination of lack of sleep and three weeks of holiday (including the week at AGU) since last I’d done anything with these experiments conspired to make me fail to realize this on time to save any of it. Sigh.

My boss tells me that “it happens”. He did it once; our PhD student did it once. He also says that it is a mistake that doesn’t tend to get made a second time. I bet! I know that I shall be really, really paranoid about the polishing in the future to be certain that I never do this again. So now I need to go back to step 1 again and seal some fresh powder (plus water plus graphite) into new capsules, and give them a couple of weeks in the piston cylinder to grow new minerals. Then I can polish them, correctly, without throwing away the important part, and analyze the results in the microprobe. Then I can add that data to our growing database, and, perhaps, someday, one of you might compare the compositions of the minerals present in your real rocks with the data from my experiments and use that to determine at what temperature and pressure your rocks probably formed. When you do, and the list pressure-temperature combinations we tried isn’t quite as extensive as you were hoping it would be, remember just how much effort goes into obtaining each data set, and how easily things go awry making it necessary to start the process over from the beginning.

Sunday, 17 January 2010

Now is not the time to look to the future; now is the time to finish up past obligations

Back in March of 2009 I sent my first letter of inquiry asking for additional information a post-doc position. After exchanging a number of e-mails on the topic and participating in an on-line interview I eventually got the job. This position commenced in July of 2009. Given that four-month lead time needed to make the arrangements for this contract, I have been thinking that come August or September I will need to start looking into options of what to do next, since my contract here ends in December. I certainly didn’t expect to see positions advertised now for a January 2011 start.

Indeed, I have not yet seen a position for a specific, already defined, job to start then. However, on Friday I saw an announcement cross the geotectonics e-mail list speaking of a Fellowship opportunity designed to bring early-career researchers, from all branches of science, into the UK for two year contracts to undertake projects of their own designing. Looking closely at the advertisement I determined that I meet all of the required qualification for application. Much to my surprise, the stated start date for the Fellowship for the successful applicants is January, 2011, or exactly when I will be free to sign another employment contract. However, the deadline for the proposal is 1 February 2010, less than two weeks from the day I saw the announcement.

I did flirt briefly with the idea of trying to come up with an application for the Fellowship. I know that two weeks isn’t really an adequate amount of time to develop a comprehensive research plan and write it up in such a way that a non-geologist will agree that the project is important and deserves to be funded. However, were I to give up things like sleeping, progress on my current research, household chores, cooking, and social life, it might be possible to craft such a packet in that amount of time. I even went so far as to send a letter of enquiry to a UK based researcher whose work I’ve admired to ask if he might have interest in being a sponsor for an application for the Fellowship (a requirement of the Fellowship is that the project be in collaboration with a UK based scientist, and the application packet is done as a joint effort between the two). I did indicate in my letter that I would understand if he’s already got too much on his plate to take on such an application with such a short deadline, but that I was willing to proceed if he were interested.

As it turns out, he already has an application packet well in progress with another post-doc, and they’ve made good progress crafting an exciting proposal with a good chance for approval. This news makes me happy on a couple of points. 1) I very much want to see the geosciences doing well and receiving funding from a variety of sources, and a good packet submitted from them, with the amount of lead time they’ve had to work on it (since they’ve known about the Fellowship opportunity for months) has a strong chance for success, and if successful, will go far towards improving the standing of the geosciences in the broader scientific community. 2) Having made a brief effort to see if chasing that Fellowship was a path I should take, I may now rest comfortably knowing that the timing was not right for me to do so at this time.

Given where I am in my career, right now is not a time to be looking forward and dropping my current and previous commitments while I try to look for future opportunities. Right now I am happily in a stable position, with an income that is sufficient for me to be able to focus on both my current research responsibilities (including completing abstracts for upcoming conferences, getting the next set of experiments up and running, doing analysis on previous experiments, and comparing my results with the work of other researchers) and finishing up the “last tasks” associated with my PhD research (publishing papers and conference talks from that work).

One of the tasks I’ve been avoiding from the later category is a summary paper, sharing the important results of my research. This one has been difficult for me to approach, because I’ve always been the sort of person who is very comfortable with what others call “too much information”. My instinct in writing up my PhD thesis was to record *everything* I’d done, summarizing both the lines of enquiry which were successful, and those which lead to dead-ends. The theory being that should anyone else later look at these samples (given that some of the samples I studied had been obtained back in the 1960’s and had been taken back out of storage for this project, it is not impossible that someone else might wish to study these samples) they would know what I’d done, and would only repeat the “mistakes” knowingly, if they wished to confirm for themselves that it really won’t work, not because they thought I’d left an avenue of investigation unexplored.

