Archive for the ‘Tutorials’ Category

Time to Get to Work

February 9, 2010 2 comments
The Ankylosaur of Destiny needs your help!

The Ankylosaur of Destiny needs your help!

Thank you to everyone for an excellent discussion going on over at the previous post. It’s really helping to clarify a number of issues – and I appreciate all of the expertise being tossed in. This is what open science is all about. Of course, the discussion continues – keep the comments rolling in!

As mentioned, we want to have a way to combine duplicate (and non-duplicate) measurements from all of the different sources for each specimen into a single entry. For instance, the Ankylosaurus magniventris specimen AMNH 5214 has four separate entries. One entry presents humerus, femur, fibula, and metatarsal lengths, another one presents only femur lengths, and so on. And, there are multiple different values given for some measurements. For instance, the femur length is given variously as 560, 536, and 542 mm (whether referring to left, right, or an unspecified side). So, we want to condense those four entries into one for the sake of further analysis (keeping the original data safe and sound, in case anyone wants to go back to them).

There is no perfect strategy, but based on our previous discussions it’s looking like the best approach is to “average and combine.” As another example, let’s consider how this would work for the Psittacosaurus mongoliensis specimen AMNH 6538.

There are two entries for this specimen, and we’ll only take a look at subsets of these entries. Two tibia lengths are presented: one at 129 mm and the other at 125 mm. So, our combined entry would use the average of these, 127 mm. Only one of the two entries presents the fibula length (given as 121.4e). In this case, we’ll assume that the estimated measurement is accurate, and enter 121.4 as the combined value (in my general experience, most of these estimated values seem to be pretty darned close, and reflect a little bit missing at the end of the bone or a similar condition; of course, it’s up to everyone to keep their eyes on exceptions to this and flag them accordingly).

Spreadsheet screen capture; click to enlarge

I’ve begun to modify the spreadsheet, so that all specimens which can have combined entries have a line for this (thanks to John Dziak for noting this). As the ceratopsians and ankylosaurs are mostly together in terms of taxonomic updating (unless anyone else spots additional problems – please flag them if you do!), they’re first targets for combination.

Here’s a proposed set of guidelines; if any other situations crop up, please post a comment and we can amend as appropriate. This is the sort of thing that will probably go into a Materials & Methods section in the paper.

Guidelines for Combining Multiple Entries for a Single Specimen

  • If values for various sides are included, please average them all into a single measurement. For instance, if a left and right humerus (in the L L and R L columns) are noted, the average would go into the “L” column. If two measurements for left humeri are included (in the L L column), the average again should go into the “L” column. And so on. . .
  • If a value is indicated as estimated (with an “e” before or after the number), it is appropriate to treat the measurement as valid (unless information indicates that the restoration is too extensive to trust the measurement).
  • If, in a set of measurements, one or more values seem to be “off” (e.g., a case where femur length is given as 342, 339, and 402 mm, respectively), flag this entry. Here, we will probably go with the more likely values (342 and 339) and dump the 402 as an outlier.
  • Each combined entry is indicated by yellow in the first few columns, and the word “combined” in the Reference column.
  • The metatarsal and metacarpal columns are in “text” format (to avoid funky autoformatting of the L/R measurements to dates). So, you will have to adjust techniques accordingly.
  • Once an entry is finished, the person who combined it puts their name in column CM (“Entry 1″) and marks the entire row as yellow.

How to Contribute

So, we’re looking for some volunteers to help combine entries. In the true spirit of crowdsourcing, the fully editable document is available here. Please make edits directly on the document (rather than downloading and resending it to me). Right now, the data down to row 531 are prepped and ready to combine, and I’ve taken care of the first few entries. As we resolve and clean up other areas of the database, those will pop up as available. As always, it’s important to check your work frequently and alert someone if you notice an error or inconsistency.

Thank you, and good luck!

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

Key Concepts: Osteology I (The Forelimb)

September 15, 2009 15 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:

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

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