Blog Orientation

Checking Out Books from the Lab

In my drive to get everything in the lab automated, I’ve set up a checkout system for the lab books. To check books in or out, use this form, or scan QR Code for Mobile Checkout App with your phone. Note that on the mobile app, you will have to type in your UW NETID, whereas on the browser form you will need to log in.


Modified CSE Format for Zotero

If you are a UW Tacoma student who uses Zotero as a reference manager (as I suggest my students do), you can now output a bibliography in the modified CSE format that we use in our science courses at UW Tacoma. The hallmarks of the modified CSE format are:

  • It’s based on the standard Council of Science Editors Author-Year format, available for Zotero here.
  • Electronic articles and e-books are cited as if they are in print, avoiding the clumsy URL and access information that is useless outside the UW campus.

So, for example, here is a bibliographic entry in the standard CSE format:

Hodges KV. 2000. Tectonics of the Himalaya and southern Tibet from two perspectives. Geological Society of America Bulletin 112:324–350. [accessed 2015 Apr 14]

Note that the link won’t work unless you have access to Geological Socienty of America publications, which most students don’t at home. The link gets even more convoluted when you are trying to find an article through EBSCOHost or another repository that stores the articles behind a paywall. I see this all the time in student papers. So instead, using this format, you can reference the article as if you had it in print:

Hodges KV. 2000. Tectonics of the Himalaya and southern Tibet from two perspectives. Geological Society of America Bulletin 112:324–350.

Easier, huh?

Here is how to download the file to the Zotero Standalone application:

  1. Download the format file here.
  2. Open Zotero
  3. Click on the Tools menu -> Preferences
  4. Click the Styles tab.
  5. Click the + button.
  6. Navigate to the file you downloaded (modified-council-of-science-editors-name-year-author-date.csl) and select it.
  7. Click OK. Now use it in good health!
Blog Uncategorized

“I am not a Computer Science Major”

Last quarter, I introduced some programming (in Glowscript) into my intro physics course. At the end of the quarter, I got evaluations from a number of students who said something like, “I’m not a computer science major. Why do I need to learn to program?” Besides being a marketable job skill, learning to program gives you a completely new way to solve problems in the physical sciences. Computer models are also a standard tool in every scientific discipline I’ve encountered, so if you are going to major in the sciences, you need to learn how they work.

Getting started in programming is easier now than it ever has been in my memory. There are a ton of resources online. You don’t even need to install software on your computer to get started (though I’d recommend you do). What follows are some recommendations for students in my lab, but they go from general to specific, so if you are not a paleomagnetist/geophysicist, you can read until you feel like stopping.

Before you start, consider what programming language to learn. I recommend that my research students learn Python for the following reasons:

  • It’s available for free.
  • Even if you want nice add-ins and an easy-to-use editor, it’s still free for academic users.
  • It’s what ESRI uses for a scripting language in ArcGIS, so if you do our GIS certificate program, you’ll use it.
  • Programming in Python is relatively straightforward and forgiving.
  • There are tons of add-in packages for all sorts of scientific purposes: if you don’t know how to write a complex piece of code, chances are someone has already done it for you.
  • There are ways to interface with all sorts of nice graphics packages like plotly and other software packages like R.
  • You can document what you do in notebooks, which you can share with the lab.
  • For paleomagnetists: Lisa Tauxe’s PMAGPY software is written in Python.

There are a few other languages you’ll want to learn for specialized purposes:

  • R, for statistics. We use it in our environmental stats course. It’s also free, has lots of add-ins, and is in wide use in academia and industry.
  • Mathematica, for specialized tasks (mainly IRM acquisition modeling). I don’t know this one all that well!
  • Matlab, for linear algebra. I don’t use Matlab so much anymore, since I can do most of the same things with Python or R… which are free. However, Matlab is widely used in geophysics.

