The Importance of Openness

Open prairie.  Image credit: Laikolosse (CC-BY-NC).
Open prairie. Not the same kind of openness as discussed below, but it looks nicer. Image credit: Laikolosse (CC-BY-NC).

On March 18, the National Science Foundation took a small step toward advancing the state of science in the world by announcing a new public access plan (more details here). It is a good start, but leaves plenty of room for improvement.

Academic publishing is dominated by for-profit publishers (Elsevier, Wiley, Springer, and others), who rake in the big bucks.

Here’s how their racket works. Academic researchers need to be able to read about the findings in their field and related fields, so rather than paying $30-40 per article, the institutional library will negotiate a year-long contract.* Because the publisher has a monopoly on research in their journals, the libraries don’t have much leverage during negotiations. Publishers will sell “bundled” journal packages, which include the journals people actually read and use, as well as a whole bunch that are extremely infrequently read. This manipulates the cost-per-article and cost-per-journal statistics.

For the researchers, library costs are generally an externality. Combine that with the need to publish in established journals if you want to land a tenure-track job, get tenured, or get promoted, and the researchers have all kinds of motivation to publish in the for-profit journal.

The system perpetuates. Researchers only publish in for-profit journals to keep their jobs, and the for-profit journals keep milking the library for everything it’s worth, safe to point out that people should publish with them because that’s what everyone reads (because that’s where people publish). It’s a vicious cycle, just like in computer software, where people write software for Windows because that’s what people use, and people use Windows because that’s what people write software for. None of that is to say that Windows is a good operating system, just a fairly well entrenched monopoly.

In the past few years, there has been an increased awareness of the need to break this cycle. Particularly, the National Institues of Health has moved to requiring that papers be made available free-of-charge on PubMed immediately upon acceptance for publication in any peer-reviewed journal. The program has been well-received by the academic community, and means that more people have access to the results of federally-funded research.

However, the NSF has been lagging behind the NIH in this front. Their recent move is a good step in the right direction. However, it still gives a 1-year embargo to preserve the profits of publishers. The rule doesn’t go into effect for quite a while, either. Only grant applications which were due or submitted after January 1, 2016 will be subject to the rule.

A few issues remain. Access to articles published before 2017 (6 months to review grant applications, plus 6 months to paper, a very generous estimate) will still be paywalled. Some of the literature I’m highlighting here on the blog is from the mid-1980s, yet access still is $30-40/article.

The real solution is open-access journals, such as PLOS One, PeerJ, or the family of journals published by the European Geophysical Union. Because of the NIH requirement, the biological and medical sciences have seen a great deal of inroads for open-access journals. Sadly, the geological sciences have generally lagged behind.

* The terms of which, both financial and otherwise, are protected under non-disclosure agreements.

Geoscientist’s Toolkit: Trained Eyeballs

A squall line approaches.  Image credit: Laikolosse (CC-BY-NC).
A squall line approaches. Image credit: Laikolosse (CC-BY-NC).

Last weekend, I attended a (free) SKYWARN training class in my area, and have become a trained severe weather spotter [NOT a storm chaser!].* In the class, we covered topics such such as safety around storms, storm development, and identification of cloud formations indicative of severe or intensifying storms.

Despite the many advances in technology—from geosynchronous weather satellites to dual-polarization radar to networked automated weather stations across the country—there are times when there is little substitute for human eyes.

Humans are very good at pattern recognition, and with a little training can identify different types of clouds, rocks, or observe that a valley was carved by a glacier. You might want to go outside sometime and take a close look at something, be it a cloud, tree, rock, or animal. What do you notice about it?

I’ll describe a few of the things I notice in the photograph above. There’s a low, dark cloud base, and toward the center-left are some disorganized clouds beneath the base. Rain is visible along the left side beyond the hill. A stiff breeze is blowing directly toward the camera, as indicated by the wavelets on the water.

With those observations in mind, I would interpret the scene in this way: a cold front is passing through, and these clouds are part of a squall line. The front has nearly reached the photographer’s location. Warm, humid air toward the right is buoyantly rising over the colder air. As it cools upon rising, the water vapor condenses and precipitates as rain. While it’s not clear from this photograph, the low-level clouds may be part of a shelf cloud, or there may be a shelf cloud above the frame of the picture. The primary hazards here would be high winds, lightning, heavy rain, and possibly some hail.

