How to Inspire a Future Paleontologist

I was sorting through some files today, and found this. Back when I was 10 years old, I knew I wanted to devote my life to paleontology, and paleontology research would be even better. So, I started writing letters to researchers I had read about in books and magazines. Some didn't respond (everyone is busy, so I can't fault them too much), and some sent really nice replies. It's those replies that propelled me into a serious career as a paleontologist. Thank you, to those who wrote back.

Little did I know that I would be visiting those collections as a researcher, only 10 years later

Life After Death At Yellowstone: An Interview with Josh Miller

In my last post, I introduced a ground-breaking study recently published in PLoS ONE, that shows how we can infer long-term trends in animal populations just from their bones. This work has big implications for ecology, conservation, and public policy, and is also a really neat piece of science. For this post, I talked to the author of the study, Josh Miller, about his work and some of the tidbits that didn't make it into the paper.

Yellowstone NP gets a lot of visitors, and you surely must have had some interactions with them during your fieldwork. How did they react to what you were doing?

JM: I work in areas that are generally well off trail and in places most Yellowstone visitors just don't see. Over the years, there are have been very few times when tourists actually ever saw my teams conducting our bone work. Most of the time, conversation with the public occur in the evenings back at camp. We generally use the public campgrounds for our homebases and my research will often come up in conversation with tourists. When folks learn what my teams and I are up to, they are always very interested and ask lots of questions. Our National Parks are an important resource, and I think people like to be reminded of their biological and scientific value. At the same time, I think it gives folks a way of looking at Yellowstone in a new and exciting way. I know lots of people who talk to us one day and keep an eye out for bones the next.

Miller studying bone survey data sheets on Northern Range, Yellowstone National Park. Photo by Scott Rose.

You looked at hundreds of bones during your survey. Was there any particular specimen that stuck out in your mind? What about it was interesting?

JM: I looked at over 20,000 bones during my work in Yellowstone. And you are right, there are a few that really stand out. Some of the most memorable bones are those of animals with severe bone maladies. In some individuals we found severe arthritis or broken bones that didn’t heal properly. Other memorable bones include rare and unusual species. One of the most exciting finds was the skull of a mountain lion. We just stumbled upon on it one afternoon walking from one transect to another. This beautiful rounded huge cat skull just lying in the grass staring up at us –a rare and amazing site.

This paper focused on bones from large animals, but surely there are a lot of small animal bones out there too - rodents, bats, rabbits, etc. Do you think they would show a similar correlation over time between abundance in life and death? Or are the taphonomic effects too different between large and small animals to expect the same pattern?

JM: Stay tuned! I kept careful attention to the bones of the small mammals we found. My bone survey teams were amazingly good at finding bones of all shapes and sizes (from bison skulls to limb bones of squirrels). One of the challenges, unfortunately, is the lack of high-quality data on the living populations in Yellowstone. One thing I'll say at the moment, however, is that the record of small-bones is surprisingly rich and diverse on the Yellowstone landscapes.

I see that you used the open source stats program R to do your data analysis. Was this something you picked up just for your dissertation work? Why did you choose R over some of the other commercial packages that are out there?

JM: I was introduced to R during the early days of my graduate work. R is a very powerful statistics language, in part, because of the large community of scientists and academics that use R and contribute to its ever-expanding utility. Another reason I use R is that I can completely control all aspects of the analysis. In canned programs, much of the analysis sits under a black box and uncovering exactly how the data were analyzed can be very difficult. But most of all, R just fits how I do science.

Thank you for your time, Josh!

Citation

Miller, J. (2011). Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape PLoS ONE, 6 (3) DOI: 10.1371/journal.pone.0018057

Note: I'm an academic editor at PLoS ONE, but had no role in the handling of this paper.

Life After Death at Yellowstone

Taphonomy - the study of what happens to an organism after it dies - is integral to reconstructing the past. Perhaps the most important lessons come in inferring ecological interactions. Did that group of animals live and die together, or were they jumbled long after death? Were all of those shark teeth with the plesiosaur bones from a feeding frenzy, or just a fluke of currents? How closely does a set of fossils represent the relative abundance of the different species during their lifetime? Such examples are numerous, and thus we commonly think of taphonomy as a study in deep time. This is certainly true, but also certainly incomplete. In fact, some of the most ground-breaking taphonomic work has been done in contemporary ecosystems. Kay Behrensmeyer, for instance, has spent decades studying bone accumulations in Kenya, and a 1927 work by Johannes Weigelt (complete with photos of dead cattle) is still considered a classic.