What do you need to get started in Python? Although Mac computers come with Python installed already, I’d recommend installing Enthought’s Canopy software under an academic license. That gives you not only Python and the Matplotlib graphics add-on, but a nice way to keep track of and edit your programs or notebooks. It’s free for students and faculty, though you do need to register with Enthought. Otherwise, it’s a bit of a headache to try to install (if you are using a PC) and/or update Python, Matplotlib, and all of the other required stuff individually.

There are lots of resources available to help you learn Python. A list of the major ones is here. For the basics – if you are still just testing it out and haven’t installed anything yet – I like because it allows you to try things out in your browser window. However, does not teach you to use the Canopy software. A Canopy academic license allows you to use the Enthought Training on Demand tutorials. The Intro to Python tutorial looks really good. Has anyone tried it? Let me know how it is! Also, Lisa Tauxe’s PMAGPY Cookbook has some notes on using Python.

As a scientist, you will also want to get familiar with the NumPy, SciPy, and Matplotlib/Pylab packages (a package is the Python term for an add-in). Tutorials for these are available at python-guide, through Enthought, and in the PMAGPY Cookbook. There’s also a cool gallery of examples for Matplotlib.

The classic Numerical Recipes by Press et al. has lots of explanations of how to do common statistical and mathematical tasks in computer code. I don’t know if there’s a Python version out now (I have an old edition for the C language), but it’s a useful place to start for scientific programming. I’ve also found the book Programming Pearls by Jon Bentley useful for some things.

Now, for the specialized paleomagnetics stuff: download and install Lisa Tauxe’s PMAGPY package. This provides you with a set of programs that you can use to plot, manipulate, analyze, and model paleomagnetic data. Most have graphical user interfaces, and Tauxe has a good set of tutorials in the PMAGPY Cookbook. But it also provides a set of functions (pieces of code for performing specific tasks) that you can use in your own programs for common plotting and data analysis tasks.

Blog Courses

TESC 419: Environmental Geophysics

Have you ever been curious how geoscientists know what’s under their feet? In Environmental Field Geophysics (TESC 419), you will learn to use seismic, magnetic, and gravity surveys to investigate the shallow subsurface environment. The course is a project-based introduction to practical geophysical tools and data analysis, along with some of the physics that makes those tools work. The 7-credit field course, scheduled for this coming Autumn quarter (2015), meets Fridays and has local field trips. It counts as a field course for the geoscience degree option. Physical geology with lab and one quarter of introductory physics are prerequisites. Please contact Peter Selkin ( soon for an add code.

Blog Research

Soil and Loess Magnetism

Magnetic minerals, because of their iron content, are sensitive indicators of chemical weathering. The magnetic properties of soils and loess (windblown silt deposits, somewhat modified by soil formation) can therefore help us understand the moisture and temperature conditions in which soil and loess landscapes formed. Other processes besides climate affect soil magnetism, however: human-made dusts, incorporated into soils, can be highly magnetic, as can the original “parent material” on which a soil formed. Fire can drastically affect magnetic properties as well. In short, the magnetic properties of soil and loess can give a tremendous amount of environmental information about a landscape, but can be challenging to tease apart.

I have several projects going that focus on analyzing magnetic properties of soil and loess, mainly in the Tacoma, Washington area and in the Patagonia region of Argentina.
My work in Tacoma will continue for the foreseeable future. One component of the work is being done in conjunction with an EPA-led soil hydrology mapping project. Another component investigates the magnetic properties of pollution from the ASARCO smelter that operated in Ruston until 1985. Because of their local nature, these studies lend themselves to student-directed projects, and may be combined with class projects in Earth materials (TESC 347) or environmental field geophysics (TESC 419). Students working on these projects have presented at regional undergraduate research conferences. Some high-quality student work has led to undergraduate co-authors on posters presented at the Geological Society of America conference. There is also work to be done on the Argentine loess deposits, and on other loess deposits in the Pacific Northwest.