Some people I’ve talked with have suggested that when taking notes and observations in the field, that the left-hand pages of the notebook should be used for observations, and the right-hand pages for interpretation. Keeping descriptions and interpretations distinct can help when an alternate interpretation is brought up, or when writing a paper with separate results and discussion sections. The results are strictly the measurements and observations, and the discussion then describes the interpretation off them.

Happy science-ing!

* If you live in the US and are interested in severe weather, you should check with your local weather office to see when and where they offer training.**

** Some places, such as the San Francisco Bay Area, don’t really have weather, so classes are few and far between. For more excitement in your meteorology, you should go to the Midwest. You could also take the online course (not necessarily accredited in your area).

A Window into the Mantle (Part 2)

Heard Island, February 23, 2015.  Scale: 250 m/pixel.  Image credit: excerpted from NASA GSFC (Aqua/MODIS).
Heard Island, February 23, 2015. Scale: 250 m/pixel. Image credit: excerpted from NASA GSFC (Aqua/MODIS) (warning: ~5 MB!).

Previously, I wrote about some of the challenges of studying the mantle. I also wrote about mass spectrometers—this was not accidental, as they were used heavily in the research discussed here. If you have not read those items already, you should do so before continuing. Also, if you are not familiar with isotopes, you may wish to get more familiar with those as well.

Although Big Ben is the dominant feature on Heard Island (seen above with a bow wave and some poorly-defined Von Karman vortices), there is a smaller volcanic edifice, Mt. Dixon, on the Laurens Peninsula (to the NW, right in the bow wave from Big Ben). Mt. Dixon is home to many lava flows, which can be seen on Google Earth, and are believed to be as young as 200 years or less.[1]

The major-element composition (Si, K, Na) of the lavas from Big Ben and Mt. Dixon can be quite different.[2] Big Ben generally has basalt and trachybasalt composition (low SiO2, moderate K2O + Na2O), while the Mt. Dixon and the other cones on the Laurens Peninsula show a much wider range, from basanite to trachyte (wide range of SiO2, generally higher K2O + Na2O).

Where things really get interesting is in looking at the isotopes. Specifically, Barling et al. looked at the isotopes of Sr, Nd, and Pb isotopes.[2,3] Some of those isotopes (86Sr, 144Nd, and 204Pb) are stable and non-radiogenic. That is, they do not decay away, nor are they formed from radioactive decay. The other isotopes studied (87Sr, 143Nd, 206Pb, and 207Pb) all are stable, but are the products of radioactive decay (87Rb, 147Sm, 238U, and 235U, respectively).

The ratio of radiogenic/non-radiogenic isotopes can be used to identify different sources, sort of like fingerprinting. To get high concentrations of radiogenic isotopes means that the rock’s history includes lots of the radioactive parent. Low concentrations of radiogenic isotopes means that the source rock has relatively little of the radioactive parent.

This is important, because although isotopes of an element are chemically similar, different elements behave differently from a chemical standpoint. Some are more often found in the crust than the mantle, while others are the opposite, depending on the compatibility of the element in mantle minerals.* Uranium is generally incompatible, and preferentially moves into the continental crust. Crustal rocks, would be likely to have a high ratio of radiogenic to non-radiogenic lead (product of uranium decay). Mantle rocks would have a lower ratio of 206Pb/204Pb, and similarly for 207Pb/204Pb.

Zindler and Hart (1986) proposed that oceanic basalts can be treated as mixtures of four components, each having a distinct chemical (and isotopic) composition.[4, via 2] Barling and Goldstein found that the Heard Island lavas exhibit a range of compositions consistent with mixing between two sources.[2] Neither of those sources matches the compositions suggested by Zindler and Hart. For the first Heard Island source, three explanations are given why that may be the case:

  1. The Heard Island source is a mixture of two Zindler and Hart sources
  2. That same Heard Island source is a fifth distinct mantle source
  3. It’s more complicated; the two Zindler and Hart sources in question define a spectrum, and the Heard Island source lies along that spectrum

Barling and Goldstein (1990) favored case 3, which they argue is reasonable given that recycling continental crust is likely to give a wide range of isotopic compositions.

Barling et al. (1994) built off of the results presented by Barling and Goldstein (1990), and focused on two main questions:

First, what is the origin of continental crustal signatures in oceanic basalts; are they inherited from the mantle source region, or are they caused by shallow contamination? If they originate in the mantle, how much continental material is present, how is it distributed and in what form, and how and when did it become incorporated into the mantle? Second, what are the origin and timing of enrichment of the sub-Indian Ocean mantle?

