Author: Sarah Werning

Sharing Paleodata (Part 3): MorphoBank

Today I am making good on an old promise to highlight more repositories for paleontological raw data. Previous posts in this series can be found here and here.

MORPHOBANK (http://morphobank.org/)

Full Disclosure: The statements about MorphoBank in the “Nitty Gritty” section were checked for accuracy by Maureen O’Leary (MorphoBank Project Director) and Seth Kaufman (software developer). The impressions are my own: I have submitted, published, and downloaded MorphoBank data.

Impressions: MorphoBank is not just a data repository, but also a collaborative tool to produce, edit, illustrate, and annotate morphological character matrices for phylogenetic analysis. It’s not a tree-making, tree-visualizing, or tree-using site; it’s a tree data site, and it’s built to accommodate large groups who are working in the same project. In service of this goal, each character or character state can be linked to an image or video of that character state, which can then be edited or annotated. MorphoBank is cloud-based, meaning you don’t have to concatenate dozens of files from collaborators to build a final matrix; everyone can see what you coded immediate (and why, if you load images). You can use MorphoBank just to create matrices, just as a media repository, or a combination.

There are lots of cool toys that make collaboration easier – these include an image annotation menu, comment screens (facilitating discussions of identity and homology), the ability to restriction which taxa/rows each person can edit (preventing people from accidentally coding/editing the wrong thing), the ability to merge many source matrices into one combined matrix, and the ability to keep all the relevant documents in one place. You can batch upload taxa, specimens, and media, which is convenient. The how-to’s are thorough and easy to use, and so is the site itself.

The matrix editor is quite user-friendly. You can create one from scratch or import from a TNT or Nexus file (and even if you don’t generate your matrix in MorphoBank, you can still host the data files there). The comments and annotations feature make it easy to discuss morphology or calls on codings with colleagues, without having to get them on the phone or in person. You can also track changes if you think someone has messed up, and assign different levels of editing ability to prevent such things from happening in the first place. I like this feature a lot, because it enables students and volunteers (and colleagues) to participate in different roles. Another cool feature is that it records and displays how many cells each team member has scored, as well as the taxa, media and citations they added.  This provides greater demonstration of exactly who did what work in a collaboration.

MorphoBank is one of the best, if not the best, repositories for 2D images.  The allowed file and image sizes are generous, and the built-in viewer enables you to zoom in/out and label/annotate your images. As a bone histologist, this is my preferred way to share my raw data – my dissertation involved over 700 large format images, and this was how I presented them to my committee. As a supplement to papers, MorphoBank is top notch: you can present detailed images at their original resolution without worrying about page sizes or file sizes, and you can show way more images than you could get into even in the most generous of journals. Having a permalink (and coming soon: DOIs) for each image means those images can be cited later, getting credit for all your work. Those permalinks also can be given to media outlets as part of your outreach or research promotion (yay broader impacts).

Overall, I have no big issues with MorphoBank, and from personal experience I can report that all the minor speedbumps I’ve experiences were quickly resolved by their excellent support team. However, there is one feature I’d like to see added that would integrate MorphoBank with other sites better: it would be nice to be able to link specimens and publications externally. For example, links from the vouchered specimens to their museum database pages, or bibliography publications to their journal page (both are features GenBank offers).

Bottom line: Grant writers should feel comfortable listing MorphoBank in their Data Management Plan because it’s safe, easy to use, and your reviewers will (should) have heard of it; reviewers should feel comfortable asking authors post data to MorphoBank when appropriate, for the same reasons. 

Postcranial skeleton of Sebecus icaeorhinus, MPEF/PV 1776. (c) 2012 Diego Pol, licensed under CC-BY-NC-ND. MorphoBank accession M106695, accessed here.

Postcranial skeleton of Sebecus icaeorhinus, MPEF/PV 1776. Image © 2012 Diego Pol, licensed under CC-BY-NC-ND. MorphoBank accession number M106695, accessed here.

MORPHOBANK: THE NITTY GRITTY

What it is: Both a collaborative tool and repository for the scientific data associated with peer-reviewed scientific publications. The focus is on data related to phylogenetic tree-building and the evolution of morphological phenotypes in general. It allows research teams to work on a single shared copy of a character matrix in real time over the Web. These data matrices can be linked to images of different anatomical characters/character states, or the images can stand on their own. “Morphology” is intepreted broadly – really, any type of phenomic data is welcome.

What it is, in their words: “…a web application for conducting phylogenetics or cladistics research on morphology. It enables teams of scientists who use anatomy to study the Tree of Life (phylogeny) to work over the web – in real time – and to do research they could not easily do using desktop programs alone.”

Who runs it: The MorphoBank Project, which has an executive committee that consists of academic researchers (including one student representative). The Project Director is Maureen O’Leary (Stony Brook University), and the Executive Committee is chaired by Nancy Simmons (American Museum of Natural History).

Who funds it: Currently: NSF (direct), with in-kind support from the American Museum of Natural History and Stony Brook University (as server hosts). Previously: American Museum of Natural History, NESCENT, NOAA (NA04OAR4700191), NSF (DBI-0743309, DEB-9903964 and EAR-0622359), San Diego Supercomputer Center, Stony Brook University.

Who uses it: Researchers who use or submit data; journals allow you to cite MorphoBank data. Project/media links could be used for media promotion and outreach as well.

Nasutoceratops titusi

Nasutoceratops titusi UMNH VP 16800. Image © Mark Loewen, licensed under CC0. MorphoBank accession number M307812, accessed here.

Cost to submit: Free.

Cost to access: Free.

Data and file types supported: Data related to systematics or morphology, including text, audio, images, video, and more. 2D images: JPEG, GIF, PNG, TIFF and PSD are allowed, but a file in CMYK or with layers may not render properly. 3D images: Three dimensional surfaces in STL and PLY format will be supported soon. Video: MPEG-4 (preferred), QuickTime, and Windows Media. Audio: MP3, AAC, AIFF or WAV.  Phylogenetics: The matrix editor/viewer accepts data in Nexus or TNT format.  Other files not in this format are stored in the Documents folder. Other: No PPT or PPTX.

File sizes allowed: Doesn’t say. In the past, my files have been limited to 40MB, but by emailing tech support I was able to request an increase in maximum file size. The image viewer sometimes has difficulty processing gigapixel images, but this can be fixed by resizing or emailing tech support.

Copyright status: Settings are currently available for Media (images, video, and the like). Your choice: CC0, CC BY, CC BY-NC, CC BY-NC-SA, CC BY-SA, CC BY-ND, CC BY-NC-ND. You can also post copyrighted media released for one-time use. Cool feature: option to upload your copyright permissions document.

Data available during peer review? Yes, if you set it up. Password protected. This is not streamlined into the journal submission process, and from personal experience, journal editors don’t pass on this info if it’s in the cover letter only. I make sure to include the login information in the body of the manuscript, so the reviewers can see it.

Allowed to post data from previous pubs? Yes, even publications published before MorphoBank existed, and they invite and encourage this practice. Example: http://morphobank.org/permalink/?P694

Skeleton Vulpavus ovatus (AMNH 11498)

Skeleton of Vulpavus ovatus (AMNH 11498). Image © American Museum of Natural History, licensed under CC BY-NC-SA. MorphoBank accession number M150920, accessed here.

Accession numbers provided? Yes. Every project gets a unique project number and stable URL (permalink), and each image gets its own accession number (similar to GenBank), assigned as you upload them. You can also assign media to folios (subsets of media), and these also get unique stable URLs. DOIs for Projects, Media and Matrices will be available before the end of April 2014 and this will be retroactive (!!!).

Data goes live when: You choose to publish the project. Data can stay as an unpublished project forever, or you can publish it when the manuscript is accepted, when embargo is lifted, when the paper is published, or any time after. You can choose to publish all or some of your files when the project is published.

Data is backed up? Yes, to tape at Stony Brook University and off-site mirror servers at the American Museum of Natural History.

Stats provided? Project views, project downloads, media views, media downloads, document downloads, data on team member efforts.

How to cite your data in your manuscript? Varies by journal, but some thoughts:

  1. Definitely cite the MorphoBank publication software. Currently, this is: O’Leary MA and SG Kaufman. 2012. MorphoBank 3.0: Web application for morphological phylogenetics and taxonomy. http://www.morphobank.org.
  2. You should additionally cite the peer-reviewed publication: O’Leary MA and SG Kaufman. 2011. MorphoBank: Phylophenomics in the “cloud”. Cladistics 27: 1-9.
  3. You should also cite your data. I recommend citing within text, something like:
    Image data available on MorphoBank: http://morphobank.org/permalink/?P494 (but where ‘494’ is replaced with your own project number). I’ve also included lists of image accession numbers as tables (for larger projects, I think this is more appropriate for the SI).

How to cite data you download? Cite the permalink (the DOI once that feature goes live) and project number, and if you refer to a particular image, the accession number.

Can update after publication? No. Once the project is published, it cannot be modified.

Eryon arctiformis (Houston Museum of Natural Science). Image by Daderot, licensed under CC0 1.0. MorphoBank accession number M326412, accessed here.

Eryon (Houston Museum of Natural Science). Image by Daderot, licensed under CC0 1.0. MorphoBank accession number M326412, accessed here.

Exciting Future Developments: The MorphoBank group is about to release a version of the Matrix Viewer that will allow you view published matrices on iPad and Android tablets (the previous, Flash-based viewer is being replaced with a new, HTML 5-based viewer). In the future, they plan to do the same for the Matrix Editor, as well. MorphoBank also talks to a new NSF-supported site called the Evolution Project (now in beta testing).  The Evolution Project allows people who have matrices in MorphoBank to crowdsource their data collection. Interested people (e.g., students, volunteers) can score cells from images (!!!).  It is designed to speed up morphological data collection.  Also coming soon: the ability to viewing CT images within the MorphoBank environment, and support for continuous characters.

Benefits in a nutshell:

  • Secure cloud storage of image and character matrix data.
  • Real-time collaborative editing of phylogenetic matrices and their associated data in the cloud.
  • Images illustrate exactly what you mean by a given character or character state. As the MB site says, “Seeing the images that document the basis for homology – a character state or a cell score – is enormously helpful to researchers during their research project.”
  • Nigh-infinite choices for: number of images, copyright, image size and resolution.
  • Batch uploads and batch edits to metadata allowed.
  • The ability to label and otherwise annotate images (without altering the original image).
  • The ability to zoom in when viewing large or high-resolution images.

Three recent paleo papers using it:
Evans SE, JR Groenke, MEH Jones, AH Turner, DW Krause. 2014. New material of Beelzebufo, a hyperossified frog (Amphibia: Anura) from the Late Cretaceous of Madagascar. PLoS ONE 9(1): e87236. MorphoBank data here.

