Preferential Preservation of Phytoliths

Scanning electron microscope image of an elephant grass phytolith after dry-ashing.[1] Image credit: Benjamin Gadet (CC-BY-SA).

As I was looking through the recently published papers in PLoS ONE (all open-access!), I came across an interesting article on the preservation of phytoliths.[2] It is an interesting and well-written paper, and is quite accessible—both in terms of copyright and of science content.

Plants often have little bits of rock in them, called phytoliths (phyto- plant, -lith rock). Phytoliths are formed within the plant by precipitating SiO₂ in a non-crystalline form (opal). These microscopic stones can help maintain the structure of the plant, perhaps among other functions. They also preserve well, because SiO₂ (glass, essentially) generally doesn’t react chemically with much in the environment.

Just like with fossilized bones or impressions of leaves, the size and shape of phytoliths can be used to identify the plant (or family of plants) which is producing them. If phytoliths are found in the geologic or archaeologic record, they can be used to determine what kinds of plants were in the area, or were being eaten. They also contain small traces of carbon, which can be used for radiocarbon dating (back to ~40 ka) or ¹³C isotope analysis.[3]

This paper is looking at what happens to various phytoliths in the archaeologic or geologic record, and whether there are preservation biases (some phytoliths being destroyed more easily than others).

The authors took samples of four different types of modern, living plants. These samples were then burned away in a 500°C furnace, leaving just ash and the microscopic rocky bits. With some further, relatively gentle treatment, they were able to isolate the phytoliths. Some of these phytoliths were mounted on microscope slides and counted to determine the relative abundance of different sizes and shapes.

Isolated phytoliths were partially dissolved for six weeks, and the Si content of the liquid was measured. The partially dissolved phytoliths were dried, mounted on microscope slides, and they too were counted to determine relative abundance of the different sizes and shapes after treatment.

Phytoliths which were small, and had a large surface-area-to-volume ratio, tended to be preferentially dissolved—this is not an unexpected result, but is important. The authors argue that based on the Si solubility, the degree of preservation can be assessed (high Si solubility means better preservation); in situations where the Si solubility is low, some of the more delicate phytoliths are likely to be missing, and a count of phytoliths under those circumstances would yield biased results.

But don’t take my word for it! Read the paper. It’s better written than my short explanation, and a fine example of scientific scholarship.

[1] Parr, J.F.; Lentfer, C.J. & Boyd, W.E. 2001, ‘A comparative analysis of wet and dry ashing techniques for the extraction of phytoliths from plant material’, Journal of Archaeological Science, vol. 28, no. 8, pp. 875-886. DOI: 10.1006/jasc.2000.0623

[2] Cabanes D. & Shahack-Gross R. (2015) Understanding Fossil Phytolith Preservation: The Role of Partial Dissolution in Paleoecology and Archaeology. PLoS ONE 10(5): e0125532. DOI:10.1371/journal.pone.0125532

[3] Looy, C.V.; Kirchholtes, R.P.J.; Mack, G.H.; Van Hoof, T.B. & Tabor, N.J. 2011, ‘“Ochoan” Quartermaster Formation of North Texas, U.S.A., Part III: First Sign of Plant Life‘ Geological Society of America Abstracts with Programs, Vol. 43, No. 5, p. 383.

Paying the Bills with Open Access

Mean and median NSF grant sizes, adjusted for inflation. Image credit: NSF.

Last week, I shared some of my opinions on open access academic journals (or journal articles). I received the following response on Twitter:

.@i_rockhopper Good points here! OA is great, but who pays for publication in these journals? Publication costs are not favored in budgets.
—Elizabeth Herndon @emh824

It is a very important part of the picture, and I have a few ideas which might be considered. Before discussion gets any further, though, I will say that there is no single magical way to make it work. Like with addressing climate change, there will need to be many small actions which collectively bring about some needed reforms—and maybe some bigger actions along the way.*[1]

My response here is based on my experience in the volcanology, geochemistry, and petrology areas of geoscience/geophysics. I know that open access varies greatly between disciplines. Some disciplines, like the NIH-funded biomedical research, have mandatory public access regulations, while others such as physics seem to have a culture of open access (arXiv.org).[3,4] Other disciplines, such as atmospheric chemistry & physics, are generally published in newer, fully open-access journals.

