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Archive for September, 2009

Andy Farke interviewed on People You Don’t Know

September 15, 2009 Leave a comment

Want to know more about your project leader Andy Farke?  He’s evidently too modest to mention it himself, but there’s an excellent audio interview with Andy up now up at People You Don’t Know.  The first half-hour of the show is all about Andy: how he got into palaeo, what his job at the Raymond M. Alf museum entails, and, yes, the Open Dinosaur Project.  Enjoy!

Categories: About Us

Update and Important Info for Contributors

September 15, 2009 3 comments

Data entry is really cranking along now! At present, we have 198 verified, 144 unverified, and around 30 entries to be compared and added to the verified list (more on this below). This adds up to around 375 total entries in the system at present – nearly double of what we had at the launch of the project. Good work, everyone!

As you may recall, we have a two-step data entry system. The first, or original entry, is compared against a duplicate entry (verification entry) typed independently by another individual (hence the multiple spreadsheets available for download). Although this is time-consuming for all involved, the extra level of confidence in our data is completely worth it. If the data are completely identical between both independent data entries, the data immediately go onto the Public Data Sheet. If there is a discrepancy between the original entry and the verification entry, we have to go back to the original paper and find the source of the confusion. At present, I would estimate that around 50 percent of all entries need to have at least some detail or another resolved before they can be checked off the list. These problems range from quite minor to rather major. Resolving the problems takes time and delays the posting of the data (sometimes by a few days, as we don’t always have time to immediately track down the relevant references).

As I’ve worked on comparing original vs. verification entries, I’ve noticed a number of common errors that we all (including me) make.  In an effort to eliminate delays caused by such errors, I thought I would highlight typical problems:

  • Failure to identify the side (left or right) that an element belongs to, or incorrectly assigning it to a side. In general, go by what the data table says. If the data table doesn’t indicate the side the element belongs to (left or right), but the text does, indicate this in a note to me in the email. This way I can more rapidly identify the source of the problem when comparing with other data entries. Make sure you type the entry into the correct column!
  • Re-identifying taxonomic assignments. I know and you probably know that many specimens once called Trachodon are now lumped into Edmontosaurus. But, please use the paper’s original taxonomy. If they call the specimen Trachodon annectens, use this name. If it really bugs you, just send a note along with your data entry. We will sort it all out at the end, before data analysis.
  • Incomplete entry of data. In large monographs (lengthy, detailed descriptions of specimens), data tables may be scattered across several widely separated pages. Make sure you check out the whole publication, to ensure that you find all of the relevant measurements. Sometimes, measurements are hidden away in the text, rather than appearing in convenient table form.
  • Using an out-of-date spreadsheet. The Verification List is updated nearly daily, and the New Data Entry spreadsheet has been updated once since the project launch. Make sure you are using the latest versions!
  • Forgetting to put your name in the appropriate column. We want to make sure you get credit for your hard work, so please remember to enter your full name on the data sheet!

The scientific success of the ODP, and the acceptance of our project within the scientific community, will hinge largely on a clear, accurate, and useful database. Working together, we’re making this a reality!

Hadrosaur Mummy

A "Trachodon" mummy, now properly called "Edmontosaurus" (after Osborn 1912)

Categories: Progress Reports

If You Haven’t Entered Data Yet. . .

September 12, 2009 11 comments

Now’s your chance! In an effort to broaden participation, I’d like to reserve the papers listed at the end of this post for those who have not yet submitted any data and do not have access to a large personal library. All of these papers are freely downloadable (and I’ve even included links!), and would be a tremendous use for the project. Please remember to download the appropriate spreadsheet, and also please post a comment indicating if you plan on entering or verifying a particular reference so that we don’t have unnecessary duplication of efforts. Check out the How-To Guide as well as the FAQs for answers to most basic questions, such as the basics of data entry. And if you have queries, don’t hesitate to post a comment here or email me.

And don’t worry. . .if you miss out on these papers, or can’t find any other open access papers, or just plain don’t feel like typing numbers into a spreadsheet, there will be plenty of other opportunities to help out with the project. Stay tuned for details.

Update

At this writing, we have 161 verified and 93 unverified entries in the database, submitted by 22 different individuals. Well done!

