Thursday, 27 August 2009

Using the correct tool for the job

I mentioned a long time back about receiving an e-mail from someone in another country with a question about the use of the program Perple_X. My initial reply to him turned out to be helpful enough that I’ve received the occasional follow up question from him, and a few months back he wrote to me with a request for me to check over the Perple_X results he’d obtained for his samples, and asked if I would be interested in being a co-author on the paper he was preparing. At the time my reply was a brief “Not now, sorry”, as I was in “frantic” mode trying to finish up my thesis before getting on an airplane, but I did add “check back when I’ve arrived in Europe, if you want”. He did, and we’ve been working on the document off and on since. After seeing the first draft I asked him if he’d done the references by hand, or if he was using a program to do them automatically. I strongly suspected I knew the answer to this question based upon the condition of that portion of the text (it can be difficult to keep references in a consistent style when adding them by hand, over the course of preparing a document). His reply confirmed my suspicions, and he asked me if I’d be kind enough to send him the copy of the program I use (EndNote). When I explained that the zip file on my computer for that program is 59,780 KB he agreed that he didn’t really want an attachment of that size (it is a pity that it is so large—my Uni library in Tassie provided the program free to all students, and so it would have felt reasonable to share it, were the folder not an unreasonably sized for mailing).

Instead I took over the sorting of the references. Step one was easy—I opened his list of references, opened up some of the on-line library databases I use, and went into assembly-line mode:

Copy the name of the first author.

Paste into database (in the field “first author”)

Change range of dates in the database search page to match that in the citation.

Hit “search”.

Select the correct result and hit “download to EndNote”.

Repeat with next reference.

Often this resulted in a single (correct) citation being suggested, but sometimes the author’s name was too common and even for a single year there were many (sometimes more than 100) choices. In that case I would glance at the paper title, choose a key word (like “melt” or “granulite”) and “search within results”. This usually got me the article in question. More rarely the reference was for a section within a book or conference proceedings and didn’t show up in one of the major databases. In that case I’d switch to GeoRef (which isn’t as nicely set up for downloading results, but has a much better geology database available) and do a bit of fiddling to get the results (once found) into EndNote. Only once or twice did I need to actually type in the data from his list into EndNote. I did, however, occasionally need to edit the data I downloaded. Sometimes accent marks or mathematical symbols don’t translate correctly, but it is easy to copy-paste the correct version into EndNote when that happens (so long as you remember to check to see if it needed).

Once I’d completed step one I then went through the document and replaced his in-line citations with EndNote field codes. This is a delightfully easy task which involves searching for the next left-hand closed parentheses in the document, if it was a citation (as opposed to some other reason to have parentheses) clicking upon the matching entry for that author(s)/date in EndNote, then pushing a single button to insert the citation within the text (and automatically adding the full reference details to the new reference list at the end of the document, if it had not yet been cited). This process revealed a number of places where he’d added a citation, but the reference wasn’t listed in his first draft list of references. I highlighted these in the document, and made a list of each occurrence for him as I went. In the time it took me to finished that process and send it back to him with a request for the list of missing references he’d completed the edits I’d suggested for the first draft and sent the document back to me.

In the time it took me to read the paper over and do a fresh round of edits he sent me a list of the “new” references, so I added them into EndNote using the same routine as before, and once again when through the document converted the previously highlighted document citations to field codes, in the process finding another handful of citations that he’d missed. Because I was curious I then compared the number of references I’ve entered into EndNote with the number that are now listed at the bottom of the document as actually cited, and, sure enough, there are more on the list than are cited in the text. This is another reason I strongly prefer to use a program for this. If a citation gets deleted from the text, it is also automatically deleted from the list. I pointed out the discrepancy to him, and suggested that he look to see which ones they are and if he wants to cite them somewhere after all. (This is not a decision I can make, while I’m useful for editing for grammar and looking at the Perple_X results he’s presented to see if he is describing them correctly, I haven’t worked with this rock type hitherto, and have not read the papers we are citing, so wouldn’t have a clue if the ones which are now “extra” should be cited or not.)

I’ve just sent that list back to him, and now he’s got a choice. I fly off to a conference tomorrow, and will have limited (if any) internet access till I return in two weeks. He can either add these last few references by hand (I gave him two copies of the document, one with the field codes intact, and one with all of the EndNote field codes converted to plain text—the latter is the one he’d have to change if he wants to do it by hand) or wait till I once again have the time (and internet access) to complete the task myself. Given the delay in the project that happened between him asking if I’d like to be on board and my being free to participate, it won’t surprise me if he chooses to do it by hand. But, if he does, I will probably still add those references to the EndNote file I created for this paper. You never know when I might need to read one of these papers, and if I do I won’t have to re-do the data entry.

