Wednesday, March 31, 2010

a little bit more of the article in progress

If anyone is coming in to this blog in the middle, I direct your attention to the posts I’ve made over the past few days, describing “active reading”, and summarizing my snail’s pace crawl through an article using this technique. It is very, very effective, and I like the amount of information I’m retaining, but it requires a chunk of time. Worth it for me, and perhaps of interest to one or two people out there, which is why I am continuing to post my notes as I make them.
Paragraph 33 describes the two schists from Elijah Ridge, lists the minerals present in each, describes the outcrop of one of them, and specifies which minerals are post-kinematic.
Paragraph 34 mentions an old study (1968) which interpreted the andalusite here as a late Buchan-style overprint, and relates it to an intrusion of a batholith ~50 Ma. Also points out that there is more andalusite to the east of the RLFZ which may be from the same body.
Paragraph 35 describes the deformation visible in these schists.
Paragraph 36 describes the garnet in these schists, and specifies the zoning pattern for garnet in one of the samples.
Paragraph 37 mentions that one of the schists (the kyanite-staurolite one) has plagioclase which has a different (zoned) composition next to the garnet than in the matrix.
Paragraph 38 describes the two occurrences of biotite from one of these schists and mentions that kyanite and sillimanite have been partially replaced by cordierite or andalusite. It also describes the manner in which broken kyanite fragments align with the foliation.
Paragraph 39 contrasts the presence of staurolite in these schists with it rarity in the Skagit Gneiss. It also mentions older studies which estimated P > 6 for staurolite-hornblende coexistence here, and points out that it has suffered brittle deformation along foliation layers.
Paragraph 40 describes the zoning pattern for garnet in the sample which wasn’t covered in paragraph 35 and points to the lovely full-colour garnet maps.
Paragraph 41 describes the plagioclase from the sample which wasn’t discussed in paragraph 37.
Paragraph 42 describes another schist sample.
Paragraph 43 continues the description of that sample, its textures, and alteration.
Here ends the section on Petrography and Mineral Chemistry (though this post summarized only the sub-section of the metapelites from Elijah Ridge). I found the organization within this section to not be as effective as some of the others—it appears to be divided by sample, but there are no additional sub headings to clue that in, and the paragraphs seem to focus on specific mineral(s) making it tough to keep track of which sample is being described where.
The next section will be on Thermometry and Barometry. Stay tuned for tomorrow, when I read and summarize it...

