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Archive for September, 2009

Developing a measurement protocol, part 1

September 16, 2009 13 comments

By now, those of you who have been entering data from the literature — and maybe even more those who have been measuring bones themselves — will have noticed that it’s not quite as straightforward as it sounds.  Some bones are crushed, distorted, broken, reconstructed, lost in soft peat for three months and recycled as firelighters.  And what exactly is the “length” of a curved bone like the femur of many ornithopods?  And where exactly is the “midshaft” that’s measured for the midshaft diameter?  And so on.

We want to develop an explicit protocol for what bones are worth including, what measurements need taking and how they should be taken.  But to do that, we’ll need your help.  We want to know what issues you’ve come up against as you’ve worked on ODP data, so we can figure out standard answers.  Post your questions as comments to this article: we’ll discuss them in the comments, and when we feel we have consensus, we’ll start to assemble a protocol document.

Our general feeling is that yes, there will be minor errors and distortions in the data, but there is no reason to suspect systematic bias and therefore not much to worry about (and not much we can do about it). Hopefully the database that we’re putting together will live forever and in the future people will revisit these specimens and submit “cleaned up” measurements in cases where that’s warranted. But that doesn’t mean we can’t be doing useful stuff in the meantime. It also doesn’t mean that we shouldn’t acknowledge these problems and fix them wherever possible.

So: (a) yes, crushing, distortion, reconstruction, measurement conventions, etc. are all valid concerns; (b) we will strive to overcome them to the extent possible, both immediately for the first paper and ultimately for the evolving database; but (c) these problems plague any large quantitative study of morphology — the only difference with the ODP is that those problems are out in the open; and (d) we don’t anticipate systematic bias and don’t think these problems are serious enough to prevent us from doing useful work right now.

Right then: questions, please!

Brachiosaurus altithorax holotype FMNH P25107, last three presacral vertebrae in right lateral view.  Sorry, I can't break the habit.

Brachiosaurus altithorax holotype FMNH P25107, last three presacral vertebrae in right lateral view. Sorry, I can't break the habit.

Categories: Basics, Tutorials

Status Report

September 16, 2009 17 comments

The ODP’s team members are amazing. Today we passed 200 verified entries – in fact, we rocketed past it to 228 verified entries! We’ve got 118 unverified entries, and ~45 that are in the que for final checking.

And now, a preliminary plot of femur length vs. tibia length (primarily ornithischians, with a few of the outgroup taxa thrown in). Want to make your own plots? Check out the publicly available data sheet!

Femur Length vs. Tibia Length

Log Femur Length vs. Log Tibia Length. Slope = 0.905, significantly different from 1.

Categories: Progress Reports

Key Concepts: Osteology I (The Forelimb)

September 15, 2009 16 comments
Forelimb of the horned dinosaur Centrosaurus apertus

Forelimb of the horned dinosaur Centrosaurus apertus

Osteology is the study of bones. Recognizing that not everyone here is completely familiar with all of the relevant names and features, this post will cover a brief tutorial of limb osteology and terminology in dinosaurs.

Broadly speaking, anatomists usually divide the skeleton into three sections: cranial (the head); axial (the vertebral column and ribs, although embryological and evolutionary histories mean that parts of the skull are sometimes lumped in here); and appendicular (the limbs). Presently, we’re only interested in the latter.

The appendicular skeleton includes forelimbs and hind limbs. Let’s start at the front in this post, and work back in a subsequent post. But before we start that, we need to introduce one more set of terms: proximal and distal (see image for their context within the forelimb). This just refers to the position along a structure relative to the main part of the body. Proximal is close to the body, and distal is away from it. Considering the humerus (upper arm bone), the elbow is at the distal end and the shoulder is at the proximal end. Within the entire leg, your toes are at the distal end and the thigh bone is at the proximal end.

The forelimb includes the pectoral girdle as well as the limb bones themselves. In dinosaurs, the pectoral girdle includes a scapula, a coracoid and a sternal plate on each side. Humans have scapulae too (most of us know them as “shoulder blades”), but our coracoids have shrunk down to little nubbins (the coracoid processes) that are fused onto the scapulae themselves. We also have clavicles (“collar bones”) as part of our pectoral girdle, but ornithischians lack this bone (although theropods preserve part of it in the furcula, or “wishbone”). In all adult ornithischians, the scapula and coracoid are fused together, and the area where they meet forms the glenoid, or shoulder socket. If the bones are fused, their total combination is then called a “scapulocoracoid.”

The humerus (or “upper arm bone”) fits into the glenoid. It’s a long bone, expanded at both ends for various muscle and bony attachments. Lots of muscles—including the famous deltoids, lats, biceps, triceps, and pectoral muscles—attach here. The “midshaft” of the humerus is exactly that – the point at the middle of bone.

A pair of bones – the ulna and radius – form the forearm. They articulate with the distal end of the humerus. They’re pretty simple, rod-like bones in most cases. The ulna usually has a process (i.e. a sticking-out bit), called the olecranon, at its proximal end for attachment of the triceps muscle.

Finally, we have the hand – more properly called the manus (Latin for “hand,” strangely enough). The manus has carpals (wrist bones), metacarpals (joining the wrist to the digits), and phalanges. Each digit (or finger) is numbered starting at the thumb. The thumb (innermost digit, for ornithischians) is I (note the Roman numeral), the index finger II, middle finger III, ring finger IV, and pinkie V.

The most proximal elements within the manus (just distal to the ulna and radius) are called the carpals. They’re often just cartilage, and even when ossified are rarely preserved (they tend to float away if the skeleton becomes disarticulated). At any rate, they’re usually non-descript little round elements in ornithischians, and we’ll pretend these bones don’t exist for the purposes of our study.

Manus of the horned dinosaur Centrosaurus (modified after Brown 1917)

Right manus of the horned dinosaur Centrosaurus (modified after Brown 1917)

Next, we have the metacarpals. If you squeeze the palm of your right hand between the thumb and index finger of your left, these are the bones you’re feeling. The number of metacarpals is variable in many dinosaurs. Humans, and most ornithischians, have five metacarpals (and hence, five fingers in most cases). Most theropods have fewer. “Metacarpal” is often abbreviated as MC. So, the first metacarpal would be MC-I, and so on.

Finally, we come to the phalanges. A single element is most properly called a phalanx (not a “phalange,” although this archaic spelling is not technically incorrect – many older publications use the terminology). The phalanges are numbered by digit (I-V) as well as their position relative to the metacarpals (given by an Arabic numeral). For instance, I-1 is the first phalanx on the first digit, and III-2 is the second phalanx on the third digit. The second-to-last phalanx is sometimes referred to as the “penultimate” phalanx.

The distal-most (terminal) phalanx is often modified into a hoof or claw. These specially modified phalanges are usually called unguals, but they are numbered just the same as regular phalanges. Even if the third and final phalanx on the third digit is a huge claw, it’s still called manual phalanx III-3.

Finally, we should mention the sternal plates. These odd bones (probably equivalent to the sternum, or breast bone, of mammals) are usually floating at the front of the chest wall. The sternals sometimes look like kidney beans (in ceratopsids) or hatchets (in other ornithischians).

It’s a blizzard of terms, but a little practice should help you become completely conversant with all of the parts of the forelimb. In an upcoming post, we’ll tackle the hindlimb. Don’t worry – many of the concepts are the same!

Categories: Key Concepts, Tutorials Tags:

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
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