(A bonus amusing side-note: I mentioned the other day that there were 10 people who will be attending next week’s conference whose papers I’ve consulted whilst doing my own research. Yesterday I received an e-mail from one of the conference coordinators letting me know of a minor change to the field trip plans, and was delighted to realize that I now recognize his name as well—his was the one most frequently cited in this paper for which I’ve just revised the reference list.)

Wednesday, 26 August 2009

Perhaps not “foot-ball sized”, but still big enough to inspire envy when compared to my whiteschist garnets

Yesterday Chris over at Highly Allochthonous commented that he treats claims of large garnets with skepticism, having been disappointed on more than one occasion when the outcrop failed to show them as large as rumor said they’d be. Therefore I did the logical thing and e-mailed the author of yesterday’s paper to ask for photos.

He graciously agreed to share, and says that the photo on the left "is of a pyrope garnet from the classical locality Case Ramello in the Dora-Maira massif. This is one of the bigger ones (see watch for scale), but there are even bigger garnets there. The slight change in color comes from a decrease in Fe from core to rim. The second garnet is smaller, ca 4 cm in diameter coexisting with large phengite and sugary quartz.”

For contrast, the below photo is of a thin section of the Tasmanian whiteschist; the largest garnet in this photo (upper left corner) is 4 mm wide.

Tuesday, 25 August 2009

Garnet Envy

While reading a paper* today which combines experimental petrology results with information obtained from natural rocks, I noticed a description of the whiteschists located in Dora-Maira massif of the Western Alps, which says that they “They display spectacular up to football-size, pinkish garnets embedded in a matrix of kyanite, quartz and phengite”. For those of you who remember my post showing the outcrop of Tasmanian whiteschist and how very small the outcrop is, you will see why I now have garnet envy. No way could my tiny little outcrop create foot-ball sized garnets! The largest one I found in my samples was only a couple of millimeters wide, though, like theirs, they are "pinkish". I wish that the article had included photos, I’d like to see those garnets…

*Hermann, J., 2003. Experimental evidence for diamond-facies metamorphism in the Dora-Maira massif. Lithos, 70(3-4), 163-182.

Sunday, 23 August 2009

The pet scientist writes another letter to her school

The following paragraphs were written in reply to the teacher at the primary school in Tasmania, Australia with whom I am long-distance partnered as a “Scientist in the School”. He suggested that I “email the students a paragraph on what you are doing in Europe”, because such a letter “can be used to generate questions from the class”. I made my reply as brief as I could manage, but it still turned out to be a full letter, rather than the requested “paragraph”.

My career as a scientist is in the process of undergoing a major transformation. I just spent the past four years working out the pressure and temperature at which Tasmanian Metamorphic rocks formed based upon the compositions of the minerals in the rocks. I did this by comparing them with the compositions of minerals formed during experiments other scientists have done. Now, instead of comparing real rocks with someone else's experiments, I shall perform my own experiments, so that others may compare their rocks with my results. To do this I have moved to Europe, where I have joined a team of scientists who do experiments.

The experiments we do require very special equipment and lots of time. First we take a powder of known composition, and then we seal it in tiny (about 3 mm wide) gold or platinum capsules. We then encase the capsules in a series of slightly larger containers, each layer chosen for specific reasons. Once we've got them all bundled up inside all of the special layers we put them into a special press, which then puts a large amount of pressure and heat on the package. We choose a temperature and pressure which is within the range at which real rocks are metamorphosed underground, and we leave it at that pressure and temperature for a few weeks. (My experiments will run at ~600-700 degrees C and 20,000 to 30,000 bars of pressure.)

During this time tiny minerals start to grow inside the capsules, just as they do in real rocks which are subjected to such extreme conditions of temperature and pressure. After they've been "cooked" long enough, we open up the package, remove and cut open the capsule, and polish the rock surface inside (it is now a rock instead of a powder because the minerals have grown from the powder, and they interlock together just as a real metamorphic rock does). Once it is polished we use a special machine called an Electron Microprobe, which allows us to analyze the composition of the minerals. It takes several hours of hard work to determine which minerals are now present inside the capsule, and what their compositions are.

Over the course of the next year I will repeat the experiment several times, each time using the same starting composition, but different pressures and temperatures. After each "run" I will make notes of which minerals, and what compositions of minerals are present in each capsule, and at what temperature and pressure they grew.