Tuesday, March 30, 2010

Yes, I think the extra time is worth it

I find that I’m liking this “active reading” stuff. It used to be that on days like yesterday, when I didn’t get around to reading my 1000 words of geologic literature till very late in the day I’d “read” it, as in my eyes would look at each word on the page, but it was more along the lines of “skimming” it, and it is somewhat doubtful how much, if any, was actually retained. Yesterday, however, I actually got meaning out of each and every paragraph I read. I know this, because it isn’t possible for me to type a sentence or three about what it says if I don’t understand it first.
Normally I’m a two-monitor kind of person. If I need to read something and type notes about it, I keep the article on one screen, and the word-processor on the other. Yesterday, on the other hand, that wasn’t possible. I’d spent the day using the electron microprobe and when it was time for the ‘probe’ operator to head home for the day I was tired, so I simply took my computer home with me, rather than bringing it back up the stairs to my office. As a result when I realized hours later that I still needed to do my 1000 for the day (I’m at 82 days in a row now this time!) I was faced with the choice of dealing without a second monitor or carrying the computer back to my office.
The solution I hit upon worked very well—I’d copy-paste a single paragraph into the document in which I was working, read it, type up my summary, then move that paragraph into an otherwise empty document. At each minor section break I’d do a word-count of the document which contained only the paragraphs I’d already read, to see if I’d done 1000 yet. As it turns out, I hit 1053 words at one of the minor section breaks, to the notes below don’t end in quite as logical of a place as the previous batch, but I was tired (Europe only just did the change to daylight savings this weekend), so called it good. It is interesting to note that my summary, including the headings “Paragraph 1, 2, etc.” took 581 words to summarize the 1053 words of the original.
When first I started reading 1000 words a day I thought of it as a 20-minute time commitment. Reading this 1053 words and typing up a summary took 54 minutes. Therefore it takes nearly three times as many minutes, but I think that the gain is more than four-fold the amount of information retained.
Here follows the summary in progress for the article Metamorphism and deformation at different structural levels in a strike-slip fault zone, Ross Lake fault, North Cascades, USA by Gordon et al 2010:
Paragraph 18 informs us that it can be difficult to find appropriate mineral assemblages for P-T estimates in the Skagit Gneiss. They mention a previous study which used 4 metapelites, and tell us that this study found 4 useful metapelites and three garnet amphibolites between the Skagit Gneiss and the Napeequa unit.
The next section focuses on the garnet amphibolites
Paragraph 19 specifies the locations for the three garnet amphibolites that yielded PT estimates and gives the units thereof.
Paragraph 20 mentions which two amphibolites (from Ruby Mt.) are migmatic adn which one isn’t (from Elijah Ridge) and gives the mineral assemblages and fabric.
Paragraph 21 describes the garnet in one of the amphibolites, giving size, general composition, mentions that it isn’t zoned (and states that this is normal for the unit), list of inclusions, and the fact that some of them display post-kinematic coronas.
Paragraph 22 describes the garnet from one of the two other samples in the other unit, mentioning their size (smaller than last paragraph), and the fact that minor growth zoning is present, and points out that the final sample is very similar to this one.
Paragraph 23 describes the hornblende of all three samples, two of which have zoning (just like the garnet from the same unit), but zoning is rare in the other sample (just like the garnet from that sample)
Paragraph 24 mentions the zoning of the plagioclase in all three samples, states that for the Ruby amphibolites the reverse (An increase to rim) zoning is more common & more variable than the normal (An decrease to rim) zoning that is present.
Paragraph 25 describes the plagioclase zoning for the Elijah ridge amphibolite, which also has more reverse than normally zoned examples. However, in this case the normal zoning is more variable than is the reverse.
Paragraph 26 mentions which sample contains clinopyroxene, and the fact that it isn’t zoned and is both in the matrix and as inclusions within the garnet.
Here ends the section on the minerals present in the amphibolites. The next section looks at the metapelites.
Paragraph 27 lists the locations (2 from Ruby Mt, and 2 from Elijah Ridge) and general assemblages of the four metapelites used in this study, and specifies which ones are structurally higher than their neighbors, and which pair is structurally higher than the other.
The next section focuses on the Ruby Mt. Metapelites.
Paragraph 28 lists the major (grt-bt-sil-ky-crd-qtz-pl) and accessory (il-zr-apt-mnz) minerals present in these rocks and point out that the sillimanite one has pseudomorphic textures hinting at former kyanite while the kyanite bearing one has some sillimanite. It also specifies the habits of the cordierite
Paragraph 29 describes the fabrics present, and where possible mentions what that says about the T at which each deformation happened.
Paragraph 30 describes the habits of garnet in one of the samples (including what is included therein) and cordierite and points out evidence for a retrograde reaction of grt-crd.
Paragraph 31 continues with the same sample as last paragraph,stating that plagioclase isn’t generally zoned, the biotite is homogeneous, and describes alignment of sillimanite with the foliation. It also reminds us that kyanite used to be stable in this sample.
Paragraph 32 moves on to the other sample, lists minerals present, compares garnet, plag, and biotite with last sample, describes the kyanite and sillimanite present.
There ends the description of the minerals in the metapelites from Ruby Mountain. The next section will describe those from Elijah Ridge.