My advisor recommended that I relegate the summary of what didn’t work to the thesis appendices, if I really wished to include them at all. As the deadline for boarding the plane to start my post-doc drew near whilst my thesis was as yet uncompleted, I finally started to decide that some dead end paths didn’t need to be included—not only was there was no time to get them in there they added no value to the overall thesis. But it was difficult to leave any of it out; I’m too used to complete, full, disclosure. I take very much to heart the cliché to tell “the truth, the full truth, and nothing but the truth”. When it comes to facts, I am very, very much a pack-rat; keep them all, they might be useful, someday.

This trait does not lend itself well to writing a concise summary sharing only the highlights of one’s research. Yet, it must be done. (Well, “must”, if I wish to stay in the academic world, where number of one’s publications is used as a measure of competence and likelihood of future progress.) Therefore, I sit here before you all, and state that since I am not preparing an application for funding for a future research project with a 1 February deadline I shall, instead, endeavour to spend this time compiling a concise, eloquent, summary of my prior research. I have resolved that by 1 February I will send a draft of such a manuscript to my thesis advisor for comment. You are my witness, and all have the right to check in and hold me accountable for this self-made commitment to my current and previous duties.

non-science things some people choose

Many years ago a friend of mine was attending the University of Alaska, Fairbanks, studying science. She was also a fairly talented musician, and one day she decided that she didn't want to be a scientist after all, but instead wanted to be a Folk Musician. She followed her dream, putting forth at least as much effort over time towards that goal as I required for the science degrees I've obtained. Over the years since she left Alaska I've followed her progress, purchased her CD's and attended her concerts whenever I could (dropped in on one in London once, just to surprise her--she didn't know I was in the country). I got to see her last month at the home of a mutual friend in Alaska (we were both “home” visiting our respective families for the holidays), but I had to leave state before any of her concerts happened.

Much to my delight, it turns out that while I can’t attend in person, the Internet has come to my rescue. Whole Wheat Radio is about to broadcast the House Concert at which she is performing—Live from Talkeetna, Alaska. She does at least one geologic song (called: A River), but I don’t know if that one will be performed tonight (well, it is evening in Alaska—the show starts at 6:00 am in my time zone, and I’ve stayed up late (getting work done) so that I can listen in. If you happen to see this on time, feel free to join me listening.

Friday, 8 January 2010

resolve to return to reading 1000 words from the geologic literature again

Now that I’ve nearly completed my travels (only one more weekend of adventures to survive till I return to Europe and my experiments) I’m finally looking at the spreadsheet wherein I track my progress on my goal of reading 1000 words from the geologic literature every day. It turns out that I have made no attempt to do this since 15 December, which has done bad things to my totals. During the 725 days which elapsed between starting this goal for the first time and submitting my thesis last June I managed to do my reading 96% of the days, with a total of 11 different times I had to re-start my count (normally only missing a single day between counts). In the 206 days since I turned in my thesis I’ve only managed to do my reading on 62% of the days, with nine different re-starts of my count, and up to three weeks at a time not reading. Clearly, I have not been giving this goal the attention it deserves, and it is time to start doing so once again. I strongly suspect that had I made the time to do such reading while travelling, I would also have made the time to do some work, since there is nothing like thinking about what others are researching to inspire one to make progress on one’s own research. Wish me luck in sticking to this goal despite having a large Medieval Themed event on this weekend’s schedule, wherein I will get to visit with many people I’ve not seen in years.

Thursday, 7 January 2010

nearly done with the post-AGU travel adventures

After a plethora of posts during AGU, I then spent the next several weeks visiting friends and family in Alaska, without making time to post. This was my first visit “home” in five and a half years, and it was wonderful. There is nothing like living or eight years in climates which have lush green grass in the winter and brown grass in the summer to really make me appreciate the beauty inherent in a snowy environment. Winter has always been my favourite time of the year, but part of what makes it my favourite is the snow. I love to see trees covered in fine crystals making them look like ice-sculptures. I love the contrast of snowy peaks and blue sky, or the way dark clouds glower over land smoothed white. Some people may have looked at me odd to be heading to Alaska for winter solstice and staying through New Years, but to me it was a perfect way to celebrate the season.

However, in addition to enjoying the weather, the visit was a constant round of socializing—hurrying from one gathering of friends or family to the next, with no time to slow down. I didn’t even make an attempt to read my 1000 words a day during this trip! It was fun, it was exhausting, and it was so worth it. Two weeks in Alaska wasn’t enough time to see everyone I would have liked to have seen, but it was enough to completely recharge my personal batteries and have me ready to enjoy working once again. I’ve got just one more large gathering of friends to attend—a Medieval themed event in California (which was added to my schedule when I realized that I could save 400 Euros on the cost of my flights by flying on the 11th instead of the first week of January) and I will return home to Europe and dive back into doing experiments once again. The peace and quiet of the lab sounds very appealing at the moment.