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The ODP at ScienceOnline2010

October 31, 2009 2 comments

scienceonline2010For those who might be interested, I will be giving a short “demo” of the Open Dinosaur Project at ScienceOnline2010, an annual conference on science and the web (Matt and Mike can’t make it, unfortunately). Because the event is so small, registration filled almost immediately (sorry! There is a wait list, though). You may not be completely out of luck, however–previous conferences have been live-blogged, streamed, twittered, or some combination thereof; look for more information on this as the time approaches. In the spirit of open science, I’ll likely be previewing the talk and soliciting input from all of you (you’re all co-authors of a sort, after all) as the time approaches.

The event is January 15-17, 2010, in Research Triangle Park, North Carolina. Find more information at the conference wiki.

Categories: Publicity

Meet the Project Participants: Diane (DeDe) Dawson

October 28, 2009 1 comment

Continuing our series of interviews, we’re happy to introduce all of you to Diane (DeDe) Dawson. In a project that relies so heavily upon the literature, it is a good thing to have a science librarian on our side!

DeDe Dawson

DeDe Dawson, collecting fossil graptolites in Nova Scotia for her M.Sc. research

Tell us a little bit about yourself. Where are you from? What do you do (professionally)? Any other interesting facts?
I am originally from the Toronto area, but have just recently moved to Saskatoon (Saskatchewan, Canada) to work at the University of Saskatchewan as the Natural Sciences Liaison Librarian. I am responsible for Geology and Chemistry subject areas, so I maintain the collections in these areas as well as provide reference and “information literacy” instruction to students and faculty. Basically, I help them find the information that they need and teach them effective literature searching skills.
I have quite a varied background. My undergraduate degree is in Biology, my main interest being evolution and zoology. I completed an honours thesis project on several trilobite species found locally (in Ontario) – collecting all the specimens myself and performing some basic morphometric analyses. Certainly I’ve always had an interest in natural history in general, and a particular fascination with fossils. So, during the summers I worked in the Vertebrate Paleontology lab of the Royal Ontario Museum in Toronto. After graduation, I remained at the ROM as a technician for several years and was lucky enough to be involved in an excursion to collect Jurassic marine reptile fossils in northern British Columbia! But it turns out though that my interests are much older… and without backbones! I ended up returning to invertebrates for my MSc thesis in Earth Sciences: graptolite phylogenetics. During the process of my Master’s thesis research I began to realize that I also really enjoyed the literature search, and while I loved paleo, I didn’t see a career in it for me. Academic librarianship presented itself as a profession more suited to me and a way to maintain my connection with the academy.

Why did you decide to participate in the ODP?
Besides my longstanding interest in all things paleo, I also have a very strong interest in open access issues and what we librarians call “scholarly communication.” Being a librarian I am all too aware of how expensive some library resources are, particularly scientific journals. The exorbitant costs often put the research published by scientists out of reach of the general public, and increasingly out of reach of budget-restricted institutions too. I realize that I am in a privileged position in having access to many of the articles that the public does not, so I want to be able to help the ODP gather this kind of data. I also want to support any effort that shares knowledge, increases collaboration across disciplines, and challenges barriers to accessing information. I am very intrigued by the concept of the ODP as a potentially new form of scholarly communication and collaboration in the sciences, and I’m eager to see how the project unfolds!

So far, what has been the best part of the ODP for you, and why?
The best part so far has been to put my library’s collection to use! I am always assisting others to use the collections here, but now I have a purpose for the collection too. I am relatively new to this library, so have not had a lot of time (or reason) to explore the stacks yet. It is very satisfying to be able to pull some of the dusty old journal volumes from the shelves and make use of them! I have also been able to identify and correct some access problems with electronic journals during this process. So I’m actually doing my job at the same time!

What have you learned from your participation in the ODP?
I have learned what a scapulocoracoid is!