A new study by paleontologist and taphonomist Josh Miller, just published in PLoS ONE, shows some of the great insights that can arise from looking at taphonomy in modern settings. Josh and his field assistants trekked through Yellowstone National Park (one of the western USA's oldest and best-known parks), cataloging the identity and physical condition of every animal bone sitting out on the surface (an elk skeleton from the project is shown at right; photo courtesy of and copyright Josh Miller). Using these data, Josh found that you can actually infer the major ups and downs of animal populations from their old bones. This is quite exciting, not just from a gee-whiz factor, but because it may be possible to infer population trends for areas where historical surveys are absent or spotty. Such data are important not only for ecologists, but for informed public policy. It sounds magical, so how was the study done?

Based on other studies (in combination with radiometric dating), it's known that bones in excellent condition usually came from animals that died only recently, whereas bones in crummy condition are from animals that died longer ago. By using the condition of the bones as a proxy for time since death, Josh estimated how long the various bones of various animals had been around. Then, based on the bone ages, he estimated the relative population of each type of animal a given number of years ago. We have very good wildlife census data for Yellowstone, and it turns out that estimates from the bones match the "real" values quite nicely. Boom years for animals (such as elk) mean lots of bones going into the system, bust years mean few bones, and these trends shows up in bone surveys.

You can read all about it at PLoS ONE, or here, here, and here. I recently talked to Josh to get a few behind-the-scenes tidbits. Stay tuned for the interview later today! [update: now posted here]

Citation
Miller, J. (2011). Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape PLoS ONE, 6 (3) DOI: 10.1371/journal.pone.0018057

Note: I'm an academic editor at PLoS ONE, but had no role in the handling of this paper.

Building Momentum for Open Data in Paleontology

Thanks to a variety of "real world" concerns and deadlines, I've been a little sparse on the blog for the past few weeks. But, that doesn't mean that important things haven't been happening elsewhere in the realm of digital paleontology. If you haven't already, take a look at and consider adding your signature to "An Open Letter in Support of Palaeontological Digital Data Archiving." Kudos to the folks who got the ball rolling on this effort! As paleontology becomes more data driven, and as more of those data are digitized, we need to get our act together as a community now.

Data Archival and the JVP

It finally happened - Journal of Vertebrate Paleontology has taken a few more tentative steps into the 21st century! Both in an editorial in the most recent issue (note: full text is paywalled), as well as in an updated version of the instructions to authors, the journal has announced a formal data archiving policy.

What does this mean?

Quoting from the JVP's new instructions to authors, "all data files needed to replicate phylogenetic or statistical analyses published in the journal should be made accessible via the JVP website as online supplementary material." In other words, if you analyzed numbers of any sort, you need to show your source data. This includes cladistic matrices (publication of these is already standard practice) as well as measurements or other data used in statistical analyses. Additional kinds of data - for instance, extraneous measurements unrelated to the study, raw field notes, or raw CT scans - are not included in this proposal (even if it's good scientific practice to make sure this information is available for posterity).

Why is this a good thing?

• Data archival allows others to build upon previous work more easily. For instance, let's say I publish a statistical analysis of molar size in the early horses Mesohippus bairdi and Mesohippus westoni. Maybe there is another worker out there who wants to look at variation in some other Mesohippus species. If my dataset is available, it is much easier for another research to quickly advance beyond my work (assuming they trust my data, of course - see below).
• Data archival allows new and unexpected uses for data (thus increasing citations). My p-values and arithmetic means of Mesohippus teeth are interesting, but not that useful outside the context of my paper. If I publish the raw data, though, other individuals can use these data (and cite my paper) in all other sorts of contexts. Maybe someone wants to throw the data in her study of horse tooth evolution (hey, it's another citation!). Maybe someone else is interested in Oligocene herbivore ecology as evidenced in molar properties (and there's another citation!).
• Data archival ensures transparency. Everyone makes statistical or analytical mistakes. Unfortunately, these mistakes may render the results of a paper highly suspect at best, or worthless at worst. With the availability of raw data, it is much easier for someone to reproduce a study or correct misuse of statistics. (as a case study from my own work, I discovered that nearly all paleopathology studies in the literature were using incorrect statistical assumptions - and a reanalysis of the data forced some new interpretations!) Additionally, taxonomy frequently changes, meaning that previous categories applied in an analysis are hopelessly outdated. Not so, if you can go back to the author's original data, make a few corrections, and rerun the analysis!
• Publicly funded research deserves to be public. So much of paleontology research is funded by government grants, or conducted on company time. It is not a good use of our limited resources to keep data locked up after the original study has been published. This is somewhat analogous to writing an NSF grant to collect fossils for one's personal collection. Why should data be any different?