O’Leary MA, et al. 2013. The placental mammal ancestor and the post K-Pg radiation of placentals. Science 339:662-667. MorphoBank data here.

Nesbitt SJ, PM Barrett, S Werning, CA Sidor, AJ Charig. 2013. The oldest dinosaur? A Middle Triassic dinosauriform from Tanzania. Biology Letters 9:5pp. MorphoBank data here.

Category: Digitization, Open Access, Open Data, Paleontology, Technology | 1 Comment

Paleo Podcasts

When I work out, I sometimes listen to a mix of aggressive electronica and high-energy dance music to get me moving. But usually, I use my gym time to catch up on podcasts. My new year’s fitness resolutions mean I’ve been updating my mp3 player with new podcasts, including some paleontology-themed ones. The problem is, when you go to iTunes and search “paleontology”, “palaeontology”, or even “dinosaurs”, you don’t get much. Here are a few for the paleo-minded.

http://www.pasttime.org/

I’ll begin with a plug for my peeps: Past Time is hosted by Stony Brook University grad students Adam Pritchard and Matt Borths. Every couple weeks they post a ~20-25 minute show on some topic relating to vertebrate paleontology, and despite the hominid focus at Stony Brook, it’s rarely about humans. In addition to their entertaining and informative banter (Adam is a perfect straight man to Matt’s charming goofiness), each episode includes an interview with a paleontologist who worked on the topic of discussion. For example, recently they chatted about all these new tyrannosaur species discovered by University of Utah scientists, with Utah professor Dr. Randy Irmis as a guest. The interviews are woven into the discussion on the topic rather than longform interviews. One really awesome feature of Past Time is that they create a “field guide” for each episode, an associated page with tons more information, photos, maps, and further reading, including links to the original scientific papers (here’s the tyrannosaur field guide). The most recent episode is “The Hobbit – An Unexpected Discovery“, which discusses the species of tiny hominids living in Indonesia just 17,000 years ago, Homo floresiensis. This show is definitely kid-friendly (no swearing, shorter), and it’s accessible to non-scientists in language/themes).

For more Past Time, head to their website, subscribe on iTunes, and follow them on Twitter and Facebook.

http://www.palaeocast.com/

You should also check out Palaeocast, a UK show hosted by Dave MarshallLaura Soul, Joe Keating, and Jon Tennant. This show is a bit longer, 30-60 minutes per episode, with a new ep every two weeks. It’s a different style than Past Time; the interviewees are the focus and they have a longer chance to explain their research. Some recent shows I liked are a general overview of marsupial evolution and a discussion of the Riversleigh fauna, both featuring Dr. Robin Beck from the University of New South Wales. Another rad aspect of Palaeocast is that they cover scientific meetings; for example, these recent eps on the Society of Vertebrate Paleontology and the Palaeontological Association annual meetings. The pages for each podcast are image-rich, with pictures from the meetings or from the scientific papers the interviewee discusses. You could play this podcast with your kids in the car (no swearing), but younger kids with short attention spans might not like the longform interviews. Adults, however, will appreciate the clarity and depth of the discussions.

For more Palaeocast, head to their website, subscribe on iTunes, and follow them on Twitter. You can also like them on Facebook.

paleo after dark

Palaeo After Dark features ”informal discussions about evolutionary biology and palaeontology… over beer”, and is hosted by four current or recent University of Kansas geology graduate students: Curtis Congreve, Amanda Falk, James Lamsdell, and Randol Wehrbein. This is also a biweekly podcast, and it’s easily the longest of the bunch (some episodes are close to two hours). This podcast is stylistically a lot different from the ones above; it’s four friends discussing topics relevant to their shared research interests or primary literature. It’s neat to get this perspective into how academics interact with each other; this is far closer to how most science conversations start than the stodgy, formal, or awkward stereotype you see in movies or Big Bang Theory. Palaeo After Dark assumes their listeners are already pretty familiar with paleontological and evolutionary terminology, so it might not be as accessible to nonscientists. It also usually takes a long time to get to the meat of the episode. For example, the gang has over 26 minutes of amusing banter before they begin this interesting discussion of dinosaur ontogeny, taxonomy, and geologic dating. Because this is an informal podcast and alcohol is involved, there is a lot of swearing, so it’s probably not kid-appropriate.

For more Palaeo After Dark, head to the website, subscribe on iTunes, and like them on Facebook.

Dragon Tongues paleontology podcast

Our final paleo-exclusive podcast is Dragon Tongues, a show so new its first episode just aired on January 7th. Hosted by Sean Willett (an undergrad! at University of Calgary who also writes a dino column for UBC Okanagan’s The Phoenix News), Dragon Tongues will air the first Wednesday every month. It’s pretty short if the first episode (15 minutes) is a good indication. The first show begins with a statement of purpose: Sean’s goal is to tell the stories of fossils and Earth history in an accessible format, with each episode focusing on a species, and each season focusing on a theme. Season 1 is about dynasties, and episode one focuses on Carcharodon megalodon. I’m excited about this podcast; Sean has a dynamite radio voice and stylistically it’s sort of a paleontology-version of This American Life. Rather than fanboy gushing over mega-sharks, he tells the story of the role C. megalodon played in understanding what fossils are, and how they shaped our understanding of past life being different. Dragon Tongues is kid-appropriate and non-scientist accessible.

For more Dragon Tongues,  follow it on Twitter and subscribe on iTunes.

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If your main source for podcasts is iTunes, that’s it. Those are the only four paleo-only podcasts they host. However, there are several other science-themed podcasts aimed for a general audience, that feature paleontological topics.

http://tetzoo.com/

Tetrapod Zoology is a relatively new podcast hosted by SciAm blogger Darren Naish and palaeoartist John Conway. As with the blog, its topics include vertebrate paleontology in addition to the biology of living tetrapods, science fiction movies, and cryptozoology. These topics are all mixed into each ~60-90 minute episode, so there are no pure-paleo shows (so far). Recent episodes include discussions of woolly rhinos, mesosaurs (fossil vertebrates somewhat closely related to reptiles), and the tail of Jeholornis (a fossil bird from the Cretaceous of China). The show jumps right into the topic, and usually begins with zoology or paleontology. It shares the tone that makes the original blog work so well; Darren and John are both genuinely interested and it shows. It would be cool if they added links to the papers/books being plugged/discussed to the website, but it’s still new, so maybe this will happen in the future. The shows are kid-friendly and generally accessible to non-scientists (they explain technical stuff), but as I said above, not paleo-exclusive.

Follow TetZoo on their website and subscribe on iTunes. Also, you really should read the blog itself.

radiolab logo

Nothing else sounds like Radiolab. You might have heard it on public radio; it’s nationally syndicated. Each week, a different topic (often scientific, sometimes news or philosophical) is explored, presented from the perspective of the hosts as if they are learning about it in real time. Clips from interviews are woven into the discussion, so listeners follow how the scientists made their discoveries and changed their thought processes. Check out this recent ep in which University of Chicago paleontologists discuss using fossil corals to track changes in the number of days per year through time. Definitely kid- and non-scientist friendly: anyone who is natively curious about the world should like it. It’s one of my favorites, even when the topic isn’t science.

Follow Radiolab on their website, Twitter, Facebook, or iTunes.

science friday

Science fans are probably already familiar with the weekly Science Friday podcast, which is also aired on public radio stations across the US. Each week, host Ira Flatow examines several topics from recently published research, including short interviews with the researchers themselves. Recent episodes include discussions with NSCU grad student Edwin Cadena about car-sized giant turtles from Colombia and a conversation about Utah’s fossil history with Utah professor Dr. Randy Irmis, science writer Brian Switek, and BYU professor Dr. Brooks Britt. And just last week, Dr. Ted Daeschler from the Academy of Natural Sciences, Philadelphia was on the show to chat about the hind limbs of Tiktaalik. Go! Subscribe! Now!

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Given that people find paleontology so fascinating, it’s really weird that there aren’t more dedicated paleo-podcasts. I would have assumed  that there would at least be one weekly or bi-weekly “dinosaur roundup” show…

Do you blast your quads to a different science podcast? Have I missed some in this list? Let me know in the comments section!

Category: Miscellaneous, Paleontology | Tagged , , | 5 Comments

The Colorado Plateau Coring Project: Getting Dates in the Triassic

Yesterday I wrote about how rocks layers are aged. After rock layers are lined up and put in relative order, they are dated radiometrically to get their age in years. Terrestrial rocks are difficult to date using relative ages alone, because the divisions of geologic time are defined based on changes in marine fossils (like ammonites and conodonts), which are rare in terrestrial rocks. We can make rough correlations if terrestrial layers are bracketed above and below by marine layers, which happens when sea level rises and oceans spill onto the edges continents. But the oceans reach continental centers  rarely, so long stretches of time may occur between the marine “brackets” that allow terrestrial correlations.

A lot of neat stuff has happened on land during the history of life, from the birth of flowering plants to the origins of humankind. If we had a better grasp on the exact dates that these important events happened, then we could place them in context of things happening elsewhere on the planet: volcanic eruptions, asteroid impacts, climate change, etc.

One time of particular interest is the Triassic Period. Not only is it bounded by two enormous mass extinctions, but the Triassic is when all the major groups of land vertebrates alive today got their start: the ancestors of crocodiles and birds, frogs and salamanders, mammals and lizards all first appear or begin to diversify in the Triassic. What caused this burst of diversity – recovery from the biggest mass extinction of all time, climate change, rifting continents, or something else?  How long did it take – was it simultaneous around the world or region; did it have pulses? The answers are in the rocks, but unfortunately, Triassic terrestrial rock layers are poorly correlated and poorly dated compared to other parts of the global geologic column.

Colorado Plateau Coring Project

Logo by Steven Seppi. Used with permission from the Colorado Plateau Coring Project.

Enter the Colorado Plateau Coring Project. The Colorado Plateau is an area covering about 130,000 square miles of Utah, Colorado, Arizona, and New Mexico. It’s well known for its dramatic geology and incredible national parks, including the Grand Canyon, Arches, Canyonlands, and Petrified Forest. It’s also rich in Triassic rocks and fossils. If the Colorado Plateau was better aligned to the global rock record and better dated radiometrically, it would be key to answering those questions above. The Colorado Plateau Coring Project (CPCP) is funded by the International Continental Drilling Program (ICDP)-funded and National Science Foundation to do just that.