Once I have enough data from a variety of different "runs", I will draw graphs that show the patterns: the relationship between which minerals are present at different temperatures and pressures, and how the compositions of those minerals change as well. Then, other scientists, at other universities, can use those graphs to compare with their real rocks, and try to work out at which temperature and pressure their rocks must have grown.

Friday, 21 August 2009

pre-conference homework

Having read more than one comment on Female Science Professor’s blog about students who failed to recognize the name of an important scientist in their field when meeting them at a conference, I decided that in addition to preparing a poster summarizing some of my recent research to present at a conference I’ll be attending later this month, I should also have an advance list at the list of delegates who are attending the conference, since the conference web page was nice enough to include one.

Comparing that list with the (Endnote) list of papers I’ve read in the course of my research reveals 10 names of people whose work I’ve consulted who will be attending the same conference as I. I now have a list of those names, and which papers of theirs I’ve got, so I can glance at them again between now and the start of the conference and be reminded of what sort of topics they research. With luck, being familiar with their work will give me topic(s) of conversation should I actually meet them in person, which will be one way to prevent shyness from keeping me in a corner not speaking to anyone. (Mine is the sort of shyness which only manifests itself if I think I don’t know anyone present.)

In the course of compiling this list there were a few people whose addresses in the program do not match the address on the paper I’ve got, so for those people I checked their department web page to see if it listed their publications or research interests, to make certain that the name of the attendee is, in fact, the same person who wrote the paper. This task was worth doing, as I found one where it turns out to be someone with the same name, but different research interests, and another where the list of the things she likes to research is very similar to my own. Therefore she might be an interesting person to speak with about her research.

If I find myself with the time/energy between now and the start of the conference, I may also go through the program looking for interesting sounding talks, not only to mark the ones I don’t wish to miss, but also to see if those authors have papers published which I’d also like to read, but haven’t seen yet. Not that I need more papers, the list of things in my “to read” pile will keep me doing my 1000 words a day of reading for a long time yet.

(Note: for those of you keeping track of such things, I’ve finally settled in to my new location sufficiently that my 1000 a day is, once again, a habit. 17 days in a row, and counting. It isn’t much, yet, but it is a start. Perhaps I might even start blogging regularly again.)

Saturday, 8 August 2009

Books I’d buy if I had a huge book buying budget.

I have been a student, and thus on a student budget, for most of my adult life. Consequently, when I receive my copy of GSAToday, I generally put the glossy bookstore flyer straight into the recycle bin without looking at it. As of last month I’m not just a student, I’m also a post-doc, with an income (though I’ll continue to count as a student, too, until the degree is actually awarded). While this income doesn’t yet translate to much in the way of spending money (having used up my savings to get here, and therefore needing more than usual from my first pay check to cover “moving in expenses”), it does mean that, for the first time, I actually looked at the flyer. This could be a mistake—were I to actually purchase everything which looks interesting, I could quickly use up all of that income I’m now making. Here is a short list of what was in the flyer which caught my eye this time, in the order listed in the flyer, and the member cost (US$) for each:

$42 The World in a Crucible: Laboratory Practice and Geological Theory at the Beginning of Geology

$34 Investigations into the Tectonics of the Tibetan Plateau

$56 When Did Plate Tectonics Begin on Planet Earth?

$63 Whence the Mountains? Inquiries into the Evolution of Orogenic Systems: A Volume in Honor of Raymond A. Price

$109 Tectonic Growth of a Collisional Continental Margin: Crustal Evolution of Southern Alaska

$67 Advances in High-Pressure Mineralogy

$49 Convergent Margin Terranes and Associated Regions: A Tribute to W.G. Ernst

$42 Earth and Mind: How Geologists Think and Learn about the Earth

$67 Tectonics, Climate and Landscape Evolution

$56 The Revolution in Geology from the Renaissance to the Enlightenment

$56 The Greenland Caledonides: Evolution of the Northeast Margin of Laurentia

$84 4-D Framework of Continental Crust

$70 Proterozoic Tectonic Evolution of the Grenville Orogen in North America

$ 42 Paleozoic and Mesozoic Tectonic Evolution of Central Asia: From Continental Assembly to Intracontinental Deformation

$70 Metamorphic Conditions along Convergent Plate Junctions

The above list got my total-I-could-spend-if-I-went-on-a-shopping-spree today to $907 (add 30% if I weren’t a GSA member). But then looking in their on-line store to create the above links revealed a few more I’d be interested in reading:

$40 Did Westward Subduction Cause Cretaceous–Tertiary Orogeny in the North American Cordillera?