Answers to some common objections

• "I have other plans for the data." Some researchers want a monopoly on their data. They have this fear in the back of their head that someone is going to go out and do exactly the same next step study planned by the original researcher. I have several responses to this. First. . .really? Second, I would remind authors that it is bad science (perhaps even unethical) to publish research results that are not transparent to scrutiny. Third, I would remind authors that they are never obligated to publish all of the tangential data. If you are publishing a paper on dentary lengths in hadrosaurs, you don't have to release the data on predentary dimensions too! Finally, I would remind authors that this is just a lame excuse to put off their own follow-up research. We all know the stories of this or that researcher who has sat on a dataset for years. Science is not being helped by keeping those data secret.
• "Interested researchers can just contact the authors." As an example of why this is a bad idea, please refer to the work of Leonard Radinsky. He published a number of wonderful morphometric studies of fossil mammals, clearly based on hundreds of measurements. But, he also passed away in 1985. Unless you have a Ouija board that actually works, it's highly unlikely that anyone will be able to exactly reproduce the results in his oft-cited "Ontogeny and phylogeny in horse evolution." Authors leave academia, pass away, or lose their data sheets all of the time. It's a pipe dream to assume that "data are available upon request." [to be fair to Radinsky, his paper did not indicate that the data were available - I just chose it as one prime example where the data are probably irrecoverable]
• "It just encourages lazy research by data miners, because you should never trust anyone else's research data." There is a grain of truth in this - inter-observer error may creep into measurements, and maybe a certain author likes to measure plaster reconstructions. But once again, this is just a lame excuse for lazy research by the person who is objecting to data transparency! After all, if you can't trust the data, you can't trust the paper, so what's the point in publishing? It's a slippery slope. The benefits far outweigh the drawbacks.
• "It's just more work for the authors." This too falls into the "lame excuse" category. If you've already gone to the trouble to put together an Excel spreadsheet for your statistical analysis, you can spend an extra 10 seconds transferring those data to the manuscript submission system. If it takes you longer than that, you may want to reconsider your data management practices.

Recommendations for JVP

I have just a handful of recommendations for the editors at JVP, based on my own experience as both a data user and a data generator. Some of these suggestions may already be incorporated, and others may be planned. Others may be impractical at this time. Either way, I think it is helpful to consider the following:

• Make sure the data files are in a usable format. Historically, supplemental information at JVP has been launched as PDF files (with some NEXUS files). This is great for casual reading, but horrible for analysis. Just try copying 3,382 measurements from a PDF table into an Excel spreadsheet, and you'll see what I mean. This does not mean you need to choose a single format - why not have the data in PDF, Excel, and raw text? Multiple formats ensure maximum usability of the data across multiple platforms (as well as flexibility in the face of future software upgrades).
• Consider a data embargo for reluctant authors. Many journals allow a six month or (maximum) one year embargo on supplemental data, to allow authors the chance to finish up any outside projects. Although I philosophically disagree with this option, I see its utility. And, it is an appropriate compromise between protecting author rights and protecting scientific integrity.
• Consider partnering with DRYAD or a similar data repository. A number of other evolutionary societies are doing this - why shouldn't SVP be a part of this?
• Solicit society input. The members of SVP and the authors of JVP probably have some great thoughts on what they would like to see in data archival. Why not solicit input from the community to find out what the community needs? This will only solidify ownership of the data archival efforts by paleontologists!
• Check out a recent publication on this very topic. Michael Whitlock recently published a great review article [paywall] on best practices in data archival - many of the points mentioned above are contained there. (thanks to Randy Irmis for passing the link along)

The Last Word

All in all, I am pleased to see JVP take these steps. Congratulations to the editors of the journal, for taking this stand for good science!