Open access publishers need to recoup their expenses, which are not trivial (significant IT costs, editorial staff, administrative staff). PLOS One and the EGU journals, among others, do this by charging article processing charges (APCs). These can be very significant: a 10-15 page paper with a couple figures and a table or two may cost $1-2k.

To put this number in context, let’s consider the typical (median) NSF award. The 2013 awards are summarized in this report (1.6 MB pdf) from the NSF, which is an interesting read.[5] For 2013, the median annualized award amount was $130k [see report, page 19]. If you have a 3-year grant which you use to publish two papers at $1300 each[6], that will use 1% of your budget.

As was pointed out earlier, funding agencies don’t like pay for publication, because it’s money you’re not spending on doing science. On the other hand, they should insist on open access because they want to maximize the number of people benefiting from the research (“broader impacts”). It is likely government funds are used to buy access to commercial journals (many times over, once for each public university and national lab), so why not reduce those costs and pay to publish things freely in the first place? Compared to the cost of bombing various countries with the latest drones, it wouldn’t take much to open up academic publishing.

There are a couple other options I can think of which may or may not work:

• Department-level funding. This would be great, but I wouldn’t hold my breath waiting for it to happen.
• University-level funding, such as from the library. Change could happen here, because a move to widespread open access would greatly reduce subscription costs. The transition is difficult, which commercial publishers will take advantage of.
• Professional societies funding their own journals. The Geological Society of America and the American Geophysical Union each have their own journals. Using a portion of memberships and other society income to support open access journals could bring about the open access change that is needed. I applaud the work the European Geophysical Union is doing with their journals (expensive though they are).[7]
• The PeerJ model. While it hasn’t been thoroughly tested yet, a flat rate of $99 for a lifetime membership and 1 paper/year seems like a good deal. It’s too bad they don’t publish geoscience.

It all seems to boil down to a problem of externalities. To the funding agency, publication costs are an externality. For libraries, open access isn’t cost-effective until they can ditch the expensive subscriptions. For established researchers, the costs of for-profit journal subscriptions are an externality. Early-career researchers are pressured by the hiring/tenure system to publish in the established, for-profit journals. And finally, the commercial publishers have a huge interest in making sure their lucrative business remains intact, and will act to make the barrier to open access [seem] as high and painful as possible.

Without some form of external impetus, widespread adoption of open access will probably remain elusive.

Those are my thoughts on funding open-access publication as of today. With further thought and discussion, they will evolve. In particular, I am looking forward to reading Cory Doctorow’s book, Information Doesn’t Want to Be Free, which treats on the issues of copyright and getting paid for creative works in the internet age.[Review]

I would be interested in hearing what your thoughts are on paying for open-access publishing, either in the comments below (open for 14 days), or on Twitter (@i_rockhopper).

—

* Due to the large number of footnotes here, they will be numbered, not asterisked.
[1] Bonus fact: global warming, or climate change, is really happening.[2]
[2] Bonus opinion: Global warming should be addressed sooner rather than later, with a major eye toward reducing our energy consumption and fossil fuel burning.
[3] I may have misrepresented the time frame under which NIH-funded work becomes publicly available in my previous post. The submission to the PubMed database must be immediate, but public access to that work may be delayed by up to one year to keep commercial publishers profitable (and libraries stuck in the position where they must maintain expensive subscriptions to stay current).
[4] Yes, arXiv is a pre-print, non-peer-reviewed repository.
[5] One unexpected tidbit I found in it was that the number of senior research personnel being supported on NSF grants is up 48% since 2005.
[6] Universities often charge overhead on grants of ~50%. This can be a lucrative “revenue stream” for underfunded “public” institutions (which may not have as much state funding as the public thinks).
[7] The EGU journals are also giving a significant financial incentive to use LaTeX (€5/page).

The Importance of Openness

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.