Calcite filled karst

Calcite filled karst

While drilling through Mount Scopus Group limestones near Yokneam, we encountered some calcite veins and karsts. While most of them were only a few millimetres thick and completely filled, some were actually wide and quite nice.

Here is a picture of the best one. You can’t really see it in the picture, but you can see right through the karst to the other side.

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Perils of field work

Field work definitely has its advantages. You have the opportunity to see wonderful places, sometimes not accessible to the general public.




This time we were sampling clays for whole rock geochemical analyses. And these were wet clays: those small lakes you see in the photographs are not common in this area. One of the consequences of a very wet December.
Now, what happens if you mix clays and water? This:


Fortunately, a tractor from a nearby agricultural settlement assisted in rescuing us from the slippery mud and we got out just before sunset.


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Reading papers on the computer

Reading papers on the computer has always been troublesome. On the one hand, you have obvious advantages: No need to print anything, so no clutter. If you use some kind of manager (I use Mendeley), everything is synced across several devices.
One of the disadvantages is that it’s on a computer screen. It’s wide, unlike the usually long A4 papers science is printed and written on. So it’s just not that convenient to read it from a computer screen.
There is a solution though – you need to rotate your computer screen! How didn’t I think of it before:
vertical screen

And on 1920×1200 resolution, it’s all crystal clear and very easy to read.

Let’s see how long it takes before I rotate it back.

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Accretionary Wedge #58: Geo signs

July’s AW is about geological signs, which is funny because I just made a post about it not long ago.

However, I have many more pictures taken from our 2011 trip to Cyprus. Apparently they like to put signs on various geological objects around:


Ultramafic rock made mostly from magnesian olivine


Just like your usual plagioclase and clinopyroxene gabbro, but it has enormous crystals


This is what they were mining around here

Now the sign geologists can’t resist to ignore:


Chromite mine in the Troodos mountains

And of course, the mandatory ambiguous sign:




And last sign for this post, one that immortalizes my name:


Tourist attractions

This is one of the attractions in the village that we were staying in, Pedoulas.


No more signs for now, but if we’re already discussing Cyprus, so here are three excellent reasons to do field work in Troodos:







The end result is a huge spreadsheet with endless amounts of numbers that I need to turn into a petrological story, somehow.


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Accretionary Wedge 57: Seeing geology elsewhere

A bit late for the June AW#57, but here is my contribution.

Being the petrographer I am, I always see interference colours. Everywhere. I’m talking about those colours known for many students in optical mineralogy as the “Michel-Lévy” colours (find it here). This phenomenon is not limited to minerals in thin section and it’s quite common. I guess the most obvious example are oil slicks on the road in a cloudy day, you can clearly see the colour changes with thickness of the oil on top of the water.

Many people never notice this kind of optical sight, and even if they do, they attribute it to the colours of the rainbow, which is a totally different thing. The following pictures are not exactly the same thing as colours in thin section because they result of reflected, rather than transmitted, light—but the colours are the same.

So here’s one from my kitchen after cooking pasta. You can even see some second order yellows in the middle!

Interference colours in the kitchen


Next picture is from underneath the toilet in our department. I hope I wasn’t giving people the wrong impression by going in there with a camera.

Interference colours in the bathroom

Last, my favourite: iridescent clouds! This is actually related to transmitted light and you can clearly see the colours change as the cloud gets thicker. We took this photo during field work in Makhtesh Ramon, looking at contact metamorphism and skarns. Just make a web search for “iridescent clouds” and you can find some really amazing photographs.

Iridescent clouds

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Misplaced geological signs

Misplaced geological signs

So we were hiking through Makhtesh Ramon and found these signs on a hill off the marked path. Apparently it was part of an old geological trail created more than 20 years ago.
Essexite is a type of magmatic rock and “TRg3″ is the abbreviation for the Triassic Gevanim formation.

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April 16, 2013 · 11:17

Installing Generic Mapping Tools (GMT) 4.5.9 on Ubuntu

Generic Mapping Tools (GMT) is an excellent set of command line tools for dealing with spatial data and creating maps. If you’re using Fedora or openSUSE you can easily install the latest version using yum or zypper. However, the latest version on the Debian and Ubuntu repositories is 4.5.7 which is almost 2 years old. If you want the latest version, you need to compile it from source. Here is how.

First, open the console/terminal and type in:

sudo apt-get install libnetcdf-dev

Put in your user password (you have to have administrator’s rights for that) and proceed. This will install some libraries that GMT needs to run.
Next, get the install script and make it executable:

chmod +x ./

Now point your web browser to
Keep everything on default, except:
A.3. YES. Use file locking
C.1. My experience shows that the NOAA server is the fastest, and the European mirrors are dreadfully slow.
C.5. Shared (dynamic) Libraries
C.8. Place GMT in subdirectories of: /usr/local

If you know that you need something else, feel free to change it. Now click the GET PARAMETERS button and save the file to wherever your file is (use pwd if you’re not sure).

The final step is to run the installation. Type:

sudo ./ GMT4param.txt

This will take a while. The first step that it does is downloading the files so you probably won’t see any progress. When it’s done it will give a message about adding something to PATH. You can ignore it. However, you might want to take the advice on adding the GMT documentation to your browser bookmarks. It’s much easier to use that instead of the terminal based manpages. To verify that it’s working, type in:


If it gives you an error, then something probably went wrong somewhere. Otherwise, you’re good to go.

The most convenient way to view graphical output of GMT is to use ps2raster and convert it to your favourite format (pdf, png, jpg). However, if you want to view the ps/eps files directly, you need a document viewer. For Kubuntu (and other KDE based distributions) you can use Okular which is excellent. However, the default viewer on GNOME is Evince. Evince has a bug that it will not display patterns made using the -Gp option. You will need to install gv then:

sudo apt-get install gv gsfonts-x11

Enjoy GMT!


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