More Reading

Berta, A., and Barrett, P. M. 2011. Editorial. Journal of Vertebrate Paleontology 31: 1. doi:10.1080/02724634.2011.546742 [paywall]

JVP Instructions to Authors [link to pdf]

Whitlock, M. C. 2011. Data archiving in ecology and evolution: best practices. Trends in Ecology & Evolution 26: 61-65. doi:10.1016/j.tree.2010.11.006. [paywall]

Nedoceratops - Random Thoughts

The last two posts here have focused on my most recently published paper, fully describing the skull of the horned dinosaur known as Nedoceratops hatcheri and critiquing the hypothesis that it, along with Torosaurus latus, is simply an older individual of what we call Triceratops. Because I've already talked about the science of the paper, and some collegial interactions, I'm going to spend this final post in the series talking about a few odds-and-ends that just didn't fit anywhere else. Most of these are little windows into the process behind the paper - from writing to review to revision. And we'll start with. . .

Open Source Composition

I'm proud to say that every single step of the authoring process for my paper happened in open source software. I wrote the manuscript in OpenOffice.org Writer, formatted most of the references in Zotero, did initial image editing (contrast adjustment and background removal) in GIMP, assembled the figures in Inkscape, and submitted the manuscript through the journal website on the browser Firefox, all of which were running on various releases of Ubuntu. Score one for open source software (and open access publishing)!

On Organizing the Paper

I'm under no illusion that everyone (?anyone?) will agree with my conclusion that Nedoceratops is a valid taxon. In fact, I'm quite accepting of the possibility that I may be wrong. But even if this is the case, I still want my paper to be useful. So, I made my best effort to separate data from interpretation in the description section of the paper. Of course, I couldn't be completely successful on this point - after all, I had to compare Nedoceratops with Triceratops and Torosaurus (the most likely candidates for synonymy) - but I like to think that I mostly achieved my goal. If nothing else, I have pretty pictures. And. . .

Speaking of Pictures

My figures went through some pretty drastic changes during the evolution of this paper. In the first round of reviews, it was pointed out that in the text I kept referring to various structures illustrated in the figures, but only a ceratopsian geek could figure out what I was talking about.

For example, we have this lovely sentence:

The narial strut is inclined rostrally towards the dorsal end of the element, and enough original bone surface is preserved to indicate that a posterior internarial flange did not project from the caudal surface of this structure (Figure 4).

My original Figure 4 looked like this:

The photo is relatively pretty, but only a die-hard ceratopsian nerd could locate the narial strut or know where to look for a posterior internarial flange if such a thing even existed in this animal. So, for my next iteration I added some labeling:

Of course, all of the abbreviations are explained in the caption (not shown here). "ns" refers to the narial strut I was talking about above. Finally, the editor mentioned that I should do a better job of indicating the "cpf" (canal at the edge of the premaxillary fossa). It wasn't just at the tip of the arrow, but over a somewhat broader area. Thus, that brings us to version 3:

This, with the extra arrows showing the position of the canal, was the version that appeared in the paper.

If I learned anything from this experience, it was about the importance of good labeling and interpretive drawings for non-expert readers. Most of the labeled interpretive drawings alongside photographs (with the exception of parts B and D in Figure 1) were added at the direct request of the editor. Looking at the end product, this addition was a major improvement to the paper. Of course, I must also admit that having relatively unlimited space in an online journal allows this luxury!

Editorial Ethics

It's probably not a surprise to many of you that I am a volunteer academic editor at PLoS ONE. And those of you who have been paying attention probably noticed that the Nedoceratops paper was just published in that very same journal. This sounds pretty problematic on the face of it.

Thankfully, PLoS ONE has pretty strict editorial controls when one of their own editors submits a paper (in addition to a competing interests policy that covers this and similar situations). My experience as a submitting author was exactly the same as for any other author. Once the "submit" button was pressed, I had to wait just like everyone else. I couldn't control which editors handled it, who reviewed it, or even have a sneak peek at the reviews on-line. In other words, the system functioned exactly as it should.

