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Quick Update

October 8, 2012 1 comment

The best way to spur work on a project is to agree to present it at a professional conference. Thus, I submitted a title (no abstract necessary) for the upcoming Southwest Regional Meeting for the Division of Vertebrate Morphology / Division of Comparative Biomechanics within the Society of Integrative & Comparative Biology (short title, isn’t it?). The beauty of this conference is that they have “5 minute talks,” where you can give short and succinct presentations of in-progress research. The ODP definitely qualifies! I’ve got a few days break from teaching (and my most time-intensive classes are completely done after the SVP meeting), so this week has the promise of productivity. Look for news on preliminary analyses, etc., in this space. Presentation is Saturday.

Oh yeah. . .I almost forgot! The submitted title was “Morphological Disparity, Locomotion and Limb Proportions in Ornithischian Dinosaurs.”

Categories: Uncategorized

Mopping Up the Data

March 8, 2012 6 comments

Thanks to Alexandre Fabre, Falko Gauß, and others, we are starting to close out some of the nagging verification entries for the data set (all of which are now accordingly updated in the public files). David Dreisigmeyer has also noted a few formatting issues and other quirks in the dataset (which I will work to correct in the next few days).

In any case, we are very close to finalizing the database. For the sake of time, I want to call attention to just a few last bits of data entry. These represent taxa and clades that are otherwise poorly represented in the sample. Some entries (e.g., those concerning the outgroup or indeterminate, fragmentary taxa) are just going to have to go by the wayside, or else we’ll never finish!

References That Have Data That Need to be Entered a First Time

Prieto-Marquez A. Cranial and appendicular ontogeny of Bactrosaurus johnsoni, a hadrosauroid dinosaur from the Late Cretaceous of northern China. Palaeontology (in press). DOI: 10.1111/j.1475-4983.2011.01053.x [link] [if this contains only disarticulated and unassociated material, it is not usable for our dataset - can anyone confirm one way or another?] [contains only disarticulated and unassociated specimens - thanks to John Dziak for checking!]

References For Data In Need of Cross-Checking

Godefroit P, Pereda Suberbiola X, Li H, Dong Z-M (1999) A new species of the ankylosaurid dinosaur Pinacosaurus from the Late Cretaceous of Inner Mongolia (P.R. China). Bulletin de l’Institut Royal des Sciences Naturelles de Belgique 69-Supp. B: 17-36.

Wang X, Pan R, Butler RJ, Barrett PM. 2011 (for 2010). The postcranial skeleton of the iguanodontian ornithopod Jinzhousaurus yangi from the Lower Cretaceous Yixian Formation of western Liaoning, China. Earth and Environmental Science Transactions of the Royal Society of Edinburgh 101: 135-159.

Zhao X, Li D, Han G, Zhao H, Liu F, Li L, Fang X (2007) Zhuchengosaurus maximus from Shandong Province. Acta Geoscientica Sinica 28: 111-122

Categories: Uncategorized

The Data Set (as it sits now)

November 12, 2010 6 comments

The ODP has accumulated a whole lot of data, and now we have to make some sense out of it. The first step was to pare it down from the original monstrous mass. Based on a very lively discussion (see this post and links therein), the data are pretty much trimmed. In addition to posting a link to those data (in response to this query by Hiro), I wanted to explain some of what I’ve done with the data.

The file, freely available as an Excel workbook, contains several spreadsheets. These are explained below, by spreadsheet:

  • To Analyze: Includes all of the data, minus highly incomplete or juvenile specimens. As you may recall, juveniles were rates as those listed as such in the literature, or individuals which were less than 2/3 the size of the largest individual for a species.
  • Deletion Candidates: The home for the highly incomplete or juvenile specimens mentioned above. We don’t want to throw them away, after all.
  • Fore Hind1 & ForeHind 2: Worksheets where I was just playing around with various ways of looking at the combined data.
  • Ratios: A whole bunch of ratios between various limb elements; it’s worth exploring. This will require a more detailed post in the not-so-distant future, to explain many of these.

You’ll probably notice the abbreviation “IM”. This refers to an intermembral index – basically, the ratio between forelimb and hind limb length. There are several ways to calculate it. These include:

  • IM1(U)=(Humerus+Ulna)/(Femur+Tibia)
  • IM2(U)=(Humerus+Ulna+MCIII)/(Femur+Tibia+MTIII)
  • IM1(R)=(Humerus+Radius)/(Femur+Tibia)
  • IM2(R)=(Humerus+Radius+MCIII)/(Femur+Tibia+MTIII)

There are several other possible ways to calculate this, but they often aren’t practical in terms of missing data (many more tibiae are known than fibulae). I would suggest that intermembral indices calculated with the radius are most desirable, for two reasons. First, the radius is a widely preserved and measured bone. Second, you don’t have to deal with the olecranon process, which exaggerates the functional length of the ulna in some animals.

