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Tuesday, January 28, 2014

Petrographic Thin Sections, Deadlines, and Nature's Stained Glass

     Deciding on this week's Partial Ellipsis of the Sun topic was harder than usual. The genetically modified organisms (GMOs) we saw on the western side of Kaua'i, guarded by several people, trucks and barbed wire, was an option. I decided that topic needed more research than driving past miles of corn (in various developmental stages) where sugar cane and pineapples used to grow ten years ago and reading a few articles. I will also read Frankenstein's Cat: Cuddling up to Biotech's Brave New Beasts by Emily Anthes before addressing this topic. (Great suggestion, Jan).

     So...deadlines to deadliness :-), on this Tuesday I decided to write about petrographic thin sections because they are something I know and they are amazing beautiful.

      Here's a piece of olivine, a magnesium iron silicate (called peridot when of gem quality):


     Amazingly beautiful, right? How about cutting a nice, clean, thin slice of this and attaching it to a glass slide. And then, how about looking at this thin slice of rock (or thin section) under a petrographic microscope? Still not impressed?

      Well, how about under crossed Nicols filters (see below) under a petrographic microscope, in thin section?

      The  two polarizing filters on a petrographic microscope work similarly to polarizing sunglasses. Each filter allows light vibrating at one particular orientation to pass through. One of the two filters is fixed. The other can be moved in and out of the light path. That filter's  polarizing direction is perpendicular to the fixed filter. 

      If you put a thin section of a rock in between the two polarizing filters (referred to as looking at the section under "crossed Nicols") it creates the stunningly beautiful portraits we see above of olivine and below of  zircon: 

     The uncrossed filter photograph of zircon, a nesosilicate, is below:

       Here's one more crossed Nicols thin section of basalt, a fast-cooling, fine-grained volcanic rock from Thailand with two large spectacular olivine crystals in the center.

       And, for completeness, a sample of basalt:

           I will end this week's illustration-rich blog with a photo of one of my favorite thin sections of gabbro, coarser-grained (i.e. slower cooling), intrusive igneous rock found near mid-oceanic rift zones (under crossed Nicols):

         The brightly colored orthopyroxene crystals are surrounded by striped plagioclase feldspar. Slower cooling produces some amazing crystals.

          Stained glass: made by nature.

          Enjoy! Next stop, a field trip to Iceland to see the mid-Atlantic ocean ridge on land to see that basalt and gabbro up close!

Petrographically yours,

Word Woman (Scientific Steph)



  1. SS,
    Thanks for the visual feast, like going to a museum of abstract art “lithographs.” The expression “Stained Glass: Made by Nature” captures it perfectly, especially the crystal-rich gabbro cross-section.

    The first olivine illustration reminded me of a detail of an ancient cave painting (showing the torso and forelegs of some critter). The “crossed nichols” (“colorized”) version looks like Ted Turner got his hands on it.

    Please briefly (if possible) define “nichols.” It’s not in my dictionary. How do they cut the thin slices, some type of diamond saw? How thin are the slices?

    The zircon slide was interesting: it looked like a gem you might see displayed on a jewelry store counter. The basalt with olivine reminds me of that kaleidoscopically psychedelic sequence in 2001: A Space Odyssey (which is an extremely oblique hint to this week’s NPR puzzle). Geology and gemstones tend to be geometric, it seems.

    Do the “slow coolers” used resemble crock pots ;-)?

    Speaking of allusions to comfort food, I will now curl up with a some buttered thin slices of olivine and a cup of hot Ovaltine.

    Welcome, Kyle!


    1. I'm familiar with polarized-light microscopy, but "nichols filter" was new to me, too, so I did some digging. The term is actually Nicol filter , named for William Nicol, who used prism of calcite to produce a polarized beam from unpolarized light. Apparently, other polarizers, like Polaroid sheets, are used today, though the term remains in use.

      Polarized-light microscopy is used in many other field, including medicine, e.g., to determine whether fluid from an arthritic joint contains crystals of uric acid (gout) or calcium pyrophosphate (pseudogout).