My authorial feet were held to the fire by Leon Claessens, the handling editor for my submission. Leon, in my opinion, did a very professional job and didn't let me get away with anything (even sending the manuscript back to me a second time for a few last corrections and improvements). The reviewers - Michael Ryan and Peter Dodson - also did their jobs (in my opinion). And, as mentioned in my last post, comments by John Scannella and Jack Horner offered additional constructive feedback.

One thing I really like about PLoS ONE is that my competing interest - as an editor at the journal - is stated up-front in the paper. Although it's somewhat scary seeing it there, I think such notices are certainly appropriate.

Final Thoughts

It's nice to finally have this paper out there - these ideas have been floating around in my head for awhile, and I've always had a secret desire to be the person to describe Nedoceratops. I'm relatively pleased with the final product (of course, there are always one or two typos that slip through, and why couldn't some of the figures in the PDF have been bigger?), and look forward to the discussion that this paper generates. Thank you to all who helped out (see the acknowledgments for a comprehensive list)!

Nedoceratops - Fun with Science

In my last post, I mentioned that I have had more fun with my recent project on Nedoceratops than anything else I've done lately. Just as a refresher, this paper described an oft-neglected horned dinosaur skull known as Nedoceratops hatcheri, and presented counter-evidence to a hypothesis (published by John Scannella and Jack Horner) that Nedoceratops, Triceratops, and Torosaurus were all the same animal. This all sounds kinda boring and academic, so where's the fun in that?

As a scientist in a small field like vertebrate paleontology, it can be awkward when you disagree with a colleague. I've heard third-hand accounts of shouting matches at scientific conferences, and have occasionally seen very heated discussions during the Q&A time at presentations. Thankfully, this sort of behavior is pretty rare. Yet, I was a little worried about what might happen when I publicly presented a counter-argument to Scannella and Horner's hypothesis.

My nightmare of a confrontation with John Scannella (left) at SVP. Maybe there wouldn't be fists involved, but at a minimum a wrestling match. He's in better shape than I am, so I would be in trouble.

Of course, I was less concerned about a shouting match, and more focused on not being a jerk in print. I've known both John Scannella and Jack Horner for a number of years, and wanted to stay on at least semi-cordial terms with them. Of course I was going to disagree with them (based on my interpretations of the available data), but I wanted to do so in a way that was fair, collegial, and honest.

So, I did something that some people might consider stupid. I sent John and Jack a copy of my unpublished, unaccepted, in-review manuscript. At the very least, I figured it was only fair that I should give them a heads-up that I would be presenting counter-arguments to their hypothesis about Triceratops and Torosaurus. More importantly, I wanted to make sure that I was representing their work fairly and accurately.

This initiated a lengthy and wide-ranging email conversation. Although I had done a decent job of representing most of their points, there were a few areas where I had inadvertently set up a straw man. I fixed those as best I could. In some (thankfully minor) areas, I needed to update information or account for some specimens I had neglected. For instance, I had grossly understated the amount of variation in the frills of various adult Triceratops (something that has only been adequately documented thanks to John's Ph.D. work). With their honest feedback, I was able to craft a much-improved version of my manuscript. It is not just a smarmy platitude to state that I genuinely appreciate their input.

Of course, I won't claim that Scannella and Horner find my counter-arguments (that Torosaurus and Triceratops are different animals) entirely convincing. And, my current opinion on the matter is not unchangeable. John and I had a nice long chat at the SVP meeting this year, comparing notes and talking about our future research plans. He has some really cool data (some of which he has presented at SVP and other conferences), and I look forward to seeing it in print. Undoubtedly, we will both modify our interpretations as new data are published.

Now why am I finding this to be so enjoyable? It's the joy of discovery, the entertainment of questioning long-held ideas (especially my own), and the pursuit of new data. After all, science shouldn't be about scoring rhetorical points, but working towards an accurate view of our world. I know beyond a doubt that we all are playing on the same team. My dialog with John (and Jack) has been engaging, challenging, and stimulating in a unique way. I've learned more about Triceratops in the past six months than I had in the past six years (to be ultra-nerdy, for instance, some specimens lack the mid-line epiparietal - neat!!!). It's just darned fun to be working on a research problem like this!

No matter how this whole issue shakes out, I think there is one thing we can all agree on right now. Horned dinosaurs are AWESOME!

John Scannella and I, with our favorite dinosaur

Coming Up: A few final thoughts on the process behind this paper.