$63 Backbone of the Americas: Shallow Subduction, Plateau Uplift, and Ridge and Terrane Collision

$42 The Origins of Geology in Italy

$28 Ultrahigh-pressure metamorphism: Deep Continental Subduction

$21 Collisional Delamination in New Guinea: The Geotectonics of Subducting Slab Breakoff

$42 Paleozoic and Mesozoic Tectonic Evolution of Central Asia: From Continental Assembly to Intracontinental Deformation

The full list comes to $1,131.00, or an average price of $53.86 for 21 books. I suppose it is for the best that I’m not actually shopping at this time—I’ve got so many papers I need to be reading at the moment that adding a pile of books that tall might make the list seem daunting. Perhaps in a month or so I’ll select just one from the list, and read it before I let myself purchase another…

Thursday, 6 August 2009

Annotating the figures in the articles I read is ever so helpful, if time consuming

Sometimes, simply reading the text of an article isn’t enough—sometimes it is truly necessary to look at the figures very closely in conjunction with the text to understand exactly what the text is saying about the figures. This is easy when the figure happens to be on the same page, and one’s eye can easily skip from one to the other, without losing one’s place. But, often, figures are located in drastically different parts of the document. With a photo-copy one can remove the staples, and set the two pages side by side (unless it is a two-sided copy and the one is on the back side of the other, of course), but many of us today prefer reading our articles in pdf on the computer screen, rather than wasting paper, particularly given the large number of articles it is needful to read both to stay on top of the current literature in one’s field, and to catch up on the “classic” papers in a field when expanding one’s research into a new direction.

The solution use to make it possible to see both the figure and the text at once is to use the “import” function of my drawing program to open the just the relevant page of the pdf and zoom in on the figure. Then I am able to display the drawing program and the pdf itself open side-by side on the screen at the same time (it is better yet when I have two monitors available!). However, for older articles the pdf often looks like a bad-photocopy (and, indeed, I suspect that in some cases the scan may well have been made from a bad photocopy rather than the original article) so zooming out far enough to see the whole figure at once often makes it difficult to see important details in the figures, but zooming in on details results in pixilation issues, which, again, can make it difficult to see.

This is where opening them in a drawing program can be very helpful, as it is possible to annotate the figure.

The figure above is figure 2 from Kepezhinskas and Khlestov (1977). The original was black and white, of course. The paper discuses Petrogenetic Grids and development thereof (as well as specifically presenting one they developed). In the course of their discussion on the development of such grids they describe an example of how it is possible to use observations of mineral assemblages in real rocks to select between two different theoretically possible arrangements of the lines on the grid. They say:

“For example, for the knot [2] including curves only with positive slopes two alternative versions are shown in Fig. 2. It may be easily seen that for the association Chd+Bt (+Q+Mu) and Cd+Gr+Chl+Mu(Q) the pressure intervals corresponding to their stability fields do not overlap one another. For the version 2a Bt+Chd characterize higher pressures, while Cd+Gr+Chl+Mu lower ones. For the version 2b one has the reverse.”

In my annotations I’ve marked the “Chd + Bt” field with a pink star in both diagrams, and the “Cd + Gr + Chl +Mu” field with a blue one. I’ve also colour-coded the various lines representing the mineral reactions so that it is easy to see how the two diagrams differ, and covered over the difficult to read text of the main labels with my own text (text added by the drawing program is clear and easy to read at any number of zoom levels, unlike the pdf of this document--alas, that layer didn't import into this post, though it shows on the jpg on my screen, so I've replaced the photo with one showing the original text). They go on to say:

"It is well known since Thompson's (1957) work that Gr+Cd+Chl+Mu is possible only at low pressures. On the other hand as reported in the literature, Chd+Bi occurs almost entirely in kyanite-sillimanite type complexes being confined frequently to especially high pressure rock series containing simultaneously glaucophane schists. It seems quite reasonable that the real thing is version 2a.

Simply reading the text, for me, does not create understanding. Combining the text with the colour-coded figure makes it easy for me to understand what they mean, and why they like 2a better than 2b. (Why, yes, I am visually-oriented with a need to “see for myself”; why do you ask?)


Kepezhinskas, K. B. and Khlestov, V. V. (1977). "The Petrogenetic Grid and Subfacies for Middle-temperature Metapelites." J. Petrology 18(1): 114-143.

Thompson, J. B., JR., 1957. The graphical analysis of mineral assemblages in pelitic schists. Am. Miner. 42, 842-58.