Perhaps some clarification is needed about what is at issue. Since it is clear there is some continental influence expressed by the Heard Island lavas, where in the history of that magma did mixing with continental crust occur? Was there a chunk of intact continental material relatively near the surface which partially melted as the basalt came upward through it? Or was there continental material which has been mixed in to the mantle beneath the Indian Ocean? If that occurred, when, and under what conditions?

Their data, and particularly the lead isotopic data (207Pb, 206Pb, and 204Pb), lead them (pardon the pun) to conclude that the component with a high-87Sr/86Sr is derived from marine (ocean) sediments subducted into the mantle at least 600 Ma before present, and probably 1–2 Ga. Modeling of the Sr isotope ratios and total concentrations, along with thermodynamic considerations, suggest that partial melting followed by partial crystallization from the magma is unlikely. That is, recycled crustal material is needed to make things work.

Barling et al. (1994) found that the overall isotopic compositions of the lavas suggest, if crustal material is indeed being recycled into the mantle, the subduction occurred around 1–2 Ga. That timing makes it far too early to be related to subduction beneath the paleo-supercontinent Gondwana.

Finally, the paper closes with the suggestion that, although Heard Island and Kerguelen Island are separated by 440 km, the two may be manifestations of the same plume head and hotspot. They note that the distance between the islands is quite small for separate hotspots, yet is obviously large for being just one hotspot. Perhaps the 2015 Heard Island expedition can collect samples which will give insight into resolving this question.


[1] Quilty, P. G.; Wheller, G. (2000) Heard Island and The McDonald Islands: a Window into the Kerguelen Plateau. Papers and Proceedings of the Royal Society of Tasmania. 133 (2), 1–12.

[2] Barling, J.; Goldstein, S. L. (1990) Extreme isotopic variations in Heard Island lavas and the nature of mantle reservoirs. Nature 348:59-62, doi 10.1038/348059a0.

[3] Barling, J.; Goldstein, S. L.; Nicholls, I. A. (1994) Geochemistry of Heard Island (Southern Indian Ocean): Characterization of an Enriched Mantle Component and Implications for Enrichment of the Sub-Indian Ocean Mantle. Journal of Petrology 35:1017-1053, doi 10.1093/petrology/35.4.1017.

[4] Zindler, A.; Hart, S. (1986) Chemical Geodynamics. Annual Review of Earth and Planetary Sciences 14:493-571, doi 10.1146/annurev.ea.14.050186.002425.

* This turns out to be crucial for things like uranium-lead dating, where the mineral zircon generally crystallizes with 10-1000 ppm U, but does not incorporate Pb. All the Pb found in a zircon can be assumed to come from uranium decay or laboratory contamination (which has a known isotopic composition).

Geoscientist’s Toolkit: Sample Bags

Sample bag and purple volcanic ash.  Yellow tag is 5 cm by 7 cm.  Image credit: Bill Mitchell
Sample bag and purple volcanic ash. Yellow tag is 5 cm by 7 cm. Image credit: Bill Mitchell

Often when in the field, it is useful to bring back samples of rock. To keep samples labeled and contained, each sample is put into its own sample bag, which is then labeled and securely tied shut.

I have used both cotton and synthetic sample bags (the one shown above is synthetic), and generally prefer the cotton. The bags are a bit sturdier, and with some of the rocks I sample being fairly pointed, they hold up more nicely in shipping. Sturdy cotton sample bags are also a bit heavier, so on expeditions where every ounce matters, the synthetic may be the bag of choice. My samples are also generally dry, but in wet environments the cotton sample bags may not be appropriate as they may degrade during shipping.

Geoscientist’s Toolkit: Mass Spectrometer

Mass spectrometer schematic. Image credit: Wikimedia Commons, based on an image by USGS.

Mass spectrometers are incredibly important pieces of analytical equipment. They have been used on Mars, around Saturn, around Mercury (the planet), and many places in between. They are even found at airport security checkpoints.

Every mass spectrometer has three primary components: an ion source, an analyzer, and a detector.

In the ion source, atoms or molecules are charged—usually by having an electron knocked off—and are focused into a beam within a vacuum chamber. Most ion sources ionize samples when they are already in high vacuum, but some ionize at ambient pressure and then pump the ions into the vacuum.

