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Archive for November, 2009

Synonym and Institutional Abbreviation List Up For Editing

November 30, 2009 24 comments

In the wake of the post the other day on upcoming tasks for the ODP, Christian Foth and Rob Taylor have submitted first passes on the list of taxonomic synonyms and institutional abbreviations (click on the links to access files for taxonomic synonyms and institutional abbreviations). To simplify things, these files should be edited directly online if at all possible. I have authorized read/write access for all users. NOTE: At present, a Google account is required to access this file. If you do not have a Google Account and do not desire one, you may email Andy (andrew.farke@gmail.com) for the file.

I would recommend that you initial any changes, corrections, or additions, just so we can keep track of the relevant contributors. Feel free to discuss concerns or differing opinions in the comment threads.

Categories: To-Do List

Big Tasks Ahead

November 24, 2009 22 comments

So now it’s time to start thinking about some of the big tasks we’ll need to do in preparation for the paper. In no particular order, these include:

  • Construct a composite phylogeny of all ornithischians (and our outgroups) for use in the quantitative comparative analysis. This will need to be in some sort of format readable by Mesquite or a similar program. This phylogeny will need to be tied to the (preferably recent) literature. It shouldn’t be necessary to run a matrix from scratch – instead, we should focus on just melding trees from various papers together into a single global phylogeny.
  • Compile a list of what all of the museum abbreviations mean (institution, city)
  • Obtain reasonably accurate age ranges for all of the taxa in the database (probably down to the stage – e.g., Maastrichtian, Bathonian, etc.). One of our analyses (as Randy Irmis will detail in a future guest post) will look at ornithischian limb morphology over time.
  • The PLoS ONE reference format uses abbreviated journal titles – but most of our titles aren’t abbreviated yet. We’ll need to get all of our references into a PLoS ONE-friendly format.
  • Anything else that should be on the list?

These are the sorts of things that anyone can work on – and many are tasks that could/should be handled by multiple individuals. Any takers?

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

The Project Heads Speak: Mike Taylor

November 18, 2009 2 comments

In the second installment of a three-part interview with Mike, Matt, and me, here’s Mike Taylor! Matt will follow tomorrow.

Mike Taylor with dorsals vertebrae A and B of Brachiosauridae indet. NHM R5937 ("The Archbishop") in right lateral view.

Mike Taylor with dorsals vertebrae A and B of Brachiosauridae indet. NHM R5937 ("The Archbishop") in right lateral view.

Do you believe you might be setting a trend?
Part of what’s so exciting is that we are in such uncharted territory.  We really have no idea whether this particular project [is] setting a trend — it’s nice to think it might be so, but equally this might end up being the one project of its kind.  It might crash and burn, or it might spiral out of our control into something really far reaching.  Three days in, it’s much too early to make concrete predictions, beyond that we’re certain to learn something.  Whatever comes out of this project in the short term, I hope that one of the long-term results is that if other people do start broadly similar large-scale collaborative projects, they’ll be able to learn from our mistakes and do a better job than we’re doing.

And this project is only a tiny part of a much bigger … I wanted to say movement, but it’s nothing as well defined as that.  It’s an ill-defined and approximate trend, but generally what’s happening is that the whole way we do science is changing in ways whose ends are hard to foresee.  Electronic publishing is no longer exotic, and some prestigious journals have no print edition; open access to online articles is increasingly widespread and journals that don’t do it are looking more and more reactionary; scientific blogging is becoming very serious in places (not least at our own Sauropod Vertebra Picture of the Week blog, http://svpow.wordpress.com/), with original research sometimes “published” in this way without recourse to journals at all; even the most staid journals are accepting citations of online resources.  Generally the trends seem to be towards decentralisation of authority, increasing openness and progressive divorcing of medium from message.  The Open Dinosaur Project fits very comfortably into that loose coalition of ideas: we’re trying to democratise science, open up data, blog the process, and make sure that the final publications are freely available to the world.