References for First-Timers

Dodson P (1986) Avaceratops lammersi: A new ceratopsid from the Judith River Formation of Montana. Proceedings of The Academy of Natural Sciences of Philadelphia 138: 305-317. [link to Google Books] (completely verified)
Dong Z (1989) On a small ornithopod (Gongbusaurus wucaiwanensis) from Kelamaili, Jungar Basin, Xinjiang, China. Vertebrata PalAsiatica 27: 140-146. [PDF of translation] (completely verified)
Galton PM, Powell HP (1980) The ornithischian dinosaur Camptosaurus prestwichii from the Upper Jurassic of England.  Palaeontology 23: 411-443. [PDF] (completely verified)
Gilmore CW (1909) Osteology of the Jurassic reptile Camptosaurus, with a revision of the species of the genus, and a description of two new species.  Proceedings of the U.S. National Museum 36: 197-332. [link to Google Books, where you can download the PDF]
Gilmore CW (1914) Osteology of the armored Dinosauria in the United States National Museum, with special reference to the genus Stegosaurus. United States National Museum Bulletin 89: 1-136. [link to Google Books, where you can download the PDF]
Hou LH (1977) A new primitive Pachycephalosauria from Anhui, China. Vertebrata PalAsiatica 15: 198–202. [PDF of translation]
Maleev E (1954)  Armored dinosaurs of Mongolia, Family Syrmosauridae. Trudy Paleontologicheskogo Instituta Akademii Nauk SSSR 48: 142-170. [PDF of translation] (completely verified)
Maleev EA (1956) Armoured dinosaurs of the Upper Cretaceous of Mongolia: Family Ankylosauridae. Akademiia nauk SSSR 62: 51-91. [in Russian] [PDF of translation] (completely verified)
Perle A, Maryanska T, and Osmolska H (1982) Goyocephale lattimorei gen. et sp. n., A new flat-headed pachycephalosaur (ornithischia, dinosauria) from the upper Cretaceous of Mongolia. Acta Palaeontologica Polonica 27: 1-4. [PDF] (completely verified)

Get an ODP T-shirt, mug or mouse-mat

September 11, 2009 3 comments

I wanted to make Open Dinosaur Project T-shirts for Andy, Matt and me to wear at SVP, so since I’ve gone to the trouble of putting them together, I figured I may as well let anyone else who wants one go ahead and get it.

Open Dinosaur Project -- the T-shirt

Open Dinosaur Project -- the T-shirt

If you want one, you can get it from the Open Dinosaur Project store on Cafepress.

Since I was there, I made mugs and mouse-mats, too.

(Note that these are all sold at cost price: we’ll not make a cent.  Just in case anyone thought we were trying to cash in on a lofty-goaled project for our own financial gain.)

Categories: Uncategorized

Update and a Mini-Tutorial

September 11, 2009 18 comments

The project is really rolling now – we have 46 project volunteers, 128 132 verified data entries and 46 56 unverified entries. Around 12 of the volunteers (representing several different countries) have submitted data, thus qualifying them for authorship. Thank you to everyone for your assistance, and your patience as we work the kinks out of the system. Several people have written in with some very helpful suggestions and requests for clarification, and some of those will be the topic of this post. Don’t be afraid to speak up, by email to me or in the comment threads! Unless we know there’s a problem or bit of confusion (no matter how slight), we can’t take steps to fix it. Really, our feelings won’t be hurt. And there’s no such thing as a stupid question.

Clarifying Some Measurements

Although we’ll have a larger tutorial on the forelimb in just a few days, I wanted to briefly discuss the scapula, coracoid, and scapulocoracoid (illustrated below). The scapula is the shoulder blade, and the coracoid is a bone that attaches to it. When the two bones fuse up (as often happens in dinosaurs), this single element is called a “scapulocoracoid.” Now, we have entries for scapula length (a maximum length of the element) and scapulocoracoid length (another maximum length), but not coracoid length. The reason for this is that almost nobody measures coracoid length the same way – some measure along the long axis, some along the axis parallel to the scapula. Because the consistency of measurements is especially questionable, we have elected not to include the coracoid in our measurement list.