Next, the ions move into the analyzer. This region separates the different ions in time or space based on the ion’s mass/charge ratio (in many cases, especially in geochemistry, the charge is +1). Although there are several different analyzer designs, the one used in isotope geochemistry is generally the magnetic sector. Here, the ions are passed through a strong magnetic field. When a charged particle moves through a magnetic field, the field exerts a force on the ion, causing its path to be deflected. Less massive ions will be deflected more sharply than more massive ions (equal force gives greater acceleration to smaller masses). This is shown in the picture above.
By changing the strength of the magnetic field, the mass(es) that reach the detector can be selected.

Finally, the ions enter the detection region. Here the current from the ion beam is amplified, and that signal is then recorded. More abundant ions will lead to higher current. Some mass spectrometers, such as the one in the schematic above, are equipped with multiple detectors to measure relative isotopic abundances of several ion masses simultaneously.

For isotope geochemistry, there are two general classes of isotope measurement: stable isotopes, and radio-isotopes.

Stable isotopes are often 1H, 2H (D), 12,13C, 14,15N, and 16,17,18O, though of course many other systems are used. These measurements can provide isotopic “fingerprints”, which can track where things are moving around, and how much mass is flowing.

Radio-isotope systems include 238U/206Pb, 235U/207Pb, 14C, 40K/40Ar, 87Rb/87Sr, and 147Sm/143Nd. These systems are generally used for geochronology, or tracking mixing between distinct sources with different chemistries and histories.

Mass spectrometry as a field is diverse in aims and equipment, but the general principles are the same: an ion source, an analyzer, and a detector. These instruments are a versatile part of the geoscientist’s toolkit.

A Window into the Mantle (Part 1)

Image credit: Randall Munroe, XKCD, CC-BY-NC.

From far out in the Solar System, the Earth appears as a pale blue dot. Carl Sagan elaborates: “On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives.”

Not only has every human being lived out their lives here, they did so on the very surface of the Earth. Beneath our feet is something many people take for granite (at least judging by counter-tops given that name), as Randall Munroe pointed out above.

The conditions far beneath our feet are vastly different than they are here at the surface. In general, as you go deeper into the Earth, the temperature rises 20-30 °C/km. Not only that, but unlike air, rocks are quite dense, so the pressure rises rapidly. One atmosphere of pressure (or the roughly-equivalent metric unit, bar), from 100 km of air pushing down on us, is equivalent to the downward pressure exerted by 3.3 meters of rock.* Going down into the Earth, pressure increases about 300 bar/km. It’s not a particularly hospitable place for fragile creatures like humans.

In short, we can’t just go down there and get a sample. We have to wait for it to come here. The thing is, sometimes things which are stable at one temperature and pressure are not stable at another. This makes it very difficult to see things as they are, and scientists have to wait for rocks from the mantle to be transported upward to the surface. Consider the following:

You are confined, for whatever reason, to the interior of the United States Senate, where the climate is controlled to be about 21 °C and there is no precipitation. If you wish to study snow, you will have to wait until there is snow in the Senate. Fortunately sometimes the chair of the Committee on the Environment and Public Works will bring in a snowball [which proves the world is not warming up some Senators are unfit for the committee responsibilities given them].

In any event, we can’t study the mantle directly, except when bits of mantle-rock are ripped up and moved along by magma and transported to the surface. Such rocks are called xenoliths [etymology: xeno- foreign, and -lithos rock]. When mantle xenoliths are brought to the surface, the minerals within them don’t last very long [geologically] before changing phase or reacting to form new minerals, just like the snowball changes from solid to a liquid. This is what a mantle xenolith looks like on Earth’s surface.

Peridotite mantle xenolith in vesicular phonotephrite (5.3 cm across at its widest) from the Peridot Mesa Flow (Middle Pleistocene, ~580 ka) at Peridot Mesa, Arizona, USA. Photo and caption by jsj1711, CC-BY.

For reasons mentioned previously, I am unable to provide a picture of a mantle rock looks like in the mantle. However, here is an artist’s impression:

Artist's impression of the Earth's mantle, as seen from the mantle.  Image credit: Bill Mitchell.
Artist’s impression of a 6-cm wide portion of the Earth’s mantle, as seen from the mantle. Image credit: Bill Mitchell.

In defense of that perhaps-shocking picture, I will point out that the mantle gets pretty hot. By 800-900 °C, objects start to glow red-orange from blackbody radiation. Also, I quibble with the XKCD cartoon shown at top; the mantle should be red and the core light yellow, not the other way around.

Volcanoes are among the places where scientists can gain insight into the mantle. Here, melted rock makes its way to the surface, and by studying the chemistry of that rock, we can understand the chemistry of the mantle.