What advice would you give those who might be interested in helping out with the ODP?
First spend some time reading through the ODP website, especially some of the tutorial postings about anatomy and what the abbreviations in the forms refer to. This has saved me from hassling the project leaders with lots of questions! Also, I found it easiest to start with verifying some of the articles already entered. This has given me a better feel for the process, and what to look for in the articles. Soon I might look for some new articles myself…

Categories: About Us, Interview

The Open Dinosaur Project in Nature

October 21, 2009 6 comments

logo150We at the ODP are excited to announce that the project is getting some publicity this week courtesy of a little journal by the name of Nature. A short letter to the editor [subscription required*], written by me, Mike, and Matt, appears in the current issue.

The letter was crafted (at Mike’s suggestion) in response to a series of articles and editorials (freely available here) in the 9 September 2009 issue of Nature, focused on the issue of data sharing and archiving. Right now, data sharing (either pre- or post-publication) is a huge concern in many fields of science. Without accessibility to original data, it is much tougher to verify results, incorporate new data into previous analyses, or use the data for new, potentially unrelated analyses. So, it should be a no-brainer to release the data underlying publications, right?

Not so fast. Some scientists are worried about being scooped (if they release data prior to publication), or losing a competitive edge to colleagues once the “exclusive” data are released (if they release data after publication). In other cases, there is no institutional support for the release of data (which requires time and money, however minimal). Furthermore, the rewards for actually releasing data can be unclear (a critical factor for scholars at the beginning of their careers, who need citations and recognition for hiring, tenure, and promotion).

All of these problems were covered in some depth in the special issue of Nature. Where does the ODP fit into this, and what does our letter add to the discussion?

We felt that the Nature articles did an excellent job of making the case for why data sharing is important to the scientific community. But, it left out one key ingredient – why data sharing is important for the world outside of professional scientists. So, we focused our correspondence on this problem.

For a field like paleontology, there is a tremendous interest in the latest (and even the not-so-latest) research findings. If you follow the Dinosaur Mailing List, the blogosphere, or any other internet venues, you will notice an active and engaged community of both professionals and amateurs. Requests for PDFs, photographs, measurements, and all sorts of additional information are quite common, reflecting an intense fascination with the field.

Public talks, popular web pages, and blogs are great for public outreach. . .but there is a demand for something more. Folks are interested in high resolution specimen photographs. . .specimen measurements. . .cladistic data matrices. So, we argue that for a field with broad public appeal like paleontology, the release of data should be a part of our public outreach efforts in addition to the immediate scientific role of data availability. People get excited by these data!

This is why we started the Open Dinosaur Project, and why we run it as openly as possible. First and foremost, it is a research project. We are collecting data to investigate some interesting questions – and we want these data to be available to other researchers! In our view, the database doesn’t do anyone any good if it stays locked up on one person’s hard drive.

Charles W. Gilmore, accidental contributor to the Open Dinosaur Project

Charles W. Gilmore, accidental contributor to the Open Dinosaur Project.

We also benefit when other researchers are open with their data – this project would not be possible if original specimen measurements weren’t published in papers. The ODP thrives on data sharing. Principal components analysis and phylogenetically independent contrasts either didn’t exist or were decades away from paleontological application when Charles W. Gilmore published his monograph on Stegosaurus back in 1914. Without putting too many words in his mouth, I think it is fair to say that he would be quite pleasantly surprised that we’re using his data for something he never intended.

Second, and just as important, the ODP is a public outreach effort. There are many, many “amateurs” who want a chance to participate in real, substantive scientific investigations, and many professional paleontologists who want to contribute to collaborative research efforts. Without the combined efforts of nearly 40 contributors from all walks of life, the ODP would only be a blog with a catchy title and cool logo. All of our project participants have made important contributions, and not just in the realm of data entry. The ongoing discussions on this blog are proof positive of the deep involvement of many, many individuals.

In sum, data sharing is something we believe in. It moves science forward, both by allowing new things to be done with old data, as well as offering opportunities to involve new people in the scientific process. If we scientists are serious about our work, and about communicating our work, data sharing is not just an option. It’s the only option.