Also, scapulocoracoid length is NOT the same as adding the lengths of the scapula and coracoid. See the diagram below for a reason why. In the example shown here, adding scapula and coracoid lengths together would slightly exceed the true measurement of scapulocoracoid length.

Scapulocoracoid of Triceratops

Scapulocoracoid of Triceratops in lateral (side) view (after Hatcher et al. 1907), showing one way to measure scapula length (1), coracoid length (2) and scapulocoracoid length (3). Note that 1+2 does not equal 3.

Our second point of clarification concerns the femoral measurements. On the spreadsheet as it was originally posted, we have length (L), minimum (or midshaft) circumference (Circ), mediolateral width at midshaft (Shaft W), and antero-posterior width at midshaft (Shaft L). Of course, the last two measurements in particular were very confusing as named. My bad. In particular, Shaft L implied a measurement very close to just plain-old length. These measurements are patterned after measurements taken by Matt Carrano, for documenting changes in femoral anatomy through dinosaur evolution. In order to avoid confusion in the future, I have now changed the column labels to Midshaft ML W and Midshaft AP L. Does this work for everyone?

Triceratops femur

Triceratops femur (after Hatcher et al., 1907) in anterior (front) view, showing 1) maximum femur length; and 2) mid-shaft mediolateral width (Midshaft ML W). Mid-shaft antero-posterior length would be perpendicular to #2.

For Those Who Are Measuring Specimens Directly

A brief note on this now, and we’ll hopefully have a more formal tutorial later. Whenever possible, we want maximum lengths of elements. Yes, we realize that this may mean slightly different anatomical landmarks on different taxa. For the present purposes of the study (and given the relative lack of standardization in overall anatomical measurements for dinosaurs), it is presumably just easier this way. Perhaps there is an interesting discussion to be had on standardizing morphometric measurements for archosaurs, though! Thinking out loud (this is an open project, after all), that would be a pretty darned cool product from the ODP. I know that some studies (Chinnery’s work on ceratopsians, for instance) have developed standard landmarks for a subset of archosaurs. . .has anyone attempted this for archosaurs as a whole? Or attempted to develop measurements that could be compared adequately with mammals?

And Don’t Forget

When you submit data, please make sure to provide a full reference for the paper in PLoS ONE format (see here for info), and include the page number for the data that you are transcribing. This will make it easier to check or double-check entries if there is a problem. Thanks!

Also, please make sure that someone hasn’t entered or re-entered the data you have your eye on. Always use the latest versions of the verification list and task list.

Looking For References? Check out the Polyglot Paleontologist! They’ve got lots of translations of dinosaur-related papers.

Tutorial 1: Finding Papers With Data (Part 1)

September 10, 2009 7 comments

As I type this, 34 35 37 individuals have expressed interest in joining the ODP. This is a tremendous response, and we are incredibly grateful for your support. If you are interested but haven’t yet notified us, it’s never too late (just send me an email indicating your interest)! So far, we have 72 75 79 108 verified and 88 85 80 53 unverified data entries – quite an expansion beyond yesterday!

Some of you are quite new to paleontology, or at least to this kind of research. You’re probably looking at this blog post or the email of welcome I sent you, wondering “What next?” So, I want to give you just a quick tutorial on the basics of finding data for entry. In future posts, we will discuss the finer points of entering data.

As you recall, we’re collecting measurements of limb bones from ornithischian dinosaurs (mostly plant eaters, if you’re not familiar with them). We’re accepting two basic kinds of data for this project: 1) measurements taken from the literature; and 2) measurements taken directly from specimens. The present post will focus primarily on #1.

The first step is finding the literature. Of course, we have a page devoted to various places to find and download open access papers that could potentially have measurements. But, this doesn’t do you much good if you don’t know what papers to look for! So, I want to give you a few hints and pointers on how to go about this.

As an example, I want to focus on downloadable PDFs from the American Museum of Natural History’s (AMNH) publications. In a very laudable move, they have made their entire run of publications freely available. Classic papers, including the original descriptions of iconic dinosaurs such as Tyrannosaurus rex, Protoceratops, Velociraptor, and more, are all here. Many of the publications’ authors did an excellent job of measuring their dinosaurs, too. So, the AMNH is going to be a key data source.