For Students
Timeline: Ongoing for the foreseeable future
Courses Required: Physical Geology w/Lab (TESC 117); Intro Stats (TMATH 110); Earth Materials, Sedimentology, and/or Physics 2 (Electricity and Magnetism) are helpful
Fieldwork: Yes
Laboratory Analyses: Bulk magnetic properties, size-fraction magnetic properties, magnetic hysteresis and components, magnetic anisotropy, reflected light microscopy, electron microscopy, UV-vis spectroscopy, particle size analysis
Data Analysis: Factor analysis and related techniques, least squares fitting
Software: Excel, Mathematica, R, Python
Conference Opportunity: Local undergraduate conferences, will need to seek additional funding for other presentations
Required Reading
Egli R. 2004. Characterization of Individual Rock Magnetic Components by Analysis of Remanence Curves, 1. Unmixing Natural Sediments. Studia Geophysica et Geodaetica 48:391–446.

Geiss CE, Egli R, Zanner CW. 2008. Direct estimates of pedogenic magnetite as a tool to reconstruct past climates from buried soils. Journal of Geophysical Research 113. doi:10.1029/2008JB005669

Glass GL. 2003. Credible Evidence Report, the ASARCO Tacoma Smelter and Regional Soil Contamination in Puget Sound. Seattle, WA: Tacoma Pierce County Health Department and Washington Department of Ecology.

Roman SA, Johnson WC, Geiss CE. 2013. Grass fires–an unlikely process to explain the magnetic properties of prairie soils. Geophysical Journal International 195:1566–1575.

Selkin PA, Strömberg CAE, Dunn RE, Kohn MJ, Carlini AA, Davies-Vollum KS, Madden RH. 2015. Climate, Dust, and Fire Across the Eocene-Oligocene Transition, Patagonia. Geology In Press.

Blog Research

Bengal Fan Rock Magnetism

Sediments eroded from the Himalayas during their 50 million years of uplift have largely been carried out to sea and deposited in great cone-shaped piles to the east and west of the Indian subcontinent. The Bengal Fan, the deposit fed by the modern Ganges and Brahmaputra rivers, is by far the larger of these sediment accumulations. In the winter of 2015, I sailed on International Ocean Drilling Program Expedition 354 to sample these sediments. We collected cores from a transect across the middle of the Bengal Fan to track the flow of detritus from the rising Himalayas to its ultimate resting place in the Bay of Bengal. Questions that the scientists on Expedition 354 are interested in answering include:

  • How has the rate of sediment flow changed through geologic time?
  • Has the source of the sediment changed as the mountains rose?
  • How has the sedimentation changed in response to changes in climate? And how has the region’s climate changed in response to the uplift of the mountains? (And: how have changes in climate affected the uplift of the mountains themselves?)
  • How do sediments spread themselves out over the massive fan deposit? 
  • Do rapid sedimentation events (turbidites) indicate storms? Earthquakes?

Over the next two to three years, I will be looking for student partners to help me address some of the questions above using the magnetic mineralogy and magnetic properties of Expedition 354 sediment samples. Magnetic minerals, for example, can help distinguish between sources of sediments. Because they are sensitive to chemical weathering, magnetic minerals may allow us to examine changes in climate over geological time. Magnetic properties of sediments can even allow us to study the physics of turbidity currents that carry sediment down the fan. As a student involved in this project, I expect you to become familiar enough with marine geology and rock magnetism to carve out part of this project that you can do yourself. Ultimately, you will gain a deep enough understanding of rock magnetic techniques to be able to collect, analyze, and interpret your own data, and to present your own findings on part of this project. High-quality research will contribute to a peer-reviewed publication and presentations at national conferences (meaning that you may have a chance to participate in a conference, and you will be a co-author on the presentation).

For Students
Timeline: Summer 2015 to 2018(?)
Courses Required: Physical Geology w/Lab (TESC 117); Sedimentology and/or Physics 2 (Electricity and Magnetism) are helpful
Fieldwork: No
Laboratory Analyses: Bulk magnetic properties, size-fraction magnetic properties, magnetic hysteresis and components, magnetic anisotropy, reflected light microscopy, UV-vis spectroscopy
Data Analysis: Factor analysis and related techniques, least squares fitting
Software: Excel, Mathematica, R, Python
Conference Opportunity: Yes, in 2016/17
Required Reading
Burbank DW. 2005. Earth science: Cracking the Himalaya. Nature 434:963–964.