      The Wikipedia article on igneous rocks does a nice job explaining the difference between fast-cooling/extrusive/fine-grained rocks and slow-cooling/intrusive/coarse-grained ones.

    2. Insomnia and Wikipedia do go so well together, don't they? Anyway, I look forward to you continuing to bridge writing and science, or gaps in our education, or mid-ocean ridges, or whatever. Should Johnny Cash's Ring of Fire be playing in the background, or would Björk be more appropriate?

    3. Fascinating about using a similar technique to determine gout versus pseudo gout. And a lot less prep time!

  2. Let's see. Firstly, thanks for your thoughts and questions, Lego and Jan. The wave of insomnia is sweeping west!

    Thin sections are indeed cut with a diamond saw to a thickness of about 30 micrometers. Thanks for the wikipedia link to igneous rocks, Jan; it is a good introduction. In general, slower cooling intrusive rocks have the bigger crystals and faster cooling extrusive rocks have the smaller or no crystals. Interesting you mention crock pots, Lego, as one of the kindergarteners' favorite projects is "Igneous Fudge," where we taste the difference between slow-cooled (granite) and fast-cooled rocks (obsidian). Half of the mixture cools in the crock pot and half on a bed of ice.

    Ah, yes, it is indeed Nicol filter, Jan. We always called them "crossed nicols." I will have to work on getting the names right, especially if I go to meet with Dr. (Mary) Temple Grandin! My second job out of college involved description of core samples in thin section and by Scanning Electron Microscope (SEM). Those are some pretty wild images. . .

    Enjoyed the bridge photo but did not see any camel spiders lurking. "Ring of Fire" or Bjork (with umlaut): that sums it up perfectly! Except that now a weird mixture of the two has now become an early-morning ear worm. . .

    1. Here are some additional spectacular thin sections:

      Be sure to check out the diogenite, a plutonic rock from a stony meteorite.

    2. Hmmmm, try this link instead:

    3. SS,
      Thanks for the answers (and, jan, thanks too for your always helpful comments and links).

      Steph, I wish I were a kindergartner in your class. Sounds like every week might be better than a visit to Willie Wonka’s!

      I had to look up “micrometer.” (It’s both a unit of measurement and an instrument of measurement!). My “research” reveals that 30 micrometers (microns) is roughly half the thickness of a sheet of copying paper or newsprint. Wouldn’t the diamond-hewn rock-slice be very brittle and difficult to work with and study?

      I suspect slide rules are now considered antiques, but do scientists still use Vernier Calipers (that’s what we called micrometers in physics class)?

      jan’s mention of solo artists Bjork (add umlaut) and “the man in black,” Johnny (add umlaut) Cash got me to pondering band names. Bjork was in the Sugarcubes (Why do/did we call those “lumps” of sugar?) and Cash was backed by the Tennessee Three (almost acceptable in last week’s NPR puzzle!) and the Highwaymen.

      Like others I know who are far too easily amused, I am always on the lookout for good band group names, and two good ones appear in your and jan’s posts: “Here they are, live on stage, it’s Igneous Fudge!” (add umlaut) and “Let’s hear it for the latest new folk/punk sensation, Pseudogout!” (add two umlauts)

      The second link to Tom Phillips works. The images are reminiscent of Chartres Cathedral. Thanks.


    4. Ok, Lego, I skipped a lot of steps:

      The original chunk of rock is significantly thicker (Figure 37 in the link above). Then, through a series of different kinds of saws, grinders, and polishers the rock is cut, ground and polished to the 30 micrometers thickness.

      I posted the link so you can see what a process it is to get an evenly polished layer rock. And as the professor points out in the link, a lot of thin sections go wrong at the last few stages...It is definitely quite an art to make a good thin section.

      Glad you liked the new images!

      Umlauts for all,

  3. Hmm.... Just checked a handy ream (500 sheets) of copy paper. Came to 50 mm, or 50,000 micrometers, which makes each sheet 100 micrometers thick.