As a start, you have to find the appropriate papers for download. Their search engine is pretty good, and available here. You’ll want to search “all publications” (the default selection). So, what next? The easiest thing is to just type in the name of a dinosaur. Remember that for now, we primarily want measurements for ornithischian dinosaurs (don’t worry, I’ll give you some names / keywords later on). As a test, try “Saurolophus” (a kind of duck-billed dinosaur).

This should bring up two papers – one from 1913 and one from 1912. Download the PDF for the one from 1913 (it’s a large file, and might take a little while), and then scroll through the pages.

Success! On page 6 (or p. 392, as paginated in the original volume) is a whole mess of measurements. And not only do they have measurements for Saurolophus, but two other dinosaurs. Humerus length, femur length – they’re all here. From this point, it’s relatively straight-forward to enter the data on the data entry sheet (which I’ll cover in a subsequent tutorial). Note that I’ve already entered the data from this paper (which should be listed on the Verification List, under “Brown 1913″), but they need to be double-checked (there’s a task for someone!).

Well and good, but if you don’t know dinosaurs, what should you look for on the AMNH website? I recommend doing a search on some of these terms (the links should take you to the search page): *hadrosaur* (the asterisks are wild-card characters to broaden the search), *ceratops* (note the wildcard characters again), *trachodon* (an archaic term for some kinds of duck-billed dinosaurs), Monoclonius, Styracosaurus (two kinds of horned dinosaurs), etc. Many all of the papers found this way contain useful data.

The following papers that might result from these searches have been entered once already, and need to be re-entered on the verification list:

Brown B (1908) The Ankylosauridae, a new family of armored dinosaurs from the Upper Cretaceous. Bulletin of the American Museum of Natural History 24: 187–201. [note - please post a comment if you are going to check this one, so we don't have unnecessary duplication of efforts]
Brown B and Schlaikjer EM (1937) The skeleton of Styracosaurus with the description of a new species. American Museum Novitates 955: 1-12.
Brown B (1913) The skeleton of Saurolophus, a crested duck-billed dinosaur from the Edmonton Cretaceous. Bulletin of the American Museum of Natural History 32: 387-393.
Brown B (1914) Leptoceratops, a new genus of Ceratopsia from the Edmonton Cretaceous of Alberta. Bulletin of the American Museum of Natural History 33: 567-580.
Brown B (1916) Corythosaurus casuarius: skeleton, musculature and epidermis. Bulletin of the American Museum of Natural History 35: 709-716.
Brown B (1917) A complete skeleton of the horned dinosaur Monoclonius, and description of a second skeleton showing skin impressions. Bulletin of the American Museum of Natural History 37: 281-306. Just verified by Tom H. Green and Ville Sinkkonen!
Gilmore CW (1933) On the dinosaurian fauna of the Iren Dabasu Formation. Bulletin of the American Museum of Natural History 67: 23-78.

These papers don’t need to be re-entered, because they’ve been done twice now:

Brown B (1913) A new trachodont dinosaur, Hypacrosaurus, from the Edmonton Cretaceous of Alberta. Bulletin of the American Museum of Natural History 32: 395–406.
Brown B (1913) The skeleton of Saurolophus, a crested duck-billed dinosaur from the Edmonton Cretaceous. Bulletin of the American Museum of Natural History 32: 387-393.
Brown B (1914) Leptoceratops, a new genus of Ceratopsia from the Edmonton Cretaceous of Alberta. Bulletin of the American Museum of Natural History 33: 567-580.
Brown B (1916) Corythosaurus casuarius: skeleton, musculature and epidermis. Bulletin of the American Museum of Natural History 35: 709-716.
Brown B (1917) A complete skeleton of the horned dinosaur Monoclonius, and description of a second skeleton showing skin impressions. Bulletin of the American Museum of Natural History 37: 281-306.
Brown B and Schlaikjer EM (1937) The skeleton of Styracosaurus with the description of a new species. American Museum Novitates 955: 1-12.
Brown B, Schlaikjer EM (1942) The skeleton of Leptoceratops with the description of a new species. American Museum Novitates 1169: 1-15.
Gilmore CW (1933) On the dinosaurian fauna of the Iren Dabasu Formation. Bulletin of the American Museum of Natural History 67: 23-78.