Petrified Forest National Park preserves an especially rich record of the terrestrial Triassic, and comprises nearly 100 million years of continuous rock layers, many rich in fossils. So it makes sense that the CPCP would begin their alignment and dating efforts here. This is a large, collaborative project involving scientists at several universities: Randall Irmis (University of Utah; Natural History Museum of Utah), George Gehrels (University of Arizona), Paul Olsen (Lamont-Dougherty Earth Observatory, Columbia University), Dennis Kent (Rutgers University), John Geissman (University of Texas at Dallas), and Roland Mundil (Berkeley Geochronology Laboratory). For the past two weeks, the team has been at Chinde Point in Petrified Forest drilling a core half a kilometer deep to get the basic rock data to align and date the Colorado Plateau.

Last week, I interviewed Randall about the details of this important research project.

Chinde Point, petrified forest

Chinde Point at Petrified Forest National Park preserves a nearly continuous sequence of Triassic rocks spanning ~100 million years. Image courtesy of the Colorado Plateau Coring Project.

SW: What are the main goals of the CPCP?

RI: The CPCP aims to recover a nearly-continuous record of sedimentary rocks from the Early Mesozoic (252-150 million years ago) of the Colorado Plateau. This record will be recovered using continuous rock cores recovered from at least five different locations around the plateau. Our first stage is to core the entire sequence of Triassic sedimentary rocks at Petrified Forest National Park; these are the Chinle and Moenkopi formations.

SW: What are you hoping to learn? Will the CPCP tell us anything about the biology of extinct animals or climate change?

RI: We hope to answer the following major questions:

  • What is the tempo of climatic and biotic change during the Triassic, such as the rise of dinosaurs?
  • How did changes in greenhouse gases (e.g., CO2) affect ecosystems and the environment during the Triassic Period?
  • What caused a sudden change in plant and animal species at about 215 million years ago – could it have been a meteorite impact that hit Quebec at about the same time?
  • How do Triassic ecosystems and environments in western North America compare with those from the same time in eastern North America, Europe, South America, and Africa?

SW: What is a core – is it a common way to study rocks? Do you find fossils in the cores?

RI: Cores are basically columnar cylinders of rock drilled from a borehole using a diamond-studded bit, which is hollow in the middle.  Cores are a common way to study subsurface rocks in the petroleum and economic geology industry.  They’re also the primary way we study deep sea sediments.  However, the application of scientific drilling (i.e., not for industry) to continents has been a fairly recent phenomenon.  Fossils can be found in the core, particularly invertebrates and microfossils, but the primary goal of the core is not to recover vertebrate fossils.

sediment cores

Triassic sediment cores from Chinde Point. Image courtesy of the Colorado Plateau Coring Project.

SW: What do you do with this column of rock once you have it?

RI: We can do almost everything with the core that one would do with traditional rock samples from surficial outcrops.  The first step is to characterize the stratigraphy and sedimentology – to understand where in section we are and what depositional environments are represented.  The core is precisely oriented relative to both north and vertical, which allows us to look at paleomagnetism to develop a magnetic polarity stratigraphy.  We will take samples for radioisotopic dating, organic and inorganic geochemistry, etc.

SW: Where will most of the research take place?

RI: Once we finish drilling, the cores will go to University of Texas-Austin to be CT scanned.  They will then travel to LacCore at University of Minnesota where the cores will be split in half lengthwise, imaged, and analyzed for natural gamma radiation and other variables.  One half will be permanently archived at LacCore, and the other half will go to Rutgers University where the science party will meet to describe the core and sample it.  Most of the actual research will happen at a host of different institutions, including but not limited to Columbia University, Rutgers University, University of Texas-Dallas, University of Arizona, Berkeley Geochronology Center, University of Utah, and University of Oslo.  In addition to the PIs (Paul Olsen, Dennis Kent, John Geissman, George Gehrels, Roland Mundil, and myself), a number of graduate students and postdocs are involved in the project, and I’m sure undergraduates will be involved as well.

CPCP fieldwork is an all day, every day operation that lasts several weeks. Image courtesy of the Colorado Plateau Coring Project.

CPCP fieldwork is an all day, every day operation that lasts several weeks. Image courtesy of the Colorado Plateau Coring Project.

SW: How does coring differ from traditional paleontology fieldwork?

RI: The timeframe of drilling varies greatly, depending on the characteristics of the rock and how long of a core you want to drill (or how many cores).  This core will be somewhere between 450-500 meters long, and we expect it to take a couple of weeks to drill.  One big difference from traditional fieldwork is that drilling occurs 24 hours a day, 7 days a week.  The equipment is so expensive that it’s best to maximize time on the site.  We work in two twelve hour shifts – in this case one from 8am to 8pm, and another from 8pm to 8am.  The crew consists of two to three drilling staff from the contracted drilling firm, and 3-5 folks on the science team who log and process the core as it comes out of the ground.

SW: Why can’t you get these data from looking at rocks on the surface?

RI: The two main keys to the core are that it gives you unambiguous stratigraphic superposition, and completely unweathered fresh rock. What the first point means is that you know that you have a single column of rock and don’t have to worry about inferences from horizontal stratigraphic correlation. In most cases the advantage of the core over sampling surficial outcrop is data quality and resolution.  For detailed sedimentologic/stratigraphic, paleomagnetic, and geochemical sampling, one would have to dig trenches at least 1-2 meters deep to reach fresh unweathered rock. The time it takes to do this limits the density of sampling to a couple of samples per meter at best, and would take many months to complete over the ~450 meters of section we are coring.  One other main benefit of our core is an innovation of my co-PI Dennis Kent – drilling the core at a 30° angle from vertical.  This means we can very precisely orient the samples for paleomagnetic work, and it gives us more rock per stratigraphic layer, which is useful when you’re taking so many samples from a 2.5 inch diameter core.

The outside of a hill is weathered and potentially chemically altered. Cores sample unaltered rock from the inside of the hill. They can also sample below ground.

Rocks on the surface are weathered and chemically altered from exposure to the environment. Cores sample unaltered, unweathered rock in a single column, and can sample far below ground, which is hard to reach with shovels and picks. Sampling at an angle results in more rock to analyze (the diagonal is longer than the vertical).

SW: Why hasn’t coring been attempted before?

RI: The proximate reason is cost – this core costs just under US $1 million, and that doesn’t include any of the science we’ll be doing.  That being said, scientific continental drilling is quickly becoming more common in deep time rocks (i.e., before the Pleistocene), particularly as specific funding sources for these types of projects are becoming available.  A broader answer is that as scientists refine their scientific questions, we need better age control and data resolution, so we haven’t necessarily needed the resolution provided by coring until recently.

SW: Why did you start with Petrified Forest?

RI: We wanted to start with a core that was both logistically manageable and maximized integration of existing data. Petrified Forest National Park has been a great partner in the project, and has been very supportive the entire way.  They’ve provided housing for the science team, and encouraged visitors to stop by to learn about CPCP.  We’re drilling in the gravel parking lot at Chinde Point, so its easy to get equipment/personnel in and out, and that way we’re also not adversely affecting any park resources.  The Triassic rocks at Petrified Forest NP and surrounding areas have been well-studied for quite a while, so there’s a very large dataset of environmental and paleontologic information that we can immediately integrate with the core to get a holistic picture of the story during the Middle and Late Triassic.

SW:  How many of these cores do you have scheduled and where else are you going to drill?

RI: Currently we are focusing on the first core at Petrified Forest National Park, which will cover nearly all of the Upper Triassic Chinle Formation and all of the Lower-Middle Triassic Moenkopi Formation.  Some late-breaking news is that we’ve just received additional supplemental funding from the International Continental Drilling Program (ICDP) to drill a second shorter core in the Chinle Fm in the southern part of the park. This will allow us to precisely test using geochronology the stratigraphic correlations that have been proposed between the northern and southern part of the park, and therefore also test the biostratigraphic schemes built on these correlations (e.g., Parker & Martz 2011).  This is particularly relevant for understanding the biotic turnover at ~215 Ma that might correlate with the Manicouagan impact event in Quebec. In the longer term, we have plans to core a total of five sites across the Colorado Plateau, which span rocks that range in age from 250 million years old to 145 million years old.  Coring of these future sites will require additional separate funding.

The Manicouagan crater in northern Quebec is an  impact crater so large it can be observed from space. The impact occurred at the end of the Triassic. Image in the public doman, originally from NASA and accessed on Wikipedia.

The Manicouagan crater in northern Quebec is an impact crater so large (70 km diameter) that it can be seen from space. The impact occurred at the end of the Triassic (~212 million years ago). Image in the public domain, originally from NASA and accessed on Wikipedia.

SW: Who is funding the CPCP, and how long did it take to get the money together for such a big endeavor?

RI: The Petrified Forest core is graciously funded by the National Science Foundation and International Continental Drilling Program.  Just the costs associated with the drilling alone are almost US $1 million.  The project was initiated with workshops in 2007 and 2009, and we submitted our first proposals for funding in late 2009.

SW: Are there economic benefits or museum exhibits planned? Will the research benefit people outside the sciences? 

RI: There are definitely plans for a strong component of outreach and communication about the results of the project, through exhibits and public programs at Petrified Forest National Park as well as at each PI’s individual institution.  In fact, the drilling site itself can be visited by anyone who is visiting the park – so we’re an active ‘living exhibit’ at the moment.  The research that will come out of the core has direct societal benefits in that it will elucidate how ecosystems change in a warming world with high CO2, something we all face with anthropogenic climate change over the next century.  The project directly or indirectly supports dozens of jobs in the drilling industry, both through the drilling contractor itself as well as a wide variety of sub-contractors for everything from drilling mud to water supply to rental of generators and work lights.

SW: Thanks so much for all your time, Randy! How can we keep track of CPCP progress between now and publication?  

RI: The best way to follow the CPCP is via our Facebook page and blog.  I should give a shout out to Steven Seppi for designing the beautiful project logo.

——-
Literature cited: Parker WG  and JW Martz. 2011. The Late Triassic (Norian) Adamanian-Revueltian tetrapod faunal transition in the Chinle Formation of Petrified Forest National Park, Arizona. Earth and Environmental Science Transactions of the Royal Society of Edinburgh 101: 231-260.

Category: Climate Change, Geology, Paleontology | Tagged , , , , | Comments Off

Geologic time vs. absolute time

Tomorrow I’ll post an interview with Dr. Randall Irmis, a geologist and paleobiologist working on the Colorado Plateau Coring Project. Today, I offer some background information on the geologic time scale and why it is so hard to figure out how old rocks are.