Citation: Farke, A. A., M. P. Taylor, and M. J. Wedel. 2009. Public databases offer one solution to mistrust and secrecy. Nature 461: 1053. [link*]

*subscription required; the publication agreement with Nature prohibits us from posting the full text of the article for six months; please contact Andy if you would like a copy of the text.

Big News Tomorrow (and a Plot)

October 20, 2009 5 comments

Late tomorrow we look forward to bringing you a Big Project Announcement (well, more of a Big Project Promotion). So, tune in then for more details.

Plot of RatiosIn the meantime, enjoy this new plot of our data. The other day Tor Bertin suggested we take a look at MT III and MC III ratios. So, here’s a chart showing the MT III:tibia ratio versus the MC III: ulna ratio. A few things to note:

  • Hadrosaurs are still very, very bizarre. Their MC IIIs are relatively longer than in any other ornithischian.
  • The vertical spread in ceratopsians is probably because both small, bipedal forms as well as large, quadrupedal forms are included in that category.
  • Basal ornithischians have very long MT IIIs. Is this a consequence of their generally small size?
  • We need more thyreophorans (stegosaurs, ankylosaurs, and the like) with MC and MT data! This group, for various reasons, is one of the remaining holes in the data set.

In the interests of full transparency, I deleted the point for for the ornithopod Lurdusaurus arenatus. Its metatarsal III length seems far too small for the size of the tibia. This may be an error in the original paper (I even went back to triple-check it!), or it could be that this taxon has tibia:metatarsal proportions completely unlike any other ornithopod.

Want to See Some Other Plots?

We’re always looking for new ways to present the data on the blog. If you have any requests, feel free to note them in the comments section.

Or better yet. . .don’t forget that the data are freely available to everyone! There is absolutely nothing stopping you from playing with the data yourself. In fact, we encourage it. Odds are quite good that, like many project participants, you’ll pick up something nobody else has noticed yet.

Categories: Data Exploration

Key Concepts: Scaling

October 19, 2009 7 comments

Allometry in a Golden RetrieverAnyone who has dealt with puppies, kittens, or human babies has probably noticed their freakish (“cute”) body proportions relative to adults. The heads are too big and the limbs too small! Fortunately, most of us grow out of this condition as we mature. The change (or lack of) in the proportions of an organism as its overall size changes is called scaling.

Scaling relationships can be compared between species, within species, or even within the same individual over the course of its development. In the present round of the ODP, we’ll be focusing on the first comparison, although many of the examples that follow will draw on within-species or within-individual scaling.

Scaling, as a whole, can be divided into two general forms: isometry and allometry. The key difference between these terms is how the different parts of an organism change in proportion to each other with increasing or decreasing overall size. Isometry (a.k.a., isometric scaling) means that everything stays the same. Here, imagine a condition in which a baby maintains its proportionately large head size into adulthood. Contrast this with the actual condition, allometry. In humans (and most other vertebrates), the head becomes proportionately smaller to the rest of the body. When different parts of the body scale at different rates, this is called an allometric scaling relationship. You can see this in the puppy and adult golden retrievers at right.

Allometry is divided into two classes – negative and positive. Our oft-cited baby’s head is a classic example of negative allometry—the head becomes relatively smaller with increasing body size. Other features might show positive allometry—for instance, the horns of male bighorn sheep grow at a much faster rate than the rest of the body. In a lamb, the horns are tiny compared to the skull. In the adult, the horns are huge!

Scaling comparisons are pretty straight-forward for linear measurements (e.g., comparing scaling of femur length relative to humerus length). Isometry is indicated by a one-for-one change in size between the two elements. But, the complications of mathematics mean that things are a little less intuitive when considering areas or volumes. Consider a cube measuring 1 mm along each side. Its volume (length x width x height) is 1 cubic mm. If we double the size to 2 mm along each side, its volume doesn’t just double, but leaps to 8 cubic mm (2 mm x 2 mm x 2 mm). Bumping the size up to 3 mm along each side, the volume is now 27 cubic mm (3 mm x 3 mm x 3 mm). Length along any given dimension has changed by a factor of 3, but volume has changed by a factor of 27 (3 cubed). Similarly, the cross-sectional area has changed by a factor of 8 (2 cubed). We won’t be doing much with areas or volumes for the present study, but this is an important attribute of scaling to keep in mind.

