Thursday, April 26, 2012

A Paleontology-Specific Impact Factor for PLoS ONE

The threads at SV-POW! are hopping right now, particularly with one commenting on open access in Journal of Vertebrate Paleontology. One question that came up is how much, if at all, the impact factor of PLoS ONE (4.411 for 2010) indicates the reach of paleontology papers in that journal. In other words, if PLoS ONE just published paleontology papers, what would its IF be?

Naturally, I had to calculate it out. I used the standard IF formula, and looked just at citations in 2010 for papers published in 2008 and 2009. Citation counts were derived from Web of Science, which is linked to from each individual article at the PLoS ONE website. Articles under consideration from 2008 and 2009 were harvested from the PLoS ONE Paleontology Collection; one or two articles in there were only tangentially paleontological, but I kept them in anyhow just for consistency.

I calculated a "paleontology IF" of 3.317 for 2010 - a little lower than 4.411 for the overall journal but still higher than in other more field-specific publications. So, not too shabby.

This omits the issue of whether or not impact factors are worth anything, but I won't delve into that here. Love it or loathe it, we scientists still like to talk about IF!

Wednesday, April 18, 2012

Introducing the Dental Microwear Image Library

Dental microwear, seen in the tiny pits and scratches on a tooth, provides lots of detailed data for inferring diet and chewing behavior in animals. Analyses are often conducted by digitizing highly magnified images of the tooth surface and counting up and classifying the various microscopic features. Animals with a certain percentage of pits and scratches may have browsing habits, whereas those with another profile may be grazers. By measuring extant animals with known diet, we can (hopefully) infer the diet of extinct animals.

Dental microwear; modified from figure 3 in Mihlbachler et al., 2012
In this age of increasingly open science, microwear studies can be problematic. A cornerstone of science is reproducibility - yet, inter-observer variation and error can greatly affect measured data. Furthermore, one study alone may generate dozens or hundreds of images. Even if you wanted to re-analyze teeth, it's pretty tough - how could you get access to the necessary images? Ideally, we want a world where anyone can access the raw image data, make their own observations, double-check published analyses, and add new data for comparison.

Thus, a new project - called the Dental Microwear Image Library, or DMIL - may change things. Assembled by Brian Lee Beatty and Matthew Mihlbachler, the website aims to become a clearinghouse for dental microwear images. This will allow greater standardization of analyses and hopefully better interpretations of paleoecology and diet for extinct organisms and modern organisms. The first data (from a recent paper in Paleontologia Electronica) are now posted, along with many other data sets.

Brian Lee Beatty (who blogs at The Aquatic Amniote and tweets as @Vanderhoofius) was kind enough to answer a few questions about the DMIL. Thanks, Brian!

Was there a particular moment or incident that inspired you to build the DMIL? If so, what was it?
As we set out to test and develop the method that Nikos Solounias and Gina Semprebon started, we found ourselves frustrated by not only the lack of information on methods that were given in most microwear papers, but also the inability for people to check their work. Interobserver error is a major cause of problems for microwear, and the only way for anyone to be aware of those differences is if they compare interpretations of microwear surfaces, not just their numbers on a spreadsheet. The DMIL was the only possible solution to the need to share such images.

How has community response been so far? Is there any particular type of skepticism that you're working to overcome?
The DMIL hasn't yet come up against skepticism, but our first paper on this method that uses it has.

What license, if any, are the data housed under? Or is it on a case-by-case basis?
There is no license for the data. We want it to be completely open-access and simply available.

How would you envision the DMIL 10 years from now? What goals might you have for the long-term?
We hope it will be a place that people can use to learn how to use the methods we are continuing to develop. I most sincerely hope that it will not only be home to our own data, but also be a place for others to deposit their data using similar methods so that more work of this sort is available in a similar, comparable format.
Authors of the recent paper in PE, along with a research assistant. Photos courtesy of Brian Lee Beatty.
For more information, check out the DMIL, or read the recent paper (open access) about the work.

Mihlbachler, Matthew C., Beatty, Brian L., Caldera-Siu, Angela, Chan, Doris, and Lee, Richard, 2012. Error rates and observer bias in dental microwear analysis using light microscopy. Palaeontologia Electronica Vol. 15, Issue 1;12A,22p.

Thursday, April 5, 2012

Open Access in the UK - Comment Now!

The Research Councils UK (an umbrella organization overseeing much of the public scientific funding in that country, as well as funding for the arts and other worthy ventures) is soliciting comments on a new open access policy [PDF]. No matter what your opinion on open access, please comment. Mike Taylor, writing at SV-POW!, has further information and instructions.

Even if you don't live in the UK, it is worth letting the Research Councils know how you feel about the policy. Why? Because science (and scientific publishing) is inherently an international endeavo(u)r. I collaborate with colleagues in the UK all of the time, and many of the best papers I read these days have their origin across the pond. But, as with most scientific literature, access sometimes ain't easy. A more open scientific literature helps all of us, and each accessible paper raises the country's profile in the scientific community. Funding agencies always want more bang for their buck (or pound), and improving accessibility is one great way to do that.

So, drop a line to by April 10 and use the subject "Open Access Feedback." Even a short sentence of support will do. Or three short sentences, as I did (basically using the argument in the paragraph above). Make your voice heard!