Earth’s history is divided into different chunks of geologic time, going all the way back to the formation of our planet. Unlike calendars or clocks, which divide time into units of equal length (e.g., days or seconds), the divisions of geologic time aren’t the same length.  For example, the Mesozoic Era was ~186 million years long, whereas the preceding Paleozoic Era lasted ~289 million years. At 2.6 million years, the Pleistocene Epoch was much shorter than the Miocene Epoch (20.4 million years long).  These divisions may seem arbitrary at first, but they’re not; geologic time is based on the succession of rock layers. Geologic time was the first method scientists used to understand the sequence of events in Earth’s history. More recently, we’ve used other methods to associate actual dates with different rock layers, thus linking geologic time (a relative method) with absolute time (= numbers of years old). This merger of geologic time and absolute time is the geologic time scale. (Don’t have a geologic time scale handy? Get one here for free!)

Geologic time is hard to sort out. The first step requires understanding the relative order of the rock layers. For almost 1000 years, we’ve recognized that rock layers are organized in the order in which they were deposited. This idea was first put forth by the Persian polymath Avicenna, and later presented more formally by the geologist and Catholic bishop Nicholas Steno. They proposed that within a vertical column of rock layers, the oldest ones are on the bottom, and the youngest are on top. Today, we call this the principle of superposition. Related to superposition is the principle of original horizontality, which just means that rock layers are more or less horizontal when they are first deposited. Horizontality is important because today’s rocks are not always in their original orientation.

According to the principle of superposition, each rock layer is younger than the one it sits on, and older than the one it lies beneath. In this image, layer I is the oldest layer, and layer A is the youngest.   Image © 2013 Sarah Werning.

Superposition: each rock layer is younger than the one it sits on, and older than the one it lies beneath. In this image, layer I is the oldest layer, and layer A is the youngest.

Of course, the real world is more complicated than the above image. After rock layers form, their position can change through faulting or deformation. For example, the entire column can become tilted, in which case the rock layers get older or younger as you move horizontally along the ground, rather than vertically up a cliff:

syncline! look it up!

Tilted rock layers in the Rainbow Basin Natural Area near Barstow, CA. The rocks were originally deposited as a stack of horizontal layers but were later tilted through geologic processes. As you move from left to right in this picture, the rock layers go from oldest to youngest. Image © 2008 Sarah Werning.

There’s no place on Earth where rock layers going back to the beginning of the planet are visible all in one place, for several reasons. First, some of the layers are underground, so even if they’re present, we can’t always see them. Second, conditions aren’t always ideal for new rock formation, so there are times/places where new rock layers aren’t deposited. Also, rock layers erode at different rates in different places. For example, if there is a river running between two hills, the old rock layers will erode faster there than at the top of the hills. New rock layers are more likely to form in the riverbed and adjacent floodplains than on the hilltops. Different rates of erosion, deposition, and tectonic activity mean that the relative order of rock layers can be difficult to sort out in some places. To illustrate, look at the first image of rock layers above, with layers A through I. Let’s pretend that after layer A was deposited, a river carved out a valley:

CPCP layers erodedDepending on which  mountain you’re on, you might not see layers B or C. Also, there is no trace of layer A in this whole region, although it may be preserved somewhere else. Now, let’s say that after some more time, sediments accumulate in the valley and new rock layers begin to form:CPCP layers eroded new These processes occur over thousands or millions of years, so we can’t observe them in real time. But we can reconstruct the relative sequence of some events. For example, Layer 1 is older than layers 2, 3, and 4, which lie on top of it (thanks, superposition!). Layer 1 is younger than layer E (and F, G, H, and I), because it sits on top of E. Based on how layers 1-4 fill in the valley, we can also conclude that the erosion creating the valley likely happened after layer C was deposited. However,  in order to figure out if layer 1 is younger than layer B, we would need to look at another mountain that preserved both B and 1 in the same vertical column.

Once you have the correct order of your rock layers sorted out, you can begin to associate the rock columns in your area with columns in other regions. If at least one rock layer stretches for miles and miles, it’s easy to confirm you’re dealing with the same layer. In the image below, you can just walk along the grey layer from point 1 to 2 to establish that it’s the same layer in both places. You might then hypothesize that the red layers are the same layer, based on their position relative to the grey layer.

CPCP walk outcrop

More often than not, aligning rock columns is more complicated than this. Parts of your column might be underground, you might be missing rock layers from erosion, and/or the layers might vary regionally in thickness. Also, not all rocks deposited at the same point in time are identical. The appearance of rock layers depends on the local chemical and environmental conditions when they formed. Layers forming under the deep ocean will look very different than those forming in a coral reef, riverbed, desert, or swamp. Even more confusing, if environmental conditions are very similar, rocks deposited at two different points in time might look similar. So what’s a geologist to do?

One line of evidence for simultaneous deposition is when two layers contain the same fossil species. This is much easier to do for oceanic rock layers, because some ocean species (e.g., foraminifera, conodonts) are found around the globe. The types and sequence of these fossils can be helpful in lining up distant rock columns.

layers with seaLet’s say columns 1, 2, and 3 are rock columns separated by thousands of miles. In this picture, fossils are white, blue layers were deposited underwater, and the other colors formed in terrestrial environments. Columns 1 and 3 are mostly terrestrial, but there are three times when the ocean invaded the land – times of high sea level or inland seas. Because the oceanic fossil species are identical, these are probably the same layers seen in column 2; if so, these layers represent the same points in time in all three columns. The sequence of the oceanic fossil species is important, too: triangles, then hearts, then circles in all three columns. It’s more evidence that we are dealing with the same overall sequence of events. If these are the same oceanic layers  in columns 1 and 3, that means that the terrestrial layers between them are roughly correlated in time (I say “roughly” because there might be erosion or deposition gaps in one or both of the columns). Using the sequence of fossil species to correlate rock layers across big distances is called biostratigraphy, and it was extremely important for understanding the basic succession of rock layers on a global scale. Biostratigraphy is still important today for oil exploration, and is also used to align bores when drilling tunnels.

Once scientists had the rock layers aligned and their basic relative sequence sorted out, they noticed large-scale patterns in the succession of the fossils at a global scale. For example,  individual species of ammonites were good for correlating very small chunks of the rock record. At the same relative point in the rock column, all ammonite species disappeared in rock formations all around the world. Globally, blastoids, trilobites, and acanthodians were common in oceanic rocks up until a certain point, after which those types of fossils were never found again. Above that point, totally different types of fossils were found, such as plesiosaurs. Similar patterns were found in oceanic fossils as in terrestrial animal and plant fossils. Because these major shifts in fossil faunas and floras occurred simultaneously all around the world, biostratigraphers recognized that they could be used to bracket and define major regions of the rock column. Smaller shifts (between species rather than faunas) could be used to bracket smaller subregions of the rock column.

This is still how geologic time divisions are defined; saying “Triassic Period” is just shorthand for “the time represented by the chunk of the global geologic column between when we first see the conodont species Hindeodus parvus, up until we start to see the ammonite Psiloceras spelae tirolicum and the foraminiferan Praegubkinella turgescens” (seriously).

Metapolygnathus praecommunisti

Triassic conodonts. Image modified from Mazza et al. (2011), figure 2.

You might be asking yourself, “Well, if the fossils define the geologic time periods, isn’t it circular to use geologic time to tell us how long ago those fossils lived?”

Good question, but no. Remember that geologic time only tells you relatively how old something is; it doesn’t give us an age in terms of number of years ago. Let’s use this analogy: my High School Era is defined as “the time between when I first started attending high school up until I graduated high school”.  In the stratigraphic column of my life, the High School Era came after the Junior High Era, before the Undergraduate Era, and partially overlapped with the I Worked At A Movie Theater Epoch. If I find an essay I wrote for Mrs. Strutzel’s AP English class, I can tell you that it was written sometime during High School Era, and therefore before Undergraduate Era. But that doesn’t tell you how old I was in high school, or how many years ago that happened.

Can you believe those early-2000s fashions? Good Lord!

Sometime during the I Worked At A Movie Theater Epoch.

To find out how old something is in terms of years, you need a different metric, one that can determine absolute time. One common way to do this is radiometric dating. Radioactive isotopes are unstable. They break down (decay) over time, until they become stable isotopes (ones that don’t decay). Each radioactive isotope decays at a specific rate and results in specific stable isotopes – these are just basic properties of the atoms themselves. To estimate when that process started, you first take a substance and figure out its ratio between the radioactive isotopes and the stable (post-decay) isotopes. Then, you can use the rate of isotopic decay (also known as the half-life) to determine how many years of decay it took to result in that ratio – in other words, how many years since the process began, when the substance was 100% radioactive isotope and 0% stable isotope.

Carbon-14 is a radioactive isotope you’ve probably heard of. We use carbon dating to determine the ages of once-living things because it is present in plant and animal tissues. Carbon-14 decays pretty fast; a rate of 50% decay every 5,730 years. That rate of decay means Carbon-14 will completely convert to the stable isotopes Carbon-12 and Carbon-13 within ~60,000 years. This is a long time compared to the High School Era, but really short compared to the age of most rocks. So, we use other isotopes to date rocks; ones that decay at a slower rate. Common methods for dating rocks include uranium-lead dating and potassium-argon dating. These isotopes have much slower rates of decay (i.e., longer half-lives): the radioactive Uranium-235 converts to Lead-207 at a rate of 50% every 704 million years, and Potassium-40 converts to Argon-40 at a rate of 50% every 1.3 billion years.

Using radiometric dating methods, we can link absolute time to geologic time. These methods have already been used to date the rock layers containing the oceanic fossils that define and bracket the divisions of geologic time. So we now know how long each major division of geologic time lasted. Radiometric methods also have been used to date some terrestrial rock layers. Rather than roughly correlating terrestrial layers based on their associations with oceanic rock layers, we can now compare dates of terrestrial layers directly. As more and more rock layers are tagged with absolute dates, the geologic time scale is getting finer and finer resolution. As a result, we have a much better understanding the timing of events in Earth’s history and in Life’s history.

Tomorrow, I’ll talk more about a major new NSF-funded project that is extremely important both for aligning rock columns (calibrating geologic time) and putting absolute dates on individual rock layers (calibrating absolute time) from the Triassic Period.

Category: Background, Geology, Paleontology | Tagged , , , , | 8 Comments

Counterpoint: Proposed USFS regulations are good for paleontology and the American people

[From time to time on The Integrative Paleontologists, we will invite guest bloggers to share alternate viewpoints about current topics. Today we feature a guest post from Matthew Brown, Vertebrate Paleontology Laboratories Manager at The University of Texas at Austin.]