So, one important analysis to be considered in ODP 1.0 is how limb bone lengths scale against each other. For instance, does the humerus increase its length at the same rate as the ulna, or metacarpals, or phalanges? Or, does the humerus get relatively shorter in larger animals? The departure from simple isometry might be for any number of reasons – perhaps larger animals need relatively more surface area for muscle attachment. Or perhaps weight limitations mean that certain bones can’t increase their size too quickly. We’ll just have to analyze the data and see what the trends are!

Image credits: Puppy image licensed under Creative Commons License 2.0; adult golden retriever in the public domain.

Key Concepts: Scaling
Anyone who has dealt with puppies, kittens, or human babies has probably noticed their freakish (“cute”) body proportions relative to adults. The heads are too big and the limbs too small! Fortunately, most of us grow out of this condition as we mature. The change (or lack of) in the proportions of an organism as its overall size changes is called scaling.

Scaling relationships can be compared between species, within species, or even within the same individual over the course of its development. In the present round of the ODP, we'll be focusing on the first comparison, although many of the examples that follow will draw on within-species or within-individual scaling.

Scaling, as a whole, can be divided into two general forms: isometry and allometry. The key difference between these terms is how the different parts of an organism change in proportion to each other with increasing or decreasing overall size. Isometry (a.k.a., isometric scaling) means that everything stays the same. Here, imagine a condition in which a baby maintains its proportionately large head size into adulthood. Contrast this with the actual condition, allometry. In humans (and most other vertebrates), the head becomes proportionately smaller to the rest of the body. This is called an allometric scaling relationship.

Allometry is divided into two classes – negative and positive. Our oft-cited baby's head is a classic example of negative allometry—the head becomes relatively smaller with increasing body size. Other features might show positive allometry—for instance, the horns of male bighorn sheep grow at a much faster rate than the rest of the body. In a lamb, the horns are tiny compared to the skull. In the adult, the horns are huge!

Scaling comparisons are pretty straight-forward for linear measurements (e.g., comparing scaling of femur length relative to humerus length). Isometry is indicated by a one-for-one change in size between the two elements. But, the complications of mathematics mean that things are a little less intuitive when considering areas or volumes. Consider a cube measuring 1 mm along each side. Its volume (length x width x height) is 1 cubic mm. If we double the size to 2 mm along each side, its volume doesn't just double, but is cubed (2 mm x 2 mm x 2 mm) to 8 cubic mm. Bumping the size up to 3 mm along each side, the volume is now 27 cubic mm (3 mm x 3 mm x 3 mm). Length along any given dimension has changed by a factor of 3, but volume has changed by a factor of 27 (3 cubed). Similarly, the cross-sectional area has changed by a factor of 8 (2 cubed). We won't be doing much with areas or volumes for the present study, but this is an important attribute of scaling to keep in mind.

So, one important analysis to be considered in ODP 1.0 is how limb bone lengths scale against each other. For instance, does the humerus increase its length at the same rate as the ulna, or metacarpals, or phalanges? Or, does the humerus get relatively shorter in larger animals? The departure from simple isometry might be for any number of reasons – perhaps larger animals need relatively more surface area for muscle attachment. Or perhaps weight limitations mean that certain bones can't increase their size too quickly. We'll just have to analyze the data and see what the trends are!

500 and beyond!

October 17, 2009 1 comment

Today, our public database of verified measurements passed 500 entries. Thirty seven contributors, ranging from students to programmers to librarians to professional paleontologists, combed nearly 130 publications and filled just under 3,500 spreadsheet cells with numerical data. Many previously unpublished measurements have also made the list. A few contributors entered data for a single specimen, and others entered data for dozens. Any way you slice it, this is an impressive effort.