France-Lanord C, Schwenk T, Klaus A. 2014. Bengal Fan: Neogene and late Paleogene record of Himalayan orogeny and climate: a transect across the Middle Bengal Fan. College Station, TX: International Ocean Discovery Program IODP Sci. Prosp. 354.

Molnar P. 1997. The rise of the Tibetan plateau: From mantle dynamics to the Indian monsoon. Astron. Geophys. 38:10–15.

Schwenk T, Spiess V. 2009. Architecture and stratigraphy of the Bengal Fan as response to tectonic and climate revealed from high-resolution seismic data. In: Kneller BC, Martinsen OJ, McCaffrey B, SEPM (Society for Sedimentary Geology), Geological Society of London, editors. External controls on deep-water depositional systems (SEPM special publication). Tulsa, Okla: SEPM (Society for Sedimentary Geology). p. 107–131.

Blog Orientation

Reversals, Part 3

Two lava flows and their magnetic directions

Blog Orientation

Reversals, Part 2

I’m finally getting back to the blog after about a week of frantic magnetometry (we discovered a bug in our magnetometer software, because of which we had to measure lots of stuff all over again!) and report-writing. Here is another in my reverse-color series on magnetic reversals.

Why do we call them magnetic reversals? Because the way some lavas are magnetized, Earth's magnetic NORTH pole would have had to be where the SOUTH pole currently is.

Blog Orientation

Basics of Magnetism 4: Reversals Part 1

Earth has a magnetic field, which is what keeps your compass lined up with the North Pole [1]. The Earth’s outer core generates that magnetic field. You may have heard before that Earth’s magnetic field has, in the past, switched its North and South Poles. This is true, and kind of amazing and mysterious, but useful at the same time. This is the first in a series of picture-posts – not quite comics – that discusses magnetic reversals, and why and how we use them. I owe Maxwell Brown for this one.

A picture of a volcano with a Roman temple on top, and a story about building stones and magnetism


[1] Previous relevant posts are under the paleomagnetism tag.


Blog Orientation Projects

A Bengal Fan Backgrounder

As I’ve been writing these blog posts, I’ve been trying to include footnotes that point you deeper into the scientific literature about paleomagnetism, rock magnetism, and the geology of the Bengal Fan. But if you’re a student planning on working with me this coming quarter, you might want a little more background than what I’ve been putting in the blog footnotes. Here are some places to start.

Note: this is not at all exhaustive or up to date. I’m trying to choose articles that I’d give to students who are taking or about to take a middle-division course in geology (e.g. sedimentology). These are not necessarily the earliest or latest, or the most relevant to the specific things we’re doing out here, but these will get you started. I may introduce a couple of more specific key ideas in future blog posts. Watch this space for more. Email me or comment if you have any suggestions!

First, if you’re just a casual reader who may be interested in working with me on a project when I get back, you might start with Diane Hanano’s blog post on deep drilling.

For a big-picture view of the growth of the Himalaya and some of the questions geologists have about it: Molnar, P. (1997) The rise of the Tibetan Plateau: From Mantle Dynamics to the Indian Monsoon. Astronomy and Geophysics 38:10-15. (Link)

Why we care about the erosion of the Himalaya: Raymo, M.E., and W.F. Ruddiman (1992) Tectonic forcing of late Cenozoic climate. Nature 359: 117-122.

For a summary of the sedimentary processes occurring on the Bengal Fan itself, with lots of maps: Curray, J.R., F.J. Emmel, and D.G. Moore. (2003) The Bengal Fan: morphology, geometry, stratigraphy, history and processes. Marine and Petroleum Geology 19: 1191-1223.