The open comment period initiated by the publication of US Forest Service draft regulations in the Federal Register has sparked intense interest from the academic paleontology community (e.g., here and here). This is a great thing! However, both public and private discussions in recent weeks suffer in some ways from a lack of big picture perspective, and illuminate persistent misunderstandings about the responsibilities of public land managers to their resources. As an academic paleontologist, I argue that the draft proposal does not endanger research on Federal lands, contrary to points made by other scientists who wish to amend the regulations. In fact, it should only serve to strengthen research. The proposed regulations are asking for basic due diligence in scientific and collections methodology.

To summarize the protests, there is dissatisfaction with the requirement for USFS permission to undertake certain kinds of research. No one in this debate has contested the public ownership of vertebrate fossils from Federal lands. Federal agencies (USFS, NPS, BLM, etc.) are in the business of resource management, which includes balancing scientific research, public enjoyment, conservation, and commercial interests. Academic researchers are but one group of stakeholders in a diverse sphere of use, and academic institutions just one type of custodian for public resources. However, there remains a misconception about the role of custodianship within the museum community. This is not unique to paleontology, by the way; a number of museum groups have expressed discontent with the Federal system, especially directed toward the National Park Service.

The argument has been made that professional paleontologists and the museums they work for are best suited to make decisions about the well being of the specimens (see links above), assuming that they are more extensively trained (i.e., they are better equipped to assess the costs and benefits of various research techniques), and because they interact more regularly with the fossils in their care through research and curation. In many cases this claim may be true; though in fairness, many academically trained research paleontologists and collections managers are employed within the federal system. These are often the same individuals responsible for issuing permits and funding research projects in the first place, and many of them have advanced degrees in geology or paleontology. But even if the preceding argument was true, let us remember that Federal specimens housed in non-Federal collections are on loan to those institutions. They retain public ownership despite being held in non-Federal collections. Keeping that in mind, consider the following thought experiment.

Let’s say that my museum borrows a specimen from your museum for my research. Deciding that my 17 years of experience as a preparator, collections manager, and researcher qualifies me to make decisions about how to best analyze your specimens, I move forward with my project with no further communication to your museum. A few years later, you visit my museum, and open a drawer to find that I have sliced up some elements for histological analysis, ground up parts for isotopic analysis, loaned the skull to a grad student to mold the teeth for microwear analysis, that the student subsequently quit the program and no one can find your skull, and that I coated the remaining bones with Elmer’s Glue to “preserve” them. I also had the skull scanned and made the CT dataset available to a commercial company, who is now selling casts for profit. I got five great papers in top journals out of these studies, but I never sent you the references. You had no idea any of this took place, and when you asked me to return the loan and any data generated, I wrote to your museum director telling them that because this isn’t your area of expertise, you don’t have any business dictating how I do my job.

The described situation is not at all uncommon for inter-museum loans; any one aspect of this scenario should be familiar to anyone who has worked in collections for any length of time. Granted, it is highly unlikely for all examples to be represented in one loan; nonetheless, you wouldn’t be happy about encountering any of these facets in a loan returned to your institution. Yet this situation is precisely the kind of unilateral decision making that museums are calling for when it comes to doing research on publicly owned fossils.

Vertebrate fossils found on Federal lands belong to the American people, and the Federal agencies, under US law, are responsible for their care. The policies of the US Forest Service, National Park Service, Bureau of Land Management, etc., are in place to protect the agencies, the resources, and the public from mismanagement. Certainly museums and researchers play a significant role as partners in the custodianship, but the Federal employees are the individuals responsible to Congress and to the public for the well being of those fossil specimens, and for balancing the needs of the diverse group of stakeholders with an interest in them. This fact cannot be changed through policy; it is regulated by United States law. It doesn’t matter if we think the policy places undue burden on researchers; the policy is written so that the agencies are compliant with Federal law.

The bottom line in these proposed regulations is accountability: accountability of the researchers to the land managers, of the land managers to Congress, and of Congress to the American people. To be sure, the Feds have not always been the greatest partners to academia, but of course the reverse is equally true. There are certainly not enough paleontologists in the Federal system; this is indeed a major problem. But that situation won’t improve if we as a scientific community fight the very regulations that lead to the creation of government research and resource management positions.

We already accept similar accountability in other aspects in our roles as shared custodians of these public resources, and they work to our ultimate benefit. For example, no museum should ever collect specimens under casual use provisions; research permits are an instrument to allow the land agencies to monitor land use, justify funding land maintenance, research projects, and government paleontology positions. It also prevents conflicting research and unnecessary destruction of public lands. Here, accountability prevents wasted public dollars and establishes that researchers are good partners in caring for fossil resources. Requiring specific permission and subsequent reporting is not an exercise in power trips. These are responsible accounting practices that demonstrate responsible use and support future research.

The core argument against the proposed provisions of USFS policy is that the expertise does not exist in the government system to make sound decisions in the best interest of specimens or research. However, this position abdicates the responsibility of researchers to educate those same land managers about the importance of their research and the resources. It also denies the federal agencies real data on how these resources are being used; data that can be used to justify further research, and further positions to enable that research. We as an academic community should be celebrating the opportunity to open positions in the Federal system for paleontologists. I have approximately 15 paleontology graduate students in my department who will graduate in the next few years. Will 15 curatorial or faculty positions in paleontology be available in that time? Probably not, given the state of most university and museum budgets. This leaves the Federal government as one of the few growth sectors in the science.

Sure, the proposed regulations may create more work for individual paleontologists. But conducting real science is hard, and the steps that the USFS and other entities are asking for strengthen the quality of that research, not hobble it. The system of permissions for sampling and analysis is a system of communication. If researchers are not communicating their desires (and research needs) to the agencies, then they are not doing their job as scientists and research partners in the use of these fossil resources. Refusal to work on Federal lands because the land managers want to know what is being collected, what is being done with the specimens, and ensuring accountability is petulant and shortsighted. The museum community reaction to proposed USFS regulations is the part of the conversation that is bad for paleontology.

Matthew A. Brown is the Vertebrate Paleontology Laboratories Manager at The University of Texas at Austin, and is closing in on 20 years of work in public and private universities, museums, and parks. He has conducted and participated in field work in NPS, BLM, USFS, and Peruvian National Park Service units, and has prepared, molded and cast, and destructively sampled fossil specimens from many of them. He is currently volunteering as Scientist-in-Residence at Petrified Forest National Park.

Category: Government, Museums, Paleontology | Tagged , , | 9 Comments

Sharing Paleodata (Part 2): Dryad

As promised, today I begin a series on repositories used for paleontological raw data. I will focusing on repositories to which data is submitted before publication, so that mention of it can appear in the manuscript. If you didn’t read the comments section of my last post, Mark Uhen and colleagues published an article about this exact topic a few months ago:

Uhen, MD, et al. 2013. From card catalogs to computers: Databases in vertebrate paleontology. Journal of Vertebrate Paleontology 33: 13-28.

I didn’t know about this article when I began planning this series, but now that I’ve read it, I think my series will complement that piece nicely. As luck would have it, I wound up gathering a lot of the same types of information about each database. To avoid immediate redundancy, I’m starting with a repository Uhen et al. did not report on, Dryad.

Print

DRYAD (http://datadryad.org/)

Full disclosure: The statements about Dryad in the “Nitty Gritty” section were checked for accuracy by Laura Wendell, Dryad Project Manager. Thanks! My impressions are my own. Also, I haven’t submitted any of my data to Dryad yet, but I have downloaded data from it.

Impressions: This repository is the most important omission from Uhen et al. (2013), especially considering that Evolution, Systematic Biology, and Journal of Paleontology are among the integrated, sponsoring journals.

There are several advantages to using Dryad. First, so many people are using it, for so many different journals. Being part of a large data clearinghouse makes your data more discoverable. Also, Dryad is big on quality control; every file is checked for usability and sensitive information before posting. You don’t have to worry about viruses or bad files. All my downloads have worked smoothly regardless of filetype. Additionally, they take care of making the data go live when the paper is published online, and you can append the file if you missed something or made an error the first time, while keeping the original file too.

Dryad hosts an impressive range of filetypes. Nexus and Excel files are among the most common, but images (2D, CT, video) and other analysis files (BEAST, Structure, etc.) are also present. Because it’s so versatile, Dryad can be used to complement other open data. For example, you can only accession sequences and annotations in GenBank, not alignments or nexus files. GenBank gets more traffic than Dryad, so the sequences should still go there, but the analysis files can go up on Dryad. It takes so much effort to get a Structure file working sometimes; why limit its use to yourself? Another thing to consider: though GenBank numbers are cited by users down the road, the original papers that produce aren’t always. When Dryad files are cited, both the dataset and the original paper tend to appear in the references section (see below). You can boost your citations this way.

The website is easy for users to navigate; you can search by keyword, author, paper title, and journal (or anything, really). The search function works quickly but isn’t especially smart (e.g., a search for ‘paleontology’ won’t bring up articles with ‘palaeontology’). Clicking on an article brings up all the data files, example citations for the article and data package, and usually a link to the original article. My colleagues who have used Dryad as submitters assure me that the submission process is smooth (it’s streamlined into the manuscript process for some journals), but I can’t speak to that.

Negatives? Hard to think of any. I wish the keywords on the article pages linked to other articles with those keywords, but that’s a small quibble. In the near future, you’ll have to pay to use Dryad – I think the price is reasonable for permanently archiving your data, but some may balk.

Bottom line: Grant writers should feel comfortable listing Dryad in their Data Management Plan because it’s safe, easy to use, and your reviewers will (should) have heard of it; reviewers should feel comfortable asking authors post data to Dryad when appropriate, for the same reasons.

dryad

The Dryad, by Evelyn De Morgan (1855-1919). Image in the public domain and accessed via Wikimedia Commons.

DRYAD: THE NITTY GRITTY

What it is: International repository for the data associated with peer-reviewed scientific publications. All types of data are welcome, but life sciences and medical data are most common.

What it is, in their words: “Dryad is a nonprofit repository for data underlying the international scientific and medical literature.”

Who runs it: Dryad, a nonprofit. The members (organizations, not individuals) elect a board of directors annually. Currently these are mostly people who work in academic publishing or information technology, or or do government, academic or industry research.

Who funds it: Initially funded by the NSF. Moving forward, Dryad will stay sustainable through a combination of membership fees and submission fees (to cover operating costs like maintaining and curating the data) and grants from private and government sources (to cover research and development costs). Dryad also hopes that funding agencies, especially those that require a data management plan, will be amenable to grantees using grant funds to pay the submission fee (more here).

Who uses it: Researchers who submit or use data; Many life sciences journals that require data to be posted on Dryad.

Cost to submit: Submitters pay an $80 fee per data package on submission (starting 1 Sept 2013), unless the journal contracts with Dryad to pay the fee, or the submitter is from an economically disadvantaged country. Additional fees apply to users who submit through non-integrated journals ($10) or have very large datasets (10+ GB; $15). Fees list here.