    I remember, in grad school, sticking micropipette electrodes into leech neurons that were about half that in diameter, just about at the limit of visibility without a microscope, which we used, of course, during the experiments. Doing the dissections, using hand-held tools, removing bits of connective tissue much smaller than that, I wondered what the selective pressure had been to evolve the ability to control movements smaller than the eye could see?

    1. Hmmmm, hoping your question is rhetorical, Jan. No answers here.

      Oh, Lego, they have digital Vernier calipers now (of course). Have you used one, Jan?

    2. The only digital calipers I've used is when I spread my thumb and forefinger apart that much when eyeballing a lesion....

    3. Not to be a nit-picker (which is what I've always imagined Pierre Vernier to have been), but I'm not sure it's correct to refer to digital calipers as digital Vernier calipers (unless, of course, they've got an analog Vernier scale as well).

    4. Jan, I was hoping you'd say that about digital calipers.

      As to digital Vernier calipers, of course you are correct...though that is how Amazon and others market them ($10 and change):

      It's quite similar to how geologists still use "crossed Nicols" even though they are not true Nicol filters now.

      Do other examples leap to mind?

  4. Your announcement of the field trip to Iceland, and legolambda's comments, put me in mind of the Magic Schoolbus series. But Ms. Frizzle would probably have taken the kids to the mid-Atlantic ridge on the seabed.

    1. Ms. Frizzle surely would!

      I picked up Godel, Escher, Bach: an Eternal Golden Braid yesterday. I am always meeting great kids at the library.

      When I asked the ~ 8-year-old boy what his name was he said "Guess." When I started to guess, his mom piped in and said "Yes, we named him Guess, thinking it would be fun." Guess has been down this road a time or two. I'm not sure but he might go along with a Will Shortz puzzle where you remove an "ES" from a word to get a name you don't have to explain every time...

      But, that might just be a Guess.

  5. So, I was intrigued by that Bridge Across Continents (also called the Leif the Lucky bridge, apparently, in honor of Leif Ericson) I linked to above, so a used a few spare minutes to find it on Google Maps. Big disappointment. It's a dinky little footbridge to nowhere, accessible by footpath from a small parking lot off the road that follows the perimeter of the island in that area, just south of Keflavik. Worse, the road itself crosses the mid-Atlantic ridge nearby, without any marking or fanfare. Looks totally missable. So, let's skip it on our field trip.

    On the other hand, it's not nearly as creepy as the Icelandic Phallological Museum, in Reykjavik....

  6. Hard to comment on that one. The legal length discussion was interesting.

    The Leif the Lucky Bridge looked intriguing. Kind of like putting your arms and legs in four states at Four Corners, U.S., you could stand there straddling two continents and ponder gabbros, plate tectonics, the mid-Atlantic rift...I wouldn't want to do that on Icelandic Highway 425.

    We may need sub field trips ;-).

  7. In an above post I wrote, “The basalt with olivine reminds me of that kaleidoscopically psychedelic sequence in 2001: A Space Odyssey (which is an extremely oblique hint to this week’s NPR puzzle).”

    The oblique hint was the word “Odyssey.” The NPR puzzle answer this week is BLOSSOM/BLOOM (Remove consecutive S’s from a word to form its synonym.) Leopold Bloom was the protagonist in Joyce’s Ulysses, which was based on the Odyssey by Homer.

    Now that’s oblique! If any reader of this blog solved the NPR puzzle on the strength (or, rather, weakness) of that hint, please let us know. You are in store for some major congratulations.


    1. How was the olivine/Ovaltine combo, lego? It is a pairing that hadn't occurred to me. One of our geologic mantras was "All that's green is olivine...unless it's epidote or..." Actually, color is generally a poor mineral indicator quality.

    2. SS,
      I also often meet interesting kids at my local library. Last week, as I sat at a library computer enjoying PEOTS, an eightish-year-old little girl and her mother descended upon a corner table nearby and began perusing stack of cookbooks. They appeared to be Indian (racial profiling). I later discovered their family had indeed moved here from New Delhi a decade ago, and that the precocious little girl had amassed a formidable English vocabulary. I peripherally noticed the girl’s attention periodically being drawn to the colorful PEOTS images on my computer screen.