So whether or not other groups in the future do things that are similar in detail to the ODP, I do think that we are trending inevitably towards the kind of scientific environment in which those KINDS of thing — things in the same SPIRIT as the ODP — are going to proliferate.  If we’re a small part of taking the world in that direction, I’ll be happy with that.

Finally, will the contribution be limited to the creation of data registers? Can people contribute in other ways?
Again, we’re feeling our way here.  What we know for sure is that volunteers — including those with no academic background — can make a real contribution in aggregating data.  For that reason, and also of course because data collection is one of the first phases of a project, that’s what we’re concentrating on now, but we’re certainly open to pushing more work onto our volunteers down the line!  In particular, there are lots of different kinds of analyses that can be run on the data, and it’s unlikely that the three of us have the necessary background to do all of them — maybe some of the project contributors can do, I don’t know, principle component analysis or something. We’ll also need people to help organize and format the project’s massive bibliography, as well as track down abbreviations and other crucial (but hard-to-find) pieces of information. Figure preparation, and especially artwork, is another obvious area where we can hope to find and and use the talents of ODP  volunteers.

Categories: About Us, Interview

The Project Heads Speak: Andy Farke

November 17, 2009 2 comments

Mike, Matt, and I recently were interviewed about the ODP by the Brazilian science publication Ciência Hoje On-line. Only a few select bits of the interview were included in the article, so the next few posts here will include our full responses (with permission from our interviewer, Ciência Hoje’s Raquel Oliveira). Exercising privilege of being project lead, and because the interview makes the most sense in this order, here are some of my responses. Mike Taylor’s will follow tomorrow, and Matt Wedel the next day.

Andy Farke

Andy Farke

Why did the group launch the project? You meant to distribute the job? From what I understood, you want to analyse a huge amount of data.
We launched this project for three reasons. First, we wanted to do some good and interesting science. In the case of collecting all of the data, we knew right away that it would have to be a task spread across many individuals. And the best way to do this seemed to be just opening up the process to anyone who wanted to help out!

Second, we wanted to get the general public excited about and involved in doing “real” science, working in cooperation with paleontologists. There is a great interest out there in paleontology, particularly dinosaurs. It’s amazing how many non-paleontologists read the technical literature! I thought, “Why not harness this enthusiasm?” There have been many people waiting for this sort of opportunity (even if they didn’t know it), and I think the response speaks for itself. In less than a week, we’ve had over 40 non-specialists indicate interest in the project, and half of these have already submitted data. I look at it as a tremendous outreach opportunity! And the information flow goes both ways–we’ve had some very insightful comments, observations and suggestions from “amateurs.” They’re making substantive contributions to the project, beyond “just” entering data.

Finally, we want to promote the concept of “open science” in paleontology. It can be a pretty secretive field, sometimes for good reason–to prevent theft of fossils from dig sites, for instance, or to avoid being “scooped” in naming a new dinosaur. But, I think there are areas where we can change this culture. For instance, lots of scientific publications are based around huge data sets of measurements. . .but often these measurements are never published, and are eventually lost as people retire, die, or switch careers. Not only does it make it difficult to reproduce the analysis (an important cornerstone of science), but it also means that it is much more difficult to build upon previous work. We’re continually re-inventing the wheel. I would never say that every piece of in-progress research should be blogged, or that every piece of data should be immediately available, but I would like more of us scientists to have data and publication availability as a higher priority. It will take time, but I am optimistic. There are many paleontologists who are starting to buy into the idea of “open science”. If some branches of physics can do it, with the arXiv website, and if molecular biology can do it, with tools like GenBank, surely paleontology can change with the times too.