Cost to access: Free to individuals and to institutions. So… free.

Data and file types supported: Most; they don’t restrict based on filetype. Files should be data, but data includes text, tables, spreadsheets, images, CT data, finite element models, video, photos, nexus files, software code, compressed file archives. Non-data files may also be submitted, if they are “integral to the publication and can be released in the public domain”.

File sizes allowed: 10GB limit per project; more is ok, but you’ll pay a small fee starting 1 September 2013.

Copyright status: All files are CC0.

Data available during peer review? Yes, depending on the journal.

Allowed to post data from previous pubs? “Data that was originally collected for another publication may be submitted as long as it is referenced by the current publication.” In other words, you need to be citing the data in a new manuscript; you’re not supposed to create projects for projects you’re completely done with. However, it’s clear from my searches that some users are uploading data from previous publications. I’m not naming names because I think it’s a good idea. Also, it seems like some journals (e.g., Systematic Biology) may be posting all their old data files to Dryad. If so, I heartily applaud the effort and suggest more journals do the same.

Accession numbers provided? A unique DOI is provided. Dryad registers it for you after checking the data. Because you list this in the publication itself, the data submission process begins early (though this varies by journal).

Data goes live when: Varies by journal, but generally, when the publication goes live online at the publisher’s site. For some journals, you can embargo data for up to a year after the paper is published. Dryad does all this for you.

Data is backed up? Yes (CLOCKSS)

Stats provided? Page views and file downloads are visible on each page.

How to cite your data in your manuscript? Dryad doesn’t have a requirement; this varies by journal anyway. Dryad recommends an in-text citation, something like:

Data available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.j2m25n82 (but where ‘j2m25n82’ is replaced with a code unique to your project).

How to cite someone else’s data you download and use in a new manuscript? Dryad doesn’t have a requirement, but recommends a data citation in-text (see above) AND in the references section. This is in addition to citing the original article, and would look something like:

Valentine JW, Jablonski D, Krug AZ, and Berke SK. 2013. The sampling and estimation of marine paleodiversity patterns: implications of a Pliocene model. Paleobiology 39(1): 1-20.
Valentine JW, Jablonski D, Krug AZ, and Berke SK. 2013. Data from: The sampling and estimation of marine paleodiversity patterns: implications of a Pliocene model. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.42577

Can update after publication? Yes (But the original version is not editable).

Benefits in a nutshell:

  • Dryad checks each submission to make sure all files work, scans for viruses, checks for copyright status and sensitive data.
  • Already linked with several journals. It’s even integrated with some journals, so data submission to Dryad is part of the manuscript submission process.
  • Can link data packages directly to/from GenBank, TreeBASE, or other specialized repositories.
  • Everyone else is using it (multi-disciplinary across the life sciences).

Three recent paleo papers using it:
Ksepka DT, Balanoff AM, Bell MA, Houseman MD (2013) Fossil grebes from the Truckee Formation (Miocene) of Nevada and a new phylogenetic analysis of Podicipediformes (Aves). Palaeontology, online in advance of printDryad data package here.

Olori JC (2013) Ontogenetic sequence reconstruction and sequence polymorphism in extinct taxa: an example using early tetrapods (Tetrapoda: Lepospondyli). Paleobiology 39(3): 400-428Dryad data package here.

Wood HM, Matzke NJ, Gillespie RG, Griswold CE (2012) Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders. Systematic Biology 62(2): 264-284. Dryad data package here.

Category: Open Access, Open Data, Paleontology, Review, Technology, Zoology | Tagged , , | 5 Comments

Sharing paleodata (Part 1): What databases are out there?

Science depends on the ability to make observations, repeat experiments, test hypotheses, and share knowledge. When a new study comes out, other researchers evaluate an author’s arguments based on the data they present and the analyses they perform. This is why most journals require that at least some of the original data be included as part of the manuscript.  Without access to the original data, science loses that critical requirement of repeatability.

Original data can be a description: “This is what the anatomy looks like, and here is a picture showing that feature”. Other times, it’s a table of measurements or a map of locations. Original data can also take the form of a chart or graph that summarizes the individual data points and reports trends for the group. Depending on the study, the number of data points you used might be 20, or 20,000. You might have to write new software to run a specific analysis. Printed in a journal, the spreadsheet or code involved could take up hundreds of pages. In these cases it’s impractical to publish all of the original data or code in printed format. But you still need that data and code for the work to be repeatable.

My particular line of research involves the examination of bone tissues in order to study the growth patterns of living and fossil animals. The primary data I use are microscopic bone tissue characters (the number or shape of bone cells, patterns or orientation of blood vessels) that vary in appearance around the slide. It’s hard to reproduce images in a print journal at the size and resolution others need to verify my observations, much less enough to capture variation around the slide.  To make my observations verifiable or repeatable, you need an enormous image – ideally, the whole slide, at high resolution and decent magnification (say, 4x or 5x). Even if the file sizes were reasonable (they’re not – I create a lot of gigapixel images), a printed version that allowed you to see all the bone cells and blood vessels would be more like a map in size than a page of a journal.

OMNH 34784 Tenonto tibia CL T1-2 BF 4xMOR tiny

It is hard to see the histological details of an image this size (click on the image for slightly larger one). Go to MorphoBank to see it large enough to examine histological details. Image (c) 2012 Sarah Werning / The Sam Noble Oklahoma Museum of Natural History.

How to solve this? Some researchers publish data to their own websites. For example, Drew Lee (Midwestern University) posts high-resolution histology images on his Paleohistology Repository. Larry Witmer’s lab (Ohio University) posts 3D visualizations of their CT data on their website, along with a bunch of downloadable interactive projects on animal anatomy. Emma Schachner (University of Utah) posts supplemental images, posters, and other ancillary images to her website, www.theropoda.com. These are pretty spectacular, but not every researcher has the time to maintain a data site, and eventually the researcher that owns them won’t be around to maintain them. So while they fill the gap now, this is not an ideal longterm solution.

Most academic journals allow you to publish online supplementary materials, including ginormous spreadsheets or software code (ginormous images are sometimes problematic – some journals limit uploaded files to 10MB). So while the data is usually out there, even in this form it’s not always accessible. You might need to subscribe to the journal to access it, or the file could get lost over time (I know the latter seems ridiculous, but unfortunately, it’s not uncommon for older papers, or when journals change publishers).

Even if the data is easy to access, comparing it in a meaningful way could require pulling together hundreds or thousands of sources. In these cases, a sort of universal clearinghouse for data would be ideal. These exist, for certain types of data. For example, almost all journals published in the US (and elsewhere) require anyone whose data includes a new genetic sequence to upload it to GenBank before publication. GenBank is a database maintained by the National Center for Biotechnology Information (NCBI), a subdivision of the National Institutes of Health (NIH). GenBank shares and synchronizes data with two similar databases (one in Europe and one in Japan) as part of the International Nucleotide Sequence Database Collection (INSDC). GenBank assigns a unique accession number to each sequence, and these are reported in the paper when it is published.

UCMP77305_Isoodon_sm

There is no standard repository for measurements or morphological data, but I outline some options below. UCMP 77305, Isoodon femur. (c) 2013 Sarah Werning

The advantage to hosting your raw data on publicly-accessible databases or data clearinghouses is clear: researchers around the globe have access to your sequences and can discover them easily, even if they weren’t familiar with your original paper before running a search. If you receive federal funding (say, from the NSF), it’s now also required. Every grant proposal submitted to NSF requires a Data Management Plan, which explains how the grantee will share “the primary data, samples, physical collections and other supporting materials created or gathered in the course of work” at “at no more than incremental cost and within a reasonable time”.

There’s no universal designated clearinghouse for bone measurements or pictures of fossil histology (yet), but a number of databases and repositories have sprung up in the last ten years that host different types of data. A few of these (for example, Dryad) have become the repository of choice for multiple journals, the first steps toward the type of data clearinghouses I described above.

Because paleontology is so interdisciplinary and draws on so many types of information, our data can be found in a number of repositories (in addition to supplemental information hosted on journals’ sites). There so many options for a paleontologist who wants to share data that it might be hard to keep them straight. Over my next few blog posts, I’ll be discussing some of the common data repositories used by paleontologists. For each of these, I’ll give pertinent information, such as funding sources/costs and site features/limitations, discuss my thoughts on usability, and highlight some recent paleo papers that take advantage of these databases. My hope is to assemble a comparative guide for paleodata repositories over the next month or so. The first of these will go up on Wednesday and discuss Dryad (mentioned above). Other sites I will discuss in the near future include Figshare, MorphoBank, and Morphbank: Biological Imaging.

repository logos

Coming soon: I review all of these. Clockwise from top left: MorphoBank, MorphBank: Biological Imaging, Dryad, Figshare.

Today, I’ll leave you with a list of some of the data repositories I’ve used and encountered in my paleontological research, along with a brief description of the type of data they host. Please post good suggestions for additions to this list in the comments.

 

SARAH’s REPOSITORY REPOSITORY

A comprehensive list of data repositories can be found at Databib. However, not all of these are data repositories in the sense that you can use them to host the data for a given manuscript (some of them just provide data summaries). Particularly useful to me is this list of  Biological Science Databases: http://databib.org/index_subjects.php#Bio

The remainder of these sites are ones you can use to host your own data (some restrictions may apply).

AMCED: http://rruff.geo.arizona.edu/AMS/amcsd.php (crystal structures)

Biomesh: http://www.biomesh.org/ (FEA models for biology)

data.gov: http://www.data.gov/ (science data generated by state- and federally-funded agencies)

Digimorph: http://www.digimorph.org/ (CT data)

Dryad: http://datadryad.org/ (all types of data)

ESA Data Registry: http://data.esa.org/esa/style/skins/esa/index.jsp (ecological and environmental data)

GenBank: (http://www.ncbi.nlm.nih.gov/genbank/ (genetic sequences)

figshare: http://figshare.com (all types of data; explanatory media including figures, presentations, and posters)

miRBase: http://www.mirbase.org/ (microRNA sequences)

MorphBank: Biological Imaging: http://www.morphbank.net/ (phylogenetic data, morphology images)

MorphoBank: http://www.morphobank.org/ (phylogenetic data, morphology images)

Movebank: https://www.movebank.org/ (animal tracking data)

Neotoma: http://www.neotomadb.org/ (paleoecological data, including faunal occurrences and pollen data)

NOAA Paleoclimatology: http://www.ncdc.noaa.gov/paleo/paleo.html (paleoclimate data)

Paleobiology Database: http://paleodb.org/ (fossil occurrence data; some measurements)

Pangaea: http://www.pangaea.de/ (earth sciences data)

Protocolpedia: http://www.protocolpedia.com/ (lab protocols)

TreeBASE: http://treebase.org/ (phylogenetic trees and supporting data/files)

ZooBank: http://zoobank.org/ (official registry of zoological nomenclature)

Category: Open Data, Paleontology | Tagged , | 6 Comments

The [Fossil] Treasure of the Sierra Nevada

The Sierra Nevada mountain range is known for its gorgeous alpine lakes, magnificent peaks, and glacier-carved valleys. It’s home to five national parks and monuments, and the only place in the world you can see giant sequoias.  In various places, the peaks above hide an extensive cave system below. Some of these caves house a scientific treasure trove of fossils, and this summer the University of California Museum of Paleontology (UCMP) is using them to uncover the long-term record of California climate change.