Monday, March 29, 2010

Active reading, continued

Yesterday I posted my understanding of the techniques of “active reading”, and shared the results of my initial glance through of an article. Today I shall share my notes from that article, Metamorphism and deformation at different structural levels in a strike-slip fault zone, Ross Lake fault, North Cascades, USA.
Skipping the abstract at the moment, and jumping straight to the article itself, here follows my notes from my first hour of active reading (plus two five-minute breaks to read blogs for pleasure) I shall continue the rest of the article in my next post, once I’ve read & made notes on the rest of it.
Paragraph 1 introduces the concept of strike-slip faults during orogenesis and raises the question “can a strike-slip fault include sufficient vertical component to drive both burial and exhumation during a single orogenic event?”
Paragraph 2 lists studies which have documented exhumation of mid- to lower-crustal rocks in strike-slip fault zones.
Paragraph 3 introduces the fact that some strike slip faults juxtapose rocks formed at very different crustal levels (metamorphic next to unmetamorphosed) and reminds us that this can sometimes be due to a vertical component to the fault movement.
Paragraph 4 introduces the field area for this study (the Skagit Gneiss & adjacent units in the transcurrent Ross Lake fault zone (RLFZ), mentions that it contains high-grade rocks from a continental arc during mid-Cretaceous shortening (and lists references, of course). It goes on to report that the exhumation of these rocks occurred in the Eocene and states that the area is of interest because it records P-T-d (pressure-temperature-deformation) histories which vary on either side of the fault. It points out that such faults usually have complex P-T-d histories, but this one is unusually well preserved.
That was the final paragraph of the introduction, therefore this is an appropriate time to look back over it and see what I think the main message is thus far. Thus far I think that their main message is that they chose this field area because they felt that the rocks exposed on either side of this strike-slip fault would contain enough information to say something about the P-T-d history of the area, and that they feel that while it is primarily a strike-slip fault, it also has a vertical component, and so can have been responsible for the exhumation which brought these rocks to the surface. The next section will cover the Eastern margin of the Skagit Gneiss, first focusing on the Ross Lake Fault Zone.
Paragraph 5 lists the location of the Skagit Gneiss and names the bounding faults
Paragraph 6 lists the general age of the Skagit Gneiss, describes the main rock types within the unit, the general structural style, lists the specific ages calculated from previous geochronological studies, and lists published geothermobarometric estimates (including the fact that the decompression was nearly isothermal).
Paragraph 7 introduces the Ross Lake Fault Zone (RLFZ), mentions that it is high-angle and has usually been dextral strike-slip (though has also experienced reverse slip in the Palaeocene and dextral-normal (down to the east) shear in the Eocene), and it briefly contrasts the high-grade & plutonic rocks on the west side with the lower-grade units on the east side, points out that the degree of difference in grade changes along the length of the fault
Paragraph 8 describes the RLFZ in more detail at the NNE margin of the Skagit Gneiss, mentioning a series of splays separating structural blocks (and naming several of the different units in different blocks), then goes on to describe specifics of the fault in two sub areas along the length just subscribed (it was necessary to compare the text to figure 2 to determine if they the paragraph had zoomed in to greater detail or if it had switched to a different region).
Paragraph 9 this paragraph describes the RLFZ in the region to the south of the last paragraph, mentioning that it is also splayed, naming the units in each splay, and pointing out the large difference in metamorphic grade across the fault in this area.
Paragraph 10 describes the segment a bit further south from last paragraph as a “left-stepping, dextral strike-slip step-over shear zone” and names the units and mentions their metamorphic grades juxtaposed by this zone.
Paragraph 11 describes the displacement history of this southern segment of the RLFZ, giving timing and direction of movement for at least three different time periods and points out that this is similar to the movements in the northern section as well.
Paragraph 12 relates the movement of this fault zone to “big picture” models about the attachment of the North Cascades and associated terranes to North America between c. 66 and 56 Ma.
This being a section break, it is time to look back over this section. This section focused specifically on the fault zone, the information known about the timing and direction of movement in the zone (including how it has changed over time) and contrasting the (sometimes very) different metamorphic grades on each side of the zone. The next section moves on to the Ruby Mountain and Elijah Ridge sub-section of the Eastern margin of the Skagit Gneiss section of the paper.
Paragraph 13 describes the units which crop out on Ruby Mountain and their deformational style, and mentions that the RLFZ should be cutting through units in this area and/or on Elijah Ridge (since it is exposed to the north and the south of this area).
Paragraph 14 describes the units on Elijah Ridge, compares them with the above mentioned Ruby Mountain units, mentions that most have an “intense constructional fabric, locally mylonitic in places”, and give the details of the one previously published P-T estimate from here (650 C, 8 kbars) pointing out that it is similar (though slightly lower than) to estimates published for the structurally deepest part of the Skagit Gneiss ~10 km to the west. It also mentions that mass balance calculations indicate that this area and the Skagit Gneiss metapelites have different protoliths.
Paragraph 15 gives more details of the units of Elijah Ridge and mentions that they have been intruded by „variably deformed and metamorphosed hornblende porphyry and hornblende gabbro, and undeformed late granitoid dykes. It also mentions the presence of schists which are interpreted as metamorphosed versions of the Methow terrane (which is mentioned in the introduction as being unmetamorphosed on the far side the RLFZ a bit to the south of this area).
Paragraph 16 compares the rocks exposed on these two peaks with those cut by the RLFZ to the north and the south of this area, but emphasizes that the location of the RLFZ in this area is unknown. It also points out that there is higher grade metamorphism of the Methow terrane rocks here than is present to the north and the south of this area and states that the driving force for that metamorphism is unknown and that the tectonic/metamorphic significance of the Skagit Gneiss-Napeequa unit contact and the origin of the constructional fabrics near the contact is unknown.
Paragraph 17 explains that the current study was undertaken to address the questions mentioned in the last paragraph, lists the areas from which they took samples and what sort of work was done on the samples (thermobarometric analysis, microstructural analysis, and 40Ar/39Ar analysis). It also directs the reader to the tables showing the analytical methods and other supporting information.
This ends the section on the Ruby Mountain and Elijah Ridge sub-section of the Eastern margin of the Skagit Gneiss section of the paper. It described the units present, compared them with units cut by the RLFZ in other areas, indicated that the location of the RLFZ in this area was unknown (but it has to be around there somewhere) and raised questions which they hoped to answer with this study. The next section will cover their results from their petrography and mineral chemistry studies.