The past week has also seen some nice mentions of the ODP in various places:

  • Citizen Science Projects blogged about the ODP this past week. For more on “citizen science” from the ODP’s perspective, check out Matt’s post on Engineering the Shiny Digital Future.
  • CBC 1’s program Spark had a featured a segment on citizen science, including a mention of the ODP! It’s worth checking out for a fun and informative background on the ideas behind open notebook science and citizen science. The link to the program is here, and you can download the MP3 of the entire podcast here. The segment on open notebook science runs from 16:00 to 23:30; ODP is discussed from 20:05 to 20:25.
  • Mathematics professor Andy Lang, a long-time supporter of open notebook science, blogged about how and why he got some of his students involved in entering data for the Open Dinosaur Project. We love to see the project integrated into an educational environment in this way!

Plot of the Moment

October 16, 2009 13 comments

Every once in awhile, it’s fun to plot up the data and see what they look like. Lately, it’s been especially fun because our data set just keeps on growing and growing! Right now, we have 425 436 455 verified entries, 190 183 unverified, and around 30 20 10 in the double-check queue. We’ve also added a few new contributors this week, which is another nice bonus. Excellent progress, everyone!

MT III vs. Tibia Length (log mm)

MT III vs. Tibia Length (log mm); click for an enlarged view. Please forgive the color scheme - in the interest of time, the defaults were used.

This time, I decided to plot tibia length versus metatarsal III length for a variety of animals (at right; click on it for an enlarged version). As in one of our earlier plots of tibiae versus femora, ankylosaurs are weird. Their metatarsals are just really, really stubby relative to the tibiae (and the tibiae were really stubby relative to the femora). Interestingly, the saurischians in our sample seem to consistently plot above the ornithischians; in other words, saurischian metatarsals are long relative to the tibia (for the basal saurischians in our sample, at least).

Some analyses of mammals have suggested that a long MT III relative to the tibia may indicate more cursorial tendencies than for animals with a short MT III. Does this perhaps hold in dinosaurs? Were saurischians speedy, and ankylosaurs plodding? Or is there a phylogenetic effect that swamps any functional signal (as suggested for the mammal patterns by some authors)? Lots of additional analyses are needed.

The plot also shows a few gaps in our verified data set. Stegosaurs, basal thyreophorans, and pachycephalosaurs are not represented at all in this plot, because we don’t have any measurements of both a third metatarsal and a tibia for any members of these groups. If you’re looking for a data entry project, these would be excellent groups upon which to focus our efforts.

Do you want to do your own analysis? You can! All of the data used to create the plot above are publicly available.

Meet the Project Participants: Rob Taylor

October 11, 2009 1 comment

Continuing our series of interviews with project participants, we’re now happy to introduce you to regular contributor Rob Taylor (no relation to Mike). Beyond Rob’s contributions to the ODP, many of you may know him for his work at The Theropod Archives – it’s a great resource for finding open access and public domain literature on those saurischian dinosaurs!

Rob Taylor at work on his database

Rob Taylor at work on his database

Tell us a little bit about yourself. Where are you from? What do you do (professionally)? Any other interesting facts?
I was born and raised in Watertown, New York, but recently settled in southeastern Pennsylvania after residing in Northern Virginia for a number of years. I’m 41, and work as a drug safety analyst, computer programmer, and database manager for a large health care IT company. Husband to Wendy – an aspiring author, ice hockey fan (with nigh onto encyclopedic knowledge of the sport, I might add), and possessor of particular fascinations with cephalopods and the Burgess Shale; father to Nick (age five, dinosaur enthusiast) and Katie (one and a half, budding dinosaur enthusiast). Katie is watching Dr. Scott and the Dinosaur Train as I type this.
And yes, count me among those who simply never outgrew their interests in dinosaurs. In 2004, seeking to further my knowledge on the subject, I began building a database of all known dinosaur and pterosaur genera, fleshing it out with whatever publicly available data I could find. It’s a project that has been rewarding on many levels. Ultimately, a partnership was forged with the Paleontological Research Institution in Ithaca, New York, where a prototype of the database was installed in their Museum of the Earth’s fossil discovery lab. Most importantly, the effort drove me to the primary literature for the first time, and allowed me to experience first-hand the benefits of open access.
Later, wanting to make my own contribution to the open access movement, I developed and launched The Theropod Archives web site. Increased work obligations have forced me to put the Archives on the back burner for a while, but followers of the project can be assured there is more to come. (There’s just the matter of a few ornithischian limb bone measurements to key in first!)