The living vertebrates of the Sierra Nevada have been studied by Berkeley scientists for over 100 years. In 1911, Joseph Grinnell (director of the Museum of Vertebrate Zoology, or MVZ) began surveying  Yosemite National Park and Sequoia National Forest. These surveys were pretty intense, especially for that time: the Yosemite Survey alone required an incredible 957 person-days of fieldwork (the equivalent of one person working around the clock for almost three years). Over 4000 specimens were collected in Yosemite alone, accompanied by 3000+ pages of field notes and 700+ photographs (Moritz et al. 2008). The notes and photos are so detailed that the specimens can all be traced to their exact collection location. In other words, we have an extremely good record of which vertebrates were hanging out in the Sierra Nevada 100 years ago, and exactly where they were living.

Yosemite Transect

Joseph Grinnell’s original (1914-1920) transect of Yosemite National Park in the Sierra Nevada, eastern California. (c) Museum of Vertebrate Zoology, accessed here.

How does that compare to what lives there today? With support from the National Science Foundation (abstract here), MVZ researchers resurveyed Grinnell’s original collection sites to find out. Their results were shocking: half the species showed significant range shifts (Moritz et al. 2008). Higher-elevation (cold-dependent) species shrank their ranges to isolated mountaintops. Formerly low elevation (warm-tolerant) species now lived higher on the mountainside, but no longer at the base. If a temperature increase of just 3°C over 100 years affected so many species, what happens when mountaintops are no longer tall enough for animals to escape the heat? This could mean big trouble if global temperatures rise even just a little more.

But what if this was all a quirk? How would you know if the last 100 years indicated an alarming new trend, a weird century, or a return to normal?  The answer is simple: we can’t know until we can link the modern record to the fossil record.  In a previous post, I mentioned that paleontology puts the living world in context. It allows us to understand the relative magnitude of changes happening in today’s world. Paleontology unlocks context much farther back in time than we get from studying the modern record alone, even when the details are really good (like the MVZ’s Sierra surveys).

Fortunately, at Cal we have the Berkeley Initiative in Global Change Biology, whose goal is to bring about exactly that type of data integration. BIGCB brings together all sorts of researchers who study the effects of climate change on past, present, and future life. Together, these groups can address and answer questions at larger scales than any one team could address on their own. All of the Berkeley Natural History Museums are sharing data, as well as the University of California field stations, reserves, and experimental forests. Thus, our fossil data is integrated with that of specimens collected in historical times, in addition to ecological and climate data, information from lab experiments, and computer models.

Melissa is one of several UC Berkeley undergrads helping to catalog the Crystal Cave site.

Melissa is one of the UCMP’s elite team of undergrads helping to catalog Pleistocene fossils from California.

This summer at the UCMP, there’s a major push to identify and catalog undescribed material from the relatively recent fossil record of California, especially in areas where we have a great record of change on the 100-year scale. Ultimately, we want to compare the 100-year trend to what we see at the the 1000-, 10,000-, and 100,000-year scales. Dr. Pat Holroyd, one of the UCMP’s museum scientists, is supervising a team of Berkeley undergrads who are identifying and cataloging of fossils from the California Pleistocene (the geologic epoch that lasted from ~2.6 million to 11,700 years ago). They’re starting in the Sierra Nevada, at a site called Crystal Cavern 1. This cave site is in El Dorado County, about halfway between the MVZ’s Yosemite Transect and its Lassen Transect.

The caves under the Sierras and their foothills are pretty recent, geologically-speaking.  Stock (1918) estimated nearby Hawver Cave to be Rancholabrean (11,000-240,000 years old) based on the fossils he found there. We don’t yet know exactly how old the Crystal Cavern 1 fossils are, because we have not yet attempted to date them using radiometric methods. This would be a great project for an interested undergraduate or graduate student!

How did the fossils get there? Sometimes, animals fall into or get lost in caves, and they die before they can find their way out. Or they can be washed in when surface waters drains into the caves. There are a lot of underground rivers in the Sierra caves, and their normal ebbs and flows can build up concentrated deposits of bones over time. Pat says that based on the original description of the locality, the fossils were preserved in a layer of mud capped by flowstone. A lot of the specimens still have this mud and flowstone on them; this is usually cleaned off before they are put in boxes in our collections.

skunk jaws

These are jawbones of the striped skunk, Mephitis mephitis. The top specimen is bone from an animal collected by UCMP scientists in the last 100 years. The bottom two specimens are newly-cataloged fossils from Crystal Cavern 1.

The team has only been working for a week, and already they’ve sorted, identified, cataloged, and curated over 350 bones. If you’re interested in tracking their progress this summer, you can see a list of specimens at the Crystal Cavern 1 locality as they get added to the UCMP database here.

I asked Pat to show me some of the Crystal Cave specimens that she and the undergraduates identified, and she gladly obliged.  The site is definitely dominated by the small mammals that Shaena recently explained were so important to understanding climate change. As you might expect from a relatively recent fossil site, most of the fossils are from species that are still alive today, some of which still live in the area. Pat showed me a lot of mammal bones; these include striped and spotted skunks, wood rats, deer mice, squirrels, mule deer, and even mountain beavers.  There are a number of birds (including owls and California quail), and even a tiny lizard jaw. But there are also some extinct animals in the mix. The largest compare well to the extinct shrub-ox Euceratherium, fossils of which have never been discovered in the Sierra Nevada.

Other interesting finds include bones with tiny tooth marks where little rodents nibbled on the remains of larger vertebrates. I include a photo  below, because it’s so cool to see evidence of fossilized behavior, like scavenging:

Tiny rodent tooth marks are visible on the edge of some of the Crystal Cavern 1 fossils.

Tiny tooth marks are visible on the edge of some of the Crystal Cavern 1 fossils, like this mule deer jaw (click for larger image).

What I like most about this team is that it’s so diverse academically – we have history and psychology majors getting hands-on experience generating scientific data alongside our biologists. Even if they don’t go on to become scientists, they’re getting a first-hand understanding of what the process of science is like: where the data come from, what it takes to acquire it, how we test our ideas, and how individual pieces of data contribute to a larger research question. Best of all, Pat told me that at the end of the summer, the undergrads are going to help her write a scientific paper describing the Crystal Cavern 1 fauna. Our students are not only contributing to a better understanding of how an ecosystem changes with climate and time, but they’re contributing original research to the scientific literature. Everyone wins!

Our crack team of undergrad catalogers is being funded by the W.M. Keck Foundation, who in 2011 awarded UC Berkeley a $1.5 million grant to integrate data from UC Berkeley’s natural history museums, field stations, and labs (abstract here). The broader research initiative is also funded in partnership with the Gordon and Betty Moore Foundation, with seed money from Berkeley’s Office of the Vice Chancellor of Research (read more about BIGCB funding here). I tip my hat to all three organizations for understanding the importance of museum collections in addressing big picture questions about things like climate change. The sooner we integrate the modern and fossil records, the sooner we can sort out how big a change we’re dealing with.

References:
Stock C. 1918. University of California Publications (Bulletin of the Department of Geology) 10: 461-515. Read the whole volume for free here!

Moritz C et al. 2008. Science 322: 261-264. You can also connect with MVZ Curator Jim Patton on ResearchGate and get it here.

Category: Climate Change, Paleontology, Zoology | Tagged , , , , , | 3 Comments

How species are like pornography: Species concepts and the fossil record

Recently I helped name a new species, an animal we think is the oldest dinosaur found to date—if not, it’s the closest cousin to dinosaurs we know of (Nesbitt et al. 2013). It was the first time I’ve named a new species of anything, though given my profession, it’s likely I’ll get to name others in the future. Our new species (Nyasasaurus parringtoni) was described based on two partial specimens, which together comprise just twelve bones: a humerus (upper arm bone) and a bunch of vertebrae (back bones). You can see and download photos of all the bones of Nyasasaurus here, for free. Now, we don’t have a lot of bones to go on, and we don’t think Nyasasaurus was a one-armed, ridiculously short-backed dinosaur with no head. And two of my co-authors have shown there are other, closely-related animals found in the same rock formation (Nesbitt et al. 2010). So how did we know we were looking at a new species?

Nyasasaurus parringtoni: If not the grandmother of all dinosaurs, certainly a cousin close enough to bring on an extended vacation. Image (c) 2012 Natural History Museum, London and Mark Witton, and available here.

Nyasasaurus parringtoni: If not the grandmother of all dinosaurs, certainly a cousin close enough to bring on an extended vacation.
Image (c) 2012 Natural History Museum, London and Mark Witton, and available here.

For that matter, how does any paleontologist know they are looking at a new species? And what do we mean by the word “species”, anyway? Unfortunately, my answer to that is: it depends on who you talk to.

One common definition of “species” goes something like this: “a group of organisms that can interbreed in nature and produce fertile offspring, but that can’t mate with other groups and produce fertile offspring”. This way of defining species is called the biological species concept, and it centers around the observation that species tend to be isolated from other species, reproductively-speaking, even when they live in the same area.

Applying the biological species concept to fossil animals is problematic because it’s difficult to prove whether or not they were reproductively isolated from each other. Finding fossil vertebrates that died in the act of mating is pretty rare (though check out these lascivious turtles), but even when you find them, that tells you more about mate choice than mating isolation. In the fossil record, the best evidence for reproductive isolation is when organisms are separated by many millions of years, but even that doesn’t rule out a really long-lived species.

So, vertebrate paleontologists tend to think about fossil species using definitions other than the biological species concept (which, if you think about it, is also not so helpful for organisms that don’t have sex, or ones that hybridize easily, like plants). One common definition we use is called the morphological species concept, which more or less means “a group of organisms that shares anatomical characteristics within the group, which are not shared with other groups of organisms”. Basically, organisms that look similar to each other and different from everything else.