Saturday, March 27, 2010

my first attempt at actually doing the “active reading” technique—part one: look over the paper without reading the details

Since I am an addicted reader of novels, the suggestions for active reading that I summarized in my last post sounded tedious and cumbersome to me when our teacher suggested them. Therefore I decided to work through one paper using those techniques here on this blog, because if I do it publicly, I will feel obligated to continue the process all the way through to the end, rather than giving up and returning to lazy reading techniques. If, at the end of this process it feels like the extra effort has been worth it, I shall let you know.
Today’s paper is Gordon et al. (2010)*. This paper was chosen for today’s reading because my PhD advisor suggested it and another article from the same issue of the journal as having structures similar to what I should be aiming at when I write the paper summarizing what I did for my PhD research. Therefore the questions I will keep in mind when reading this paper are:

1) What structure did they choose, and how effective do I feel it is in presenting their work? 2) How many different techniques did they use for this project, and how did they organize their presentation of these various techniques? 3) How effective is that organizational method? 4) Would another order be more appropriate? 5) Do they indicate how much more work they undertook in addition to the specific results they share? 6) Is there any indication as to how they selected these specific results? 7) How do their results and the presentation thereof lead to the conclusions they draw? 8) Do their results and the subsequent discussion convince me that their conclusions are appropriate? 9) Why or why not?

Step one in the active reading is simply to look over the entire thing. This is a 20 page document, the first 17 of which contain text, tables, and figures. The headings used in this article reduce to the following outline:

INTRODUCTION
GEOLOGICAL OVERVIEW OF THE SKAGIT GNEISS AND ROSS LAKE FAULT
. Eastern margin of the Skagit Gniess
. Ross Lake Fault Zone
. Ruby Mountain and Elijah Ridge
PETROGRAPHY AND MINERAL CHEMISTRY
. Garnet amphibolite
. Metapelitic rocks
. . Ruby Mountain Metapelites
. . Elijah Ridge Metapelites
THERMOMETRY AND BAROMETRY
. Thermometry
. Barometry
P-T PATHS
MICROSTRUCTURAL ANALYSIS
40Ar/39Ar RESULTS
DISCUSSION
. Previous interpretations of Ruby Mt-Elijah Ridge tectonic history
. Re-evaluation of Ruby Mt Elijah Ridge tectonometamorphic history