      “What’s your name?” I asked her.
      “Surmise,” she responded.
      I knew only a smattering of Indian girls’ names (Indira, of course, Toru, Amrita, Sarojini, Sudha and Kamala). So I began with the most likely.
      “Indira?” I surmised. She seemed bemused by this.
      Her mother piped in, saying, “Yes, we named her Surmise, thinking it would be fun.”
      Site that proves I am not lying:

      But sometimes, I confess, I do make it up as I go merrily along. For example, when I wrote “I will now curl up with a some buttered thin slices of olivine and a cup of hot Ovaltine,” that was not completely truthy. Regrettably I inadvertently misspoke, and I am sorry to any of you who may be offended by that.

      Here is the bottom line, “what you must take away” from that stretched-taut truth: From the “slices of OLIVINE,” the takeaway is that “It was a LIE.” From the “cup of hot OVALTINE,” the takeaway is that “It was a TALE.” Truth be told, after some rearrangement of pillows, I curled up with a glass of VINO, then a second glass of VINO.

      Speaking of ingestion: Actually, the color green is generally a good indicator of food quality, at least according to the moldy samples in my refrigerator research. (I get a lot of false positives with my jars of olives, however.)

      In Vino Veritas

    3. Lego,
      Slightly confused here...Your link shows Surmi as a name but not Surmise. My writing about "Guess" as a boy's name was absolutely true. Hmmmm, not sure about your "Surmise" name, especially given the lie-tale-vino issue. Kindly illuminate further unless you are busy with green things ;-).

    4. SS,
      Yeah but, yeah but… I have scoured baby-name sites and “Guess” is nowhere to be found either! (The closest I could find was “?” of “? and the Mysterions” fame.) If Denver-area parents are nutty enough to name their kid “Guess,” does it not stand to reason that New Delhi-rooted parents might be nu…

      Wait, wait, wait! This charade must end! Olivine, Ovaltine, and now, Surmise. It’s a tangled trinity of tales, a three-pack of lies! Conversely, your contention about meeting a boy named Guess (full name: Guess Gene Denim?) is plausible, believable and, as you swear upon a stack of books that need to be reshelved, “absolutely true.” I take you at your word, woman.

      Am I busy with green things? Oh yes I am. Busy grappling with my envy -- envy for the likes of people who actually encounter and engage Guesses, launch blogs, concoct igneous fudge, and fudge neither scientific data nor either mundane or eternal truths…

      …as opposed to minting counterfeits, casting shadows and blowing smoke.

      Hey, this opening a vein is even better than opening a vino… or two.

    5. As long as you don't take those names in "vein." ;-) Thanks for the scoop, lego.

      I did wish Guess could have let the "Who's on first?" scenario play out. That would have been fun!

  8. Eight-Year-Old What’s-His-Name
    (Cast: SS = Scientific Steph, G = Guess, GM = Guess’s Mother)

    SS: So, little boy, what’s your name?
    G: Guess.
    SS: Gus?
    G: No, Guess.
    SS: Yes, guess your name, right?
    G: Yes, Guess, my name.
    SS: Okay. Are you Ernest?
    G: Yes, I am earnest.
    GM (overhearing): You are not Ernest. That is a bad Guess! (to SS) Guess, his name.
    SS: (to GM) He lie?
    GM: Eli? No!
    SS: But you said he was not earnest.
    GM; Yes, he is not Ernest. Guess!
    SS: Eli?
    GM: No, did you not hear what I said before? Guess!
    SS: Willie?
    G (interjecting): I did not lie. I will never lie. I am earnest.
    GM: He is not Ernest.
    SS: Please! No more guessing games. Will one of you just tell me the name?
    G and GM (simultaneously): Yes. Guess!
    SS (losing patience): Surmi?
    G and GM (simultaneously): Huh?


    1. Oh, it's way more fun over here today. I laughed out loud. Thanks, Lego!