How do you think the academia will react to the Open Dino?
Already, we’ve noticed an interesting mixture of excitement and skepticism. Some people have looked at the project and said, “Wow, why didn’t I think of that?!” They’re excited about the possibilities. And others have said, “Well, there are so many potential problems, scientifically and organizationally, that it will never succeed.” By opening up the project, by blogging about it, we want to be able to address any concerns about the structure and science of the project essentially in real-time. Some legitimate concern does stem from the fact that we’re pulling data from the published literature – how do you know that all of these scientists measured bones consistently, for instance. So, we’re focusing on a set of relatively simple bone lengths that should hopefully be more consistently measured. For the large-scale evolutionary analysis that we’re conducting, I suspect that minor variation in measurement style from paleontologist-to-paleontologist is a rather small problem.

On another note, I think there is some reaction – positive and negative – to the fact that the project is going to be so transparent. By blogging the project, all of our successes and mistakes will be out there for the world to see. I think some folks will like that, and others won’t.

Categories: About Us, Interview

The ODP in Portuguese

November 16, 2009 2 comments

The Open Dinosaur Project is featured as one of the inaugural articles for the newly designed website of the Brazilian science news publication, Ciência Hoje On-line.  The article is in Portuguese, but a somewhat-readable translation is available through the wonders of Google Translate.

Look for expanded versions of the interviews behind the article soon!

Categories: Publicity

Speaking of the Bipedal / Quadrupedal Transition. . .

November 11, 2009 5 comments
Aardonyx, after Yates et al. in press

Aardonyx, after Yates et al. in press

Dedicated readers of the blog likely remember that one of the core research goals of this project is to examine the bipedal/quadrupedal transition in ornithischian dinosaurs. Of course, ornithischians weren’t the only group to experience such locomotor changes during their evolution! A new paper on the bipedal/quadrupedal transition in sauropodomorphs (the saurischian dinosaur group including animals like Plateosaurus, Apatosaurus, and Brachiosaurus) has just appeared on Proceedings of the Royal Society B‘s FirstCite. This paper, headed up by Adam Yates, details the anatomy of Aardonyx, an early sauropodomorph from the Early Jurassic of South Africa. The authors posit that the new critter was a habitual biped, although it had many features that presaged the anatomy of later quadrupedal forms.

The paper has already been covered in some depth elsewhere in the blogosphere – check out posts by senior author Adam Yates, Dave Hone, Sid Perkins, and Bill Parker for more.

If you haven’t contributed data to the Open Dinosaur Project yet, and are looking for something to do, this might be a good one! The supplementary information (freely available) is chock-full of measurements.

Citation
Yates, A. M., Bonnan, M. F., Neveling, J., Chinsamy, A., and M. G. Blackbeard. In press. A new transitional sauropodomorph dinosaur from the Early Jurassic of South Africa and the evolution of sauropod feeding and quadrupedalism. Proceedings of the Royal Society B. doi:10.1098/rspb.2009.1440. Published online 10 November 2009. [subscription required for full access]

Categories: Relevant Research

Big Announcement – A Whole Pile of Data!

November 6, 2009 1 comment

Awhile back, I had alluded to some big announcements for the project. Announcement 1 was, of course, our little contribution in Nature. Now it’s time for Announcement 2.

We at the ODP are very, very happy to announce the contribution of a huge chunk of original measurements from Matt Carrano at the Smithsonian Institution. Matt has graciously offered the core of his dissertation data set (and then some), with measurements from over 600 specimens relevant to the ornithischian component of this project. The database is particularly full of measurements from the hindlimb, including a number of never-before-published data points.

Combining the data submitted by all of us with the Carrano ornithischian dataset, we now have nearly 1,200 individual verified entries in the ODP database! That’s a 21-fold increase over what we had at the launch of the project. Great work everyone, and a huge thank you to Matt for his generosity. As before, the entire dataset is freely available for download and use by anyone.

So what does a plot generated with the gigantic database look like? Now you know!

MT III vs. Tibia L

Log Length of MT III regressed on Log Length of Tibia. Slope=0.852 (significantly different from 1); r^2=0.928

Categories: Progress Reports
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