There you have it! Comments?

Categories: Uncategorized

Paring Down the Data

March 19, 2010 15 comments

Awhile back, I brought up the issue of how to handle specimens with multiple individuals, as well as juvenile individuals, and a lively discussion ensued. The general conclusions were:

  1. Any ratios must be calculated for individual specimens, not from Frankensteinian averages of elements from different specimens. It is OK to average ratios across specimens, just not the raw measurements.
  2. Extremely young juveniles should be excluded, as they may differ in body proportions from adults of the same or closely related species.

With this in mind, I’ve started to go through the data set to flag obviously small juveniles. I would propose that we use body size rather than sexual maturity or LAGs as an indicator. Recent studies (e.g., this one on pachycephalosaurs by Horner and Goodwin) have shown that some near-adult size dinosaurs are probably not fully mature. I suggest that we assume that the limb proportions approximate those of adults sufficiently in these individuals (even if the skull morphology doesn’t). This will allow us to keep a few interesting taxa in. For instance, Fruitadens is not fully adult, but probably pretty close to it (according to histology; see the original paper). It’d be a shame to ignore the world’s smallest known ornithischian!

This is pretty straightforward for taxa known from only single specimens of obviously young juveniles (e.g., Avaceratops, Nipponosaurus, etc.). These taxa can be pretty safely removed.

What about animals like Stegosaurus armatus, where we have many specimens of various sizes, from tiny to gigantic? Here, I suggest cutting the specimens that are smaller than 2/3 the size of the largest specimen in one or more measurements (modifying a suggestion from William Miller). This 2/3 is a completely arbitrary cut-off, but I feel that it removes the smallest individuals while recognizing that indeterminate growth means adults can have a range of sizes.

As an example, the longest Stegosaurus femur, from YPM 1853, is 1,334 mm in length. Two-thirds of this is 889 mm, so any specimen with a femur smaller than this would be cut. This includes YPM 1856 (883 mm), DNM 2438 (308 mm), and many more. Of course, we can use our judgment for specimens close to the line. Because some specimens lack a femur, we would look at other elements (e.g., the humerus) to narrow the sample down more.

This elimination method will give us a rarefied data set, with the most egregious juveniles out of the picture. I suggest that we then use the average of the ratios from the trimmed sample for further analysis. In cases where we need actual bone lengths, I suggest using the largest specimen with sufficiently complete data necessary for the analysis.

For Everyone to Check
Following these criteria, I have posted a new Google spreadsheet here. It has two worksheets. The first, titled “To Analyze” (you can find the tabs along the bottom of the screen), has specimens that should be considered for removal marked with a greenish color. Do you agree? Disagree? See another specimen that should be removed? Let me know in the comments.

The second worksheet, titled “Deletion Candidates,” has specimens and taxa that I think should be excluded from the final analysis. The reasoning is given in the final column. Examples include, “can’t match with actual specimen” (for cases where it looks like derivative data given without citation that couldn’t be tied to a particular specimen), “non-diagnostic taxon of uncertain affinity” (should be obvious), etc. Once again, please check it over. Do you agree? Disagree? Say something in the comments here.

Categories: Uncategorized

Meet the Project Participants: David Dreisigmeyer

March 7, 2010 Leave a comment

It’s been a long time since we’ve featured one of our project participants. . .so, here’s a chat with a relative newcomer to the ODP, David Dreisigmeyer.

Tell us a little bit about yourself. Where are you from? What do you do (professionally)? Any other interesting facts?
I’m originally from Pennsylvania, where I attended Juniata College for my undergraduate degree in Pre-law.  After taking a year off, I relocated to Boulder, CO and then started grad school at Colorado State University (in Fort Collins, CO).  After a year in the Economics Department I switched over to the Mathematics Department.  I was first introduced to data/pattern analysis here while working with Michael Kirby.  After my M.S., I moved over to the Electrical Engineering Department for my Ph.D., specializing in signal processing and mathematical physics.