Why did you decide to participate in the ODP?
When I think about it, much of the effort I’ve put into my dinosaur projects has been about wanting to approximate the scientific experience. I’m grateful that there seems to be growing recognition among the scientific community that dedicated amateurs and knowledgeable enthusiasts might bring something to the table. Honestly, the opportunity to contribute to actual science – dinosaur science, no less! – is something I’ve always dreamed of. (And then there’s that carrot-on-a-stick offering of a publication credit dangling out front…)

So far, what has been the best part of the ODP for you, and why?
It’s the feeling of satisfaction that comes with making an actual contribution to science, coupled with a sense of excitement over being involved in a project that’s clearly breaking new ground.

What have you learned from your participation in the ODP?
Certainly those early tutorials were very useful in shoring up my knowledge of appendicular anatomy; however, the real surprise was in learning that I seem to absorb and retain a lot more when going at a scientific paper with a specific purpose in mind.

What advice would you give those who might be interested in helping out with the ODP?
I would suggest taking the time to review each work in its entirety, even though most measurements of interest may fall predictably within a single section of the paper. Read the figure captions, review the plate explanations, and note any additional information that could potentially be useful to evaluators in the email that accompanies your submission. The data presented in tables can sometimes be misleading if viewed out of context!

Categories: About Us, Interview

The ODP at One Month

October 8, 2009 2 comments
by Armchair Caver; CC BY-NC 2.0

Cake by Armchair Caver; CC BY-NC 2.0

Happy Birthday, ODP!

It’s now been one month since the official launch of this project. We started out with three project contributors (me, Matt, and Mike) and 147 verified and unverified data entries. As of this morning, 34 project members from around the world have contributed 637 unique entries. If you count original entries and verification entries separately, this is a grand total of 1,153 submissions!

If you haven’t already, take a few moments to enter some data. It’s painless, really! And if you have any questions or problems, there are lots of people who can help you out. Good luck, and here’s looking forward to the next month of data collection!

Categories: Progress Reports

The Road Ahead

October 7, 2009 9 comments
Measuring Protoceratops

Measuring Protoceratops

Despite the fact that the blog has been quiet, there is a lot going on behind the scenes at ODP. In the next week or two, you can (hopefully) look forward to some Big Announcements – for reasons that (hopefully) will be apparent, we’re keeping this one under our hat for now.

Presently, we have 394 verified and 197 unverified entries, with another 25 entries in the double-check queue. Great work, team! Our data entry is moving along very nicely. The system of entering and re-entering data has been paying dividends, too. Many errors, small and large, have been caught this way. Thank you to everyone who has made the ODP a success so far!

We are still very much looking for data of all sorts. Right now, the most useful data are measurements from associated skeletons – specimens where more than one bone from the same individual was found together. Specimens of isolated elements (a lone humerus, or a lone femur) are also welcome, but are presently much less useful for the research goals at hand. Because we are comparing bones across the skeleton, an isolated tibia or the like won’t likely make it into the final analytical mix. A few basal theropods and sauropodomorphs are also useful for outgroup comparison, but we won’t need a whole ton of those until the later phases of the project.

At this point, I thought it would be useful to lay out a rough timeline for Phase I of the project, based on discussions that Matt, Mike, and I had a few months back. Here goes:

ODP Timeline (Subject to Change)

  • 8 September 2009: Launch of ODP and Phase I of Data Collection (ornithischian dinosaurs)
  • 1 February 2010: Finish data collection, begin data analysis
  • 1 March 2010: Finish data analysis, begin writing the paper
  • 1 April 2010: Submit paper to journal

If it looks like data submission is beginning to taper off, we may move up the data analysis phase a little bit. Otherwise, we want to stick to the schedule as much as possible.

Thoughts? Questions? Comments?

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