The article contains 13 figures.
Figure 1 contains both a simplified geologic map of the region of study area and an annotated Google Earth image (the latter is in colour in the pdf version). The notes include details of sample locations, locations of geological units, and pressure temperature estimates.
Figure 2 is a closer-scale geologic map of just the fault zone region
Figure 3 shows a series of cross-sections across the region.
Figure 4 contains colour photomicrograph of thin sections of two samples
Figure 5 contains colour photomicrograph of thin sections of three samples
Figure 6 contains colour photomicrograph of thin sections of three samples
Figure 7 contains both a colour photomicrograph of one thin section and major element x-ray maps for the garnet in that thin section for Mn, Fe, and Mg (this garnet is obviously much richer in Fe than Mg or Mn)
Figure 8 contains both a colour photomicrograph of another thin section and major element x-ray maps for the garnet in that thin section for Ca, Mn and Fe, (this garnet has a core which is Ca-poor and a rim (nearly as thick as the core) which is Ca-rich—the core is richer in Mn than the rim. Both the core and rim contain a similar amount of Fe overall, but there is an Fe-poor region at the core-rim boundary, which could be related to the greater quantity of inclusions in that region (my observation, not what the caption said))
Figure 9 is a P-T diagram showing the estimates obtained for various samples plotting in a clump just above the ky-sil boundary in the range 600-800 C and 7-11 kbars. It also includes arrows to show the near-isothermal decompression they infer for these samples based upon mineral assemblages and textures.
Figure 10 contains two (colour) photomicrographs of the orthogneiss, showing two different grain sizes.
Figure 11 contains field photos illustrating intense constrictional fabrics to two different rock types from the region.
Figure 12 contains Muscovite 40Ar/39Ar age spectra for two different samples.
Figure 13 contains a map-view cartoon sketch of the transpressional step-over and duplex structures of the region.

Of the questions I asked myself at the beginning, I feel that just looking at the headings and figures permits me to answer the following:

1) They present an introduction and regional geology, followed by six different sections presenting each of their different types of results, followed by a discussion section where they first list previous interpretations of the area and then share how they feel their new data modifies those interpretations (Isn’t it funny how I can state that with confidence, even though I have yet to actually read the paper and so have no idea what their interpretation is, nor what the older interpretations might have been?)
2) The six techniques they used are geological mapping, petrography/mineral chemistry analysis, thermobarometric calculations, P-T paths, microstructural analysis, and geochronology, listed in that order. The order may well have been chosen because one must first do the field work and obtain the samples before anything else happens. The microstructural section could just as easily have come before the petrography/mineral chemistry section, but that work is essential for the geothermobarometric calculations, which, in turn, is essential to determine a P-T path. The age dating could have been presented at any point after the field work, unless 40Ar/39Ar technique requires information obtained in the petrography/mineral chemistry section.
3), 4) How effective is that organizational method? The organizational method looks logical thus far, I’d have to actually read the paper to see if it is truly effective and if another would have been more appropriate.

The remaining questions can’t be answered till I read the text itself. This post is now quite long enough, so I will take a break from “reading” this paper and share with you my progress to this point. Stay tuned for my paragraph by paragraph summaries of this paper, once I’ve done them.


*Gordon, S.M., Whitney, D.L., Miller, R.B., McLean, N., and Seaton, N.C.A., 2010, Metamorphism and deformation at different structural levels in a strike-slip fault zone, Ross Lake fault, North Cascades, USA: Journal of Metamorphic Geology, 28, 117-136.