Go away, Larry. I'm trying to stay reproductively isolated from you. Image (c) 2007 José Nestor Cardoso, and available here on a CC BY-SA 3.0.

Go away, Larry. I’m trying to stay reproductively isolated from you.
Image  (c) 2007 José Nestor Cardoso, and available here on a CC BY-SA 3.0

Another common way we think about fossil species is the phylogenetic species concept, which requires an analysis of evolutionary relationships. Under this definition, species are the smallest groups of organisms that both share a common ancestor and are evolutionarily distinct from all the other groups on the tree. Anatomical characteristics are the data we use to reconstruct evolutionary relationships for fossil species, so in reality, most fossil vertebrate species are described using a hybrid method that takes into account both anatomy and evolutionary relationships. In the Nyasasaurus example above, the combination of anatomical features we see in those twelve bones are unique, and they fall out in a novel position on the dinosaur family tree.

It may be surprising that different scientists define species in different ways. A lot of this depends on what type of organism that person does their research on, because many definitions work really well for a particular group of organisms, but are completely inapplicable to other groups of organisms. If you’re a paleontologist, you won’t have much use for a definition that requires showing genetic isolation or genetic similarity, because it will be difficult to apply to most fossil organisms. Similarly, a bacteriologist might not find the morphological species concept too helpful when trying to sort out thousands of species that look identical under the microscope.

Interestingly, the idea that experts should determine which characteristics and species definition are most biologically relevant to the organisms they work on and define species that way is its own species concept: the taxonomic species concept. Though I feel that this is probably the most practical species concept (it’s basically what goes on now), it does have that unsatisfying “I know it when I see it” quality. Who would have guessed that species and pornography could be identified using the same, Supreme Court-sanctioned method?

lewd and lascivious turtles

New species or turtle porn? I know it when I see it.
Image from Joyce et al. (2012), available here.

The difficulty of finding and agreeing on a universal definition for “species” has led some biologists to doubt whether species are biologically real entities at all (Mishler 2010). Rather, they argue that species are arbitrary constructs that biologists impose on the natural world. I think that this viewpoint is a bit extreme; when organisms pass on their DNA in fundamentally different ways (sex vs. no sex, for example), why should we expect a one-size-fits-all definition of species to work?

However, if you use the taxonomic species concept, you have to acknowledge that all species are not exactly biologically equivalent to each other, because we use different methods to parse out what a species in each group. And our opinion of what a species is might be very different from the organisms’ opinion. With genetic data cheaper than ever to obtain, we’re just starting to discover how many species we’ve been lumping together because they look so similar. Despite anatomical similarity, these species have clearly been genetically isolated for many years. We call these groups “cryptic species”, and some types of organisms are much more likely to have cryptic species than other (see Bickford et al. 2007 for a review).

We already know that the fossil record is incomplete; even as good as it is, not every species will be preserved. Right off the bat, any estimate of past species diversity based on fossils is an underestimate. But even among the species we know about and have described, we’re going to miss all the cryptic species. Genetic studies of fossils are still technologically impossible for taxa that have been extinct for hundreds of millions of years, and the skeleton (or a small part of it, in the case of Nyasasaurus) is often all we have to go on. So what we call a fossil “species” might actually have involved several genetically distinct, reproductively isolated groups back in the day.

Now that we’re on the same page regarding how paleontologists think about fossil species, I’ll cover more of the nuts and bolts of how we figure out something is new to science next time. For more on species concepts, go here for the basicshere for a longer list, and here for a very thorough explanation.

References 

Bickford D, et al. 2007. Cryptic species as a window on diversity and conservation. TRENDS in Ecology and Evolution 22: 148-155.

Joyce WG, et al. 2012. Caught in the act: the first record of copulating fossil vertebrates. Biology Letters 8: 846-848.

Mishler BD. 2010. Species are not uniquely real biological entities. pp 110-122 in: Ayala FJ and R Arp, Eds.  Contemporary Debates in Philosophy of Biology. Wiley-Blackwell, Singapore. 440pp.

Nesbitt SJ, et al. 2010. Ecologically distinct dinosaurian sister group shows early diversification of Ornithodira. Nature 464: 95-98.

Nesbitt SJ, et al. 2013. The oldest dinosaur? A Middle Triassic dinosauriform from Tanzania. Biology Letters 9: 3pp.

Category: Background, Paleontology, Zoology | Tagged , , | 5 Comments

Why Paleontology Is Relevant

In these times of budget cuts and belt-tightening, you might wonder why our government,  universities, and museums should fund paleontological research. After all, there are bridges to repair, children to educate, and fires to put out. Few would disagree the latter problems all deserve our attention and our tax dollars. But what about paleontology?

When trimming budgetary fat, why isn’t paleontology something that falls clearly in the “non-essential” column? Is it even relevant to today’s world? Does it provide value to other scientific fields? Professional paleontologists understand why our field is relevant and can articulate that to an academic audience, but I don’t know how well we communicate its value to the public. These are the five “public-friendly” justifications I hear most often:

  • “Paleontologists teach anatomy at many medical schools.”
  • “Fossils play an important role in oil discovery.”
  • “Paleontology is a good ‘gateway drug’ to the other sciences.”
  • “Paleontology is a good way to teach critical thinking skills.”
  • “Paleontology is inherently interesting; it doesn’t need further justification.”

These responses are pretty abysmal, in my opinion. Yes, they’re all true, but I personally wouldn’t blame the government, university, or natural history museum who instantly defunded paleontological science based on any of them.

I didn't go to medical school to be called MISTER T, buddy.

I pity the fool who didn’t learn  anatomy from a paleontologist.
Image accessed here.

I think there is a better way to articulate the importance of paleontology, one that focuses on its scientific necessity and directly links our field to today’s world:

Paleontology is the study of the history of life. Because that history is written in the fossil and geological record, paleontology allows us to place living organisms in both evolutionary (life-historical) and geological (earth-historical) context. It is this contextual background that allows us to interpret the significance of characteristics of living organisms, and the significance of biological events occurring today.

The benefits of having such context are not limited to:

  • Determining the evolutionary identity of living and past organisms
  • Determining cause-and-effect relationships (How do things actually change under x, y, z conditions? )
  • Gaining predictive power with regards to rare events that have been experienced in the past, and may be experienced again in the future
  • Understanding the relative magnitude of changes happening in today’s world

These are above and beyond any of the fringe benefits that paleontology also facilitates (“gateway science”, critical thinking skills, anatomy instructors, it’s inherently cool, etc.).

And tonight Mr. Kite is topping the bill

You *might* think my feathers originally evolved to enable flight, if all my non-flying dino-ancestors didn’t have them too.
Image (c) 2006 Thomas Kraft CC BY-SA 2.5; accessed on Wikipedia.

Now, I’m not arguing that you can’t figure out some of these things without paleontology. We use many lines of evidence in addition to the fossil record of anatomy to determine the evolutionary identity and relationships of organisms, including DNA and developmental sequences, which often aren’t preserved in fossils (but sometimes are!). You can infer the evolutionary history of some body parts or characteristics when you the understand relationships among organisms, and you can often test function of individual body parts directly. But in all these cases, your data are improved by observing the direct record of change through time that only the fossil record provides.

The fossil record is the only source of natural (as opposed to experimental or theoretical) examples of what happens to living organisms under conditions the Earth is not experiencing today. For example, let’s say you want to know what happens to animals when the Earth gets much hotter – maybe five or seven degrees warmer than today’s average annual temperature. The last time this happened was during the Miocene (~14.8 million years ago), but it’s been that hot several times in Earth’s history. The fossil record shows that temperature increases have similar effects every time they happen. For example, warm-adapted animals expand their range north- and southward from tropical regions, so animals like crocodylians and monitor lizards live happily in places like Canada and Europe (Böhme 2003). Ectotherms get much, much bigger (think 42-foot snakes; Head et al. 2009).

Because these changes happen when temperatures go up and the reverse happens when temps go down, we can infer a cause-and-effect relationship between global temperature and various aspects of animal biology based on actual evidence. It happened before. It will happen again, if conditions are right. This is why paleontology is critical for predicting the effects of climate change at several scales.

Canadian croc

An expat from the Miocene.
Image accessed here.

In cases where you want to understand the magnitude of current change, the fossil record is again your only source of context. For example, many vertebrate species have gone extinct in the last 500 years. Some of these extinctions resulted from habitat loss (e.g., the dodo) or overhunting (the dodo and the moa), some indirectly from climate change, and some from disease (chytrid fungus in amphibians, or white-nose fungus in bats). Many, many more species are threatened with extinction (“critically endangered” means they’re not likely to last long, folks). If all of these species do go extinct in the next century, how bad would that be? Are we experiencing normal levels of extinction, or are we experiencing a mass extinction? The answer requires knowing what the normal rates are, and how mass extinctions are different. That understanding can only come from the fossil record.

To answer the above question, in 2011, Anthony Barnosky and colleagues published a study in Nature that compared the modern rates of extinction to those during the “Big Five” mass extinctions (times where 75% of the world’s species went extinct in a short amount of time). They determined that if only the species we consider critically-endangered go extinct over the next 100 years, at that rate would mean it would take 890-2270 years to reach 75% extinction (mass extinction levels). If, however, all the species we consider “threatened” also go extinct, we’ll hit that point within 540 years. Both of these are blinks of an eye in geological terms (faster than the end-Cretaceous extinction that wiped out the non-bird dinosaurs), but over two hundred years or two millenia we might be able to reverse some of these trends. They also showed the duration required to get to 75% is longer than the duration of some (though not all) of the “Big Five” extinctions. Some good news: we’re not experiencing mass-extinction level rates right now.

Extinction rates for different types of animals. White numbers: % of species in each group that went extinct in the last 500 years. Black numbers: % of threatened species, plus those that have gone extinct in the wild. Asterisks indicate groups with data for only a few species.
Image from: Barnosky et al. (2011), Nature.

I think if we were asked why studying American history or world history is important, we could make all of these same arguments and come up with a similar list of benefits. In fact, The American Historical Association did just that. This parallel between the relevance of life’s history and the relevance of our cultural history is a good one. When paleontology is reduced to cataloging the weird things that once were, it instantly becomes as irrelevant to our own time as cultural or political history would be, if it were reduced to a list of things that once happened.

References:

Barnosky AD, et al. 2011. Nature 471: 51-57.

Böhme M. 2003. Palaeogeography, Palaeoclimatology, Palaeoecology 195: 389-401.

Head JJ, et al. 2009. Nature 457: 715-717.

Category: Background, Miscellaneous, Paleontology, Zoology | Tagged , | 16 Comments