However, the rock at a volcano is not necessarily all from the mantle. Continental crust is less dense than mantle rocks, and tends to float. Continents and the mountains upon them can be weathered into sand and silt, transported down streams—or even by the wind—and settle into the ocean. In areas of subduction, such as around the Pacific rim and in Indonesia, those little bits of continent can get pushed down into the mantle, where they melt and rise back to the surface.

Volcanoes can also form on top of a mantle hotspot. Kilauea is an example of this, as are all the Hawaiian volcanoes.

What about Heard Island? Is it a hotspot volcano, or something else? And where does the magma come from? An excellent set of questions! Before we dive into the papers by Jane Barling and others on the subject [1, 2], we will need to cover a few more topics to understand the work being done!

[1] Barling, J.; Goldstein, S. L. (1990) Extreme isotopic variations in Heard Island lavas and the nature of mantle reservoirs. Nature 348:59-62, doi 10.1038/348059a0.

[2] Barling, J.; Goldstein, S. L.; Nicholls, I. A. (1994) Geochemistry of Heard Island (Southern Indian Ocean): Characterization of an Enriched Mantle Component and Implications for Enrichment of the Sub-Indian Ocean Mantle. Journal of Petrology 35:1017-1053, doi 10.1093/petrology/35.4.1017.

* The math:

The density of rock is ~3 g/cm3, or 3*103 kg/m3. One bar is 105 kg/s2/m in SI base units.

Pressure = density * height * g [ed: little-g, 9.8 m/s2], and we’ll round g up to 10.

Height = pressure / (density * g), which works out to about 3.3 m.

Part 2

Geoscientist’s Toolkit: LaTeX

A LaTeX file.  Image/text credit: Bill Mitchell.
A LaTeX file. Image/text credit: Bill Mitchell.

LaTeX is a typesetting program used for preparing documents—generally articles and books, but sometimes posters and presentation slides. It is available for Linux, Mac, and Windows, and is free, open-source software. The primary output file format these days is PDF, but other options are available.

When you are putting together a document with figures, citations, and sections which get moved around, it is tough to use a common word processing program and maintain sanity. However, because LaTeX is a markup language (like HTML, the HyperText Markup Language), it is explicit which text is grouped where. For instance, suppose you are trying to have both superscripts and subscripts following a letter, such as in CO32-. If you need to edit the superscripts or subscripts in Word, it can get confused easily. In LaTeX, it is explicit which parts are superscript and which are subscript. A little more work up front saves a lot of frustration later.

Above is a small excerpt from my dissertation, written in LaTeX. I am not sure I would have survived grad school had I attempted to write my dissertation in a word processor.

Yes, there is a learning curve to using LaTeX, and you don’t see changes in the finished document immediately when you make them in your text editor, but there are tons of advantages.

First, the format is all plain text, so it will be readable for a long time and across platforms (although the OpenDocument formats are attempting to make word processor documents future-compatible). Plain text is also very convenient when combined with things like version control software. Track changes isn’t just for word processors!

LaTeX separates the content from the formatting. Most of the formatting is done automatically. Yes, you manually specify that something is a emphasized, or is part of a quote, or a heading, but LaTeX will make sure that the formatting is consistent throughout (unless you intervene), and the defaults are generally good.

One place where LaTeX really shines is in mathematical equations. Greek letters and many mathematical symbols are input as commands such as \beta or \sqrt{n}, so your hands need never leave the keyboard. Once typeset, the equations are neat and properly sized.

Many journals accept submissions in LaTeX, if they do not outright encourage its use, because it is easy to keep the formatting consistent from article to article. The fonts will match, the font sizes will match, and in general things are awesome and look professional.

I have given several presentations made with LaTeX (pdf output). The outline slides are automatically maintained, and slide headers/footers can show where in the presentation you are. Those indicators link to the sections if you click on the section name, and it’s all done automatically. LaTeX is totally worth the effort of learning, and do it soon while you can take your time and experiment. Writing your dissertation while learning LaTeX is a recipe for unhappiness.

So, now that you’re ready to get started, here are some tutorials and reference materials:

It really bothers me when the justification for doing something slow, inefficient, and expensive is “that’s what most people use, and I can’t be bothered to learn something new.” There comes a time to do things differently, and a good ecosystem is one where there are several options based around open standards. Case in point: USB ports are great! The proprietary charger connection on my (old-school) phone? Awful. Lock-in is expensive. Choose open source.