All of the rest of them haven’t been entered even the first time! Do you think we can get all of the relevant AMNH publications entered and double-checked before the end of the week?

A Few Quick Pointers

Much of this information is already contained in the FAQs and How-To Guide, but given the length of these documents it’s easy to overlook a few key points. Future tutorials will also address aspects of this in more detail, but I figured it would be helpful to talk about some of it right now.

  • Units: Please enter all measurements in millimeters. If the paper gives the measurements in centimeters, please do the conversion (multiply by 10) while entering the data.
  • Before Entering Data: Check to see if the paper is listed on the Tasks for Contributors page. Papers on the finished list are already closed out, and don’t need to be entered in any form. Papers on the other list need to be re-entered on the verification spreadsheet. If you don’t see the paper on either reference, odds are good that nobody has gotten to it yet.
  • Why Do We Need Data from the Literature Entered by Two Contributors? When keying in data from a paper, it’s very, very easy to mistype a number, or enter data into the wrong column, or miss a measurement altogether. In order to make our database as reliable as possible, we independently check all entries from the literature. Believe it or not, project contributors have caught several mistakes that I made when entering data on my own.
  • Bibliographic Data. I really, really appreciate it if you send me a formatted bibliographic entry for each paper that you input. We need to be building the bibliography from day 1, and it’s a lot easier to do it now than in a mad rush while preparing the final publication. Please send a formatted bibliographic entry to me with each entry. See here for info on how we would like the entries formatted. The examples on the Tasks page might also be helpful.
  • How I find out if someone has entered data from a paper already? Check out the list on the Tasks for Contributors page.

Do you have any other questions? Ask them in the comments section, and we’ll do our best to address them!

Categories: Tutorials

Progress Report: Day 1

September 9, 2009 20 comments

Wow, it has been a whirlwind of activity at the Open Dinosaur Project! After our official launch less than 24 hours ago, things have really begun to happen. Before we begin some background and tutorial posts, I just want to highlight a few items.

Sign-Up

The response has been great so far, in terms of volunteer numbers. We have nearly 30 people who have expressed interest, from all walks of life – professional paleontologists, mathematicians, artists, physicists, high school students, graduate students, computer programmers, librarians, and more. If you haven’t signed up already, it’s not too late! See the link in the sidebar for more information.

Publicity

Thank you to all of those who assisted in publicizing the launch – we had over 1,700 hits in the first day! In particular, thanks to Bora at Blog Around the Clock, Glyn at open…., Andrea at Theropoda, Darren at Tetrapod Zoology, Tor at Thoughts and Ideas from a Paleopunker, Dave Hone of Dave Hone’s Archosaur Musings, Bill at Chinleana, Gavin at Open Access News, Luis at Ciência Ao Natural, A Primate of Modern Aspect, Brian at Dinosaur Tracking, Jeremy at Denim and Tweed, and all of the other bloggers out there. Did we miss your post? Let us know, and we’ll add it to the list!

Data Entry

We had a nice stockpile of data before the launch, and project participants have already begun to add to this. Tor Bertin and Daniel Najib provided several entries, and Frank Varriale provided important data for a number of ankylosaur, stegosaur, and ceratopsid specimens that he measured personally. There are 55 verified and 92 unverified entries to date. Do you have a spare minute? Enter some data and send them on over! Let’s try and surpass 100 verified and unverified entries as soon as possible!

A First Look at the Data

Throughout the course of the project, we’re going to post some visualizations of the data in various forms. Hopefully it will be a good motivation to spur us forward in data collection, as well as an inspiration for new research questions and directions. The graph below shows humerus length versus femur length, for ceratopsian (horned) dinosaurs and thyreophorans (the group including stegosaurs and ankylosaurs). Do you want to conduct your own analyses? The data are freely available here (Google account log-in required; you may also email Andy Farke for a copy of the spreadsheet if you don’t have a Google account).

Humerus Length vs. Femur Length

Humerus Length vs. Femur Length

(note – the axes on the graph have been updated)

Categories: Progress Reports

Introducing the Open Dinosaur Project

September 8, 2009 15 comments

Hello, and thanks for dropping by at the Open Dinosaur Project.  This blog is part of a wider project, in which we hope — with your help — to make some science.  We want to put together a paper on the multiple independent transitions from bipedality to quadrupedality in ornithischians, and we want to involve everyone who’s interested in helping out.  We’ll get to the details later, but the basic idea is to amass a huge database of measurements of the limb bones of ornithischian dinosaurs, to which we can apply various statistical techniques.  Hopefully we’ll figure out how these transitions happened — for example, whether ceratopsians, thyreophorans and ornithopods all made it in the same way or differently.