Active reading techniques to improve understanding & retention

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

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

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

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

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

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

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

Wednesday, March 24, 2010

Taking a short break from a course in writing to post about it

I am currently half way through a short course on Successful Scientific Writing: from Proposal to Publication. I am really enjoying this class, and getting much out of it. I will, doubtless, be sharing further details on the course once it is over, but since I’ve got an hour before class starts this morning I thought I’d take a moment to share one of the very useful tools they gave us to improve our writing.
Treat your writing like a game of dominoes. When playing dominoes if the first tile placed is a 5-6 the second tile needs to contain either a five or a six spot side, which is placed up against the matching side of the first tile. This approach is also useful in writing. The first sentence in a paragraph introduces the topic, and the next sentence contains a word or words which link back to the first sentence and then adds additional information on that topic. Each subsequent sentence in the paragraph ideally contains a word or phrase which links it back to the sentence which immediately precedes it.
Likewise each paragraph, which by their very nature, often introduce new topics should contain something which links back to what has already been written in addition to providing new information. (Sometimes the “link” can be a contrast such as “However,…”.
This tool alone can make a huge difference. Before the class began we were assigned the task of writing a “200-word abstract describing your current research project. The abstract should be concrete, but simple enough to be understood by researchers not only in your own field but also adjoining fields (i.e. researchers in physics, chemistry, etc.)”. Yesterday afternoon we broke into pairs to evaluate these abstracts. One of the two I read contained ten sentences in four paragraphs. In looking over it I noticed that it didn’t obey the rules of the domino game. Therefore I searched each sentence to discover which ones were related. My suggestion to the author consisted of re-arranging his thoughts. I numbered each of his sentences (1-10) and assigned letters (A-G) to the new locations for the sentences which I felt would improve the flow of the abstract. The “map” for the changes I suggest looks like this:

A: sentence one
B: sentence five
C: sentence two
D: sentence ten
E: sentences three and four
F: sentences six and seven
G: sentences eight and nine.

One of today’s assignments is to revise our abstracts using this tool, and all of the other useful tools they’ve given us thus far. I am looking forward to seeing the changes in my abstract as a result of this course, and anticipate that future papers will be much easier to write than previous ones. I strongly recommend taking such a course from a good teacher.

Monday, March 22, 2010

Traveling, again

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

Friday, March 19, 2010

the mass balance of cookies

Part of my time/energy the past few days has been focused upon getting things set up correctly to make Mathmatica work for mass balance calculations. Mathmatica is a powerful tool that can do amazing calculations *if* the user first sets up the data files exactly correctly, and then creates (or, more commonly, edits previously existing) files which tells it what to calculate and where to find the data files upon which to perform the calculations. Now that I’ve got it working, I thought I’d take a moment and share with you a bit about what mass balance calculations are.

Anyone who has ever decided to do lots of baking for a party understands how to look at the various recipes, make note of how much of each ingredient is needed, and then add up the totals for any ingredient which appears in more than one recipe.

Imagine that I decided to make three batches of blond brownies, 2 of oatmeal current cookies, 2 batches of vanilla cookies, and 4 batches of peanut butter cookies. Using the recipes below that would mean that all of the combined cookies would contain a total of 6 cups of oats, 14 cups of flour, 5.5 teaspoons of baking powder, 4.5 teaspoons of salt 1 cup of honey, 4 cups of brown sugar, 2.5 cups of white sugar, 6 cups of butter, 11 eggs, 6 teaspoons of vanilla, 2 cups of peanut butter, 1.5 cups of nuts, 1.5 cups of chocolate chips, 1⅓ cups of currants and 1 teaspoon of cinnamon.

Now, what if I gave you that pile of ingredients, and the recipes, but didn’t tell you how many batches of each one to make, but I did require you to follow the recipes exactly and to use up all of every single ingredient, without wasting anything.

That is what mathmatica is doing for the mass balance calculations. We tell it the starting bulk composition (the list of ingredients), and the recipes (the composition of each mineral that is present, and the list of all the minerals that are present) and ask it how much (how many batches) of each mineral can be made from those ingredients.