The Dreisigmeyer Family (David, Lisa and Dyson at Pueblo Bonito (Chaco Canyon, NM)

The Dreisigmeyer Family (David, Lisa and Dyson) at Pueblo Bonito (Chaco Canyon, NM)

After grad school, I moved back to the Math Department at CSU for a postdoc in image processing and dimensionality reduction.  After this, we (myself, my wife Lisa and our son Dyson) moved to Los Alamos for a second postdoc.  During this time I did signal and image processing and some protein modeling.  Now we’re in Pennsylvania while I’m at Pitt on a visiting position in the Medical School and the Math Department.  Currently, in addition to the ODP, I’m doing some modeling of the influenza virus (epidemiology and evolution), ecology and some fault detection methods.  I’m also just starting to help out on a developmental aid database.

My wife and I are really into climbing.  We loved New Mexico, especially the trail running (and seeing those bears nice and close up like).  Ghost Ranch was absolutely amazing (the hiking, not those other things you may be thinking of).  And if you have the chance to visit Chaco Canyon you should definitely do so.  My other interest are the American Revolution and history (a la Susan Wise Bauer).

Why did you decide to participate in the ODP?
First of all I always wanted to be a paleontologist until I was about twelve.  A couple months ago I decided to look back into it (after spending some time reading about the field again).  But, how could someone like me actually do research in this field?  A google search on ‘data analysis dinosaur’ led me to the ODP.  This what I had been looking for.  And it was open source — double bonus!

So far, what has been the best part of the ODP for you, and why?
Being able to deal with the data, both the analysis and the ‘cleaning’.  Since I’m a data analyst I love… data.  And, I can’t imagine neater data than dino data.

What have you learned from your participation in the ODP?
Working with paleontologists is a great experience.  It’s awesome to learn about the questions the field is interested in examining.

What advice would you give those who might be interested in helping out with the ODP?
Check everything.  In a database this large, put together ‘by hand’, there’s bound to be some errors, it’s unavoidable.  By having everyone help everyone else out the final product is only improved.

Categories: Uncategorized

Almost Done Aging Our Dinosaurs!

March 5, 2010 2 comments

Thank you to Rob Taylor, David Button, Christian Foth, ReBecca Hunt, Chris Noto, and Jordan Mallon for their work filling in the ages/dates for our dinosaur spreadsheet, as well as helping to update some of the taxonomy. We have just a handful of taxa to deal with now. These include:

  • Finding the ages of: Dyoplosaurus, Zhejiangosaurus, Pseudolagosuchus, Mandschurosaurus, Camptosaurus aphanoectes, Machaeroprosopus, Pantydraco, Loricatosaurus, and Stegosaurus mjosi.
  • How should we treat Iguanodon hollingtonensis? It’s synonymized with I. fittoni, but is that even a valid species anymore?

If you know of any references that can help answer these questions, please feel free to enter the data on the Google Spreadsheet. Thank you!

Categories: Uncategorized

ScienceOnline2010 Update

January 16, 2010 3 comments

My presentation on the ODP came and went, and seemed to be very well received. I’ve had a fantastic time talking with other folks leading and participating in citizen science efforts, and there is plenty to follow up on. Look for more news in the days to come.

And, once I get info on where the YouTube video is posted, I’ll add a link here.

Thank you to all of our participants – your efforts knocked their socks off!

The Project Heads Speak: Matt Wedel

November 19, 2009 Leave a comment

In the final installment of our three part interview series, Matt Wedel shares his thoughts about the Open Dinosaur Project. See part 1 and part 2 for interviews with Andy and Mike.

Matt with another sauropod vertebra

[It] seems (it may be totally wrong) that the project might be more appealing for those who are not professional paleontologists (as you mentioned on the blog, “high school students, school teachers, plumbers“). Why would a experienced researcher be interested in contributing to it?

For some experienced researchers, the project might offer an opportunity to do something new and different. That’s the case for two of the three project leaders (Mike Taylor and Matt Wedel), both of whom typically work on sauropod dinosaurs. The project might also appeal to junior faculty members who are working on building their CVs, and hopefully it will appeal to workers at every career stage who are interested in making science more open (and making more open science). We also hope that some people who have large collections of otherwise unpublished measurements would be interested in contributing, to make their data more available and to boost the project. Of course we realize that the project will not appeal to everyone, and that does not necessarily mean that anything is wrong with either the project or the people who decide not to participate. It’s a big world and there are only so many things that one can meaningfully pursue. We’re not trying to coerce or cajole people into participating. We just want to make the opportunity to contribute open to everyone, and we will be grateful to everyone who chooses to participate. The response already has been very gratifying, and confirms our suspicion that the pool of people who are interested in doing science is not limited to those who hold advanced degrees or are employed as scientists.

Categories: Uncategorized

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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