Who are “we”, I hear you ask.  The core ODP team is Andy Farke (curator at the Raymond M. Alf Museum of Paleontology, Claremont, California), Matt Wedel (Western University of Health Sciences, Pomona, California) and Mike Taylor (University College London).  We’re all researching and publishing scientists, specialising in dinosaurs — although up until now Matt and Mike have concentrated on sauropods.

As for who you are: if you care about dinosaurs, and want to make some science, then you can be involved.  It doesn’t matter whether you’re a seasoned professional palaeontologist, a high-school kid or a retired used-car salesman: so long as you can conduct yourself like a professional, you’re welcome here.

And now, for the gory details. . .

Once Again, The Research
We will create a comprehensive database of skeletal measurements for ornithischian dinosaurs, with the goal of investigating the evolution of locomotion and limb proportions in this group.

Why Ornithischians?
In terms of locomotion, ornithischians–the group of dinosaurs including stegosaurs, ankylosaurs, iguanodonts, horned dinosaurs, “duck-billed” dinosaurs, and more–are ridiculously diverse. From a bipedal ancestor, ornithischians evolved quadrupedality at least three times–in thyreophorans (ankylosaurs+stegosaurs), ornithopods (iguanodonts, duck bills, and relatives), and ceratopsians (the horned dinosaurs). This is an intriguing transition, but one that has received almost no study.

The Big Questions
A number of questions are driving the project. Some of them may be answered immediately. Some may be answered later. Some may turn out to be unanswerable in the present study. This is all part of how science works! From the very start, we want to keep the spirit of inquiry open and freely accessible for everyone.

  • Why did ornithischians evolve quadrupedality multiple times? Was it consistently associated with an increase in body size?
  • Did different groups of quadrupedal ornithischians arrive at this body form in similar ways, or did they have different strategies?
  • How diverse was the body plan of ornithischian dinosaurs?
  • Did different clades of ornithischians scale the relative proportions of their limb bones in different ways?

Constructing the Database
A huge, virtually untapped resource of skeletal measurements resides in the published scientific literature. In order to put these measurements to good use, it is necessary to place the data into a form that can be analyzed mathematically. Essentially, we aim to construct a giant spreadsheet with as many measurements for ornithischian dinosaur limb bones as possible. For simplicity, we will focus on bone lengths and diameters along the shaft. From the forelimb, we will look at the scapula, coracoid, sternal plates, humerus, radius, ulna, and manus (“hand”). Within the hind limb, we will look at the femur, tibia, fibula, and pes (“foot”).

In the old days, this would require a lot of time in the library stacks. Some aspects of the project may still require this. But, a number of scientific papers are now freely available to the general public! So, anyone with an internet connection can help out.

Who Can Participate?
Anyone! We do not care about your age, education, previous paleontological experience, or geographic location. You don’t have to be a professional paleontologist – just a person who is willing to act professionally in the accurate and ethical collection, analysis, and interpretation of real scientific data.

What Can I Do?
It’s simple! Just locate the necessary scientific papers, and start entering data into our spreadsheet. If you have access to real specimens, you may enter these data.

What Do I Get Out of This?
Two things – 1) the thrill of participating in real scientific research; and 2) an opportunity for authorship on a scientific paper. Yes, you read that correctly. All contributors to the database are given the option of joining us as authors for the final published paper. If you opt out of authorship, you will still be listed in the acknowledgments (unless you request otherwise).

How Do I Sign Up?
Simply drop an email to project head Andy Farke – andrew.farke@gmail.com – with your name and preferred email address. If you have an institutional affiliation, please include that also. . .but remember that a formal academic affiliation is not required!

Help! I’m Lost!
Never fear. . .we’re going to publish a series of tutorials in the next few days outlining how to search for scientific literature, what measurements to look for, and other important introductory pieces for those new at the research game.

Categories: Basics
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