I don’t truly understand how it is doing it, but it uses a “monte carlo sampling” to do this. We tell it how many tries to make (100 tries takes only a few seconds) and it tries various combinations of how much of each mineral (how many batches of cookies). I think that it may be comparing the ingredients needed for each of its guesses with the list of ingredients actually present. The larger the number of tries we tell it to make (my boss suggests that it should be at least 1000), the more accurate the results will be.


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Blond Brownies

1 c. sifted flour

½ t b. powder
½ t b. soda
½ t salt
⅓ c. butter
1 c. brown sugar
1 egg
1 t vanilla
½ c. chopped nuts
½ c. chocolate chips

Sift flour, baking powder, baking soda & salt together. Add nuts and mix well.


Melt butter & add sugar and mix well. Cool. Add eggs & vanilla to butter/sugar and mix well.

Add flour mixture, a small amount at a time, mixing well after each addition. Add chocolate chips and turn into greased pan 9 x 9 x 2 (inches)

Bake at 375 for 20-25 min.
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Oatmeal Current Cookies

Put 2/3 cup of currents into a cup, and cover (just till the liquid shows at the top layer of currents) with a blend of 1/2 apple juice, 1/2 lemongrass tea, put into the microwave on full power for thirty seconds, then let stand till cool.

In one bowl mix:

3 c oats

1 c flour
1 t salt
½ t backing soda
A dash of cinnamon

In another bowl mix till light and fluffy:

1 c soft butter
½ cup light brown sugar
3/4 c raw sugar
1 egg

Add the cooled juice/currents to the butter mixture, and fold in the oat mixture. If too sticky, add a small amount more flour. Roll into 2 – 3 cm balls, place on greased paper, bake at about 180 C for 7 to 10 minutes till they are only barely golden brown. Cool on a wire rack.

Note: I used the juice/tea blend because that is what I put on my muesli in the mornings for breakfast, so I had it on hand. You could use all juice, for a sweeter result, or all tea, for a less sweet result, if you wanted.
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Vanilla cookies

½ cup butter

½ cup sugar
¼ tsp vanilla
1 egg
2 cups plain flour
1 tsp baking powder
egg or milk for glazing
pinch salt

Preheat oven to 160ºC.

Cream butter sugar and vanilla. Beat egg and add. Add sifted flour and baking powder. knead lightly. Roll out part of the mixture at a time, keeping remainder cool. Cut shapes. Put onto greased pan Glaze with a little egg or milk, dust with cinnamon or Place a piece of cherry or almond on each. Bake 10 minutes to pale gold
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Peanut butter cookies

½ cup butter
½ cup peanut butter (natural style--chunky)
1¼ cups all purpose flour
1/2 cup sugar
¼ cup honey
1 egg
½ tsp baking soda
½ tsp baking powder
½ tsp vanilla

Mix butter and peanut butter well. Add sugar. Add ½ cup of flour, honey, egg,

baking soda, baking powder and vanilla. Beat till thoroughly combined.

Beat in remaining flour.

Shape dough into 1 inch balls. Place 2 inches apart on an ungreased cookie sheet. Flatten with a fork.

Bake in oven at 375 for 7 to 9 minutes or till bottoms are lightly brown.

Cool cookies on a wire rack.
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Wednesday, March 10, 2010

advice to my co-author

* Don’t submit the manuscript to a publisher before it has been edited for grammar, spelling, punctuation, and clarity of communication.

* Read the text you’ve written out loud in order to find places with awkward phrasing, unclear sentences, and bad grammar.

* If you do submit a manuscript full of errors and they send you back a review suggesting that there are major problems with the document don’t wait to tell your co-author, who speaks English as a native language, until six days before the revised manuscript is due to be turned in. Properly cleaning up that many problems with a document really takes more time than that.

* Don’t attempt to keep track of citations by hand, use a reliable program designed to keep track of citations for you.

* If you do attempt to do citations by hand, include the list of cited papers when you send the manuscript to your co-author so that she will have something to work with when converting the document to using her citation-tracking program of choice.

* If you attempt to do citations by hand, be consistent in the format you use—do not switch between ALL CAPS for some author names and normal capitalization for others. (Really, one should just use a program to take care of the citations—the time it takes to learn to use one is well rewarded with the consistent results.)

* Once you send the list of references to your co-author, it should actually contain all of the references you cite in the text. Seven references from the first three pages of the document which do not appear on the list is unacceptable. Learn to use a program to keep track of citations!

* It is better to spend the time to get the document into a form of which you can feel proud *before* submitting it to a journal in which you would like it to be published.

* Manuscripts are more concise if you don’t repeat the same thing in slightly different words in the very next paragraph.

* When you need to describe the many different occurrences of minerals within the sample it is helpful to first make a list and organize it, to prevent the paragraphs from wandering, full of needless repetition, and hard to follow.

* Avoid the use of negative phrasings such as “are not uncommon”.

* If the reviewer complains that the figures don’t match the in-text figure references send more than just the first two figures along with the manuscript if you wish your co-author’s help in resolving that issue.

Monday, March 8, 2010

Geospeedometry

Today whilst reading my 1000 words from the geologic literature (61 days in a row this time, and counting) I encountered a term that either I have never seen before, or I somehow managed to overlook it on other occasions. “Geospeedometry” was coined by Lasaga (1983), who related the cooling rate calculated for minerals based upon the diffusion of atoms within minerals with the time it takes for the “exhumation” of the rocks within which the minerals grew. What does this mean?

Metamorphic rocks form when any preexisting rock is subjected to increased temperatures and/or pressures for sufficient time to grow new minerals which are stable at the new conditions. One very common way for this to occur is for the rock to be taken sufficiently deep below the surface of the earth that both the temperature and pressure are elevated. If it were to happen that a package of rocks were to be taken to such pressures and temperatures and held there until all new minerals grew to replace the original minerals, and then those rocks were to be very slowly brought to the surface so that new minerals continued to grow to replace older minerals during the changing conditions the ultimate result would be a rock which contains only minerals which are stable at surface conditions. However, it happens often that the metamorphic rocks containing minerals which grew at elevated pressure and temperatures are brought back to the surface too quickly for those minerals to be replaced by their lower pressure/temperature counterparts. As a result we have a record of the conditions at which the metamorphism happened. The process of bringing the rocks back to the surface is called “exhumation”, and it refers to great quantities of over-lying rock going away (often due to a combination of faults bring up underlying rocks, and erosion carrying away broken bits of overlying rocks).

Ever since geologists realized that each mineral has a specific range of temperatures and pressures at which it will grow people have been attempting to figure out how to relate the list of minerals present in a given rock with the temperature and pressure at which it formed. The next logical question after the conditions of formation have been determined is one of “how long”. How long did the minerals take to grow? How long (or how quickly) did it take to get this rock from where it formed to the surface of the earth? Those people who study compositional zoning in minerals and calculate the rate of diffusion of atoms within the minerals and who then relate those numbers to the time it took for the diffusion to occur describe what they are doing as “geospeedometry”. Since the term was coined in 1983 there have been 52 papers which list that term in their title, abstract, or key words that have been entered into the Scopus database. One each published in 1983 and 1984, and then a six year break before the next was published. Since 1990 there have been one to five papers on geospeedometry published a year, save for 1993, which didn’t have any.

It is interesting to me that even after completing a PhD and making a point to try to read papers from the geologic literature on a daily basis, I am still encountering terms that are new to me, though they have been around for decades.

Lasaga AC. 1983. Geospeedometry: an extension of geothermometry. In Kinetics and Equilibrium in Mineral Reactions, ed. SK Saxena, Adv. Phys. Geochem., 2:81–114. Berlin: Springer-Verlag

Saturday, March 6, 2010

open access journal articles on the tectonics of Chile

I haven't posted about any of the major earthquakes which have happened recently, since my research focuses upon another direction entirely (and I've been very busy working, even if I had wanted to). However, I was very pleased to see an e-mail today from the Geological Society of London, who has made has made available a range of papers on the Lyell Collection covering the tectonics of the Chile region. Anyone wishing a greater understanding of that particular earthquake is encouraged to take advantage of this offer and enjoy the free access to these papers (good till the end of April, 2010).