Home > Housekeeping, To-Do List > Summertime, open ignorance, and finishing the project

Summertime, open ignorance, and finishing the project

Hi, all. Thanks for your patience this spring. Sorry we’ve let things lie fallow for so long. Many thanks to everyone for keeping things ticking over while we were AWOL.

Like Andy said in the last post, it’s time to wrestle this thing to the ground and stick a knife through its heart (I may be paraphrasing a bit). Andy, Mike, and I have cleared some protected time in our summer schedules to finish the analyses and write the paper. The next two weeks may be a bit quiet on our end as we all work to get other things tied up and off our desks–and as Andy moves his residence!–but we should be ready to hit it hard by the second week of June.

There is a lot of work to be done, and there are lots of ways to contribute to the paper for everyone who wants to be involved, right now and continuing through the summer. I’ll give some suggestions in a minute. But first, an admission.

We don’t really know what we’re doing here. That’s obvious with the social side of the project, because nothing like this has been attempted before, at least not on this scale or with this degree of openness. But it’s also true on the scientific side. None of us (Andy, Mike, or I) has ever written a paper on this topic. There are some specific analyses that we need for the paper that we’ve never run before. So we are very much learning as we go–this is the open ignorance I alluded to in the title. This isn’t by accident. We could have chosen to do something simpler and less ambitious–perhaps repeat a project that we’d already done before with only the names of the critters changed. But we wanted to learn from the project–from you, the contributors, and alongside you–and to grow as scientists from having participated in it. And we want the final product to be a truly collaborative effort, and not to simply walk everyone through a series of moves that we already know by heart.

And it is working. We have been amazed at the level of enthusiasm and commitment that you have brought to the project, and our only regret is that we have not reciprocated with the sustained level of effort that you, and the project, deserve. So we’re committing ourselves to getting this done, starting now.

How can you contribute? Here are some suggestions:

  • Update the database. New taxa continue to be described, new descriptions of established taxa continue to be published, and older publications continue to become available. So if you have been wanting to do some (more) good old-fashioned ODP gruntwork, there’s still a little time.
  • Suggest relevant references, or read up on the ones that are already suggested. It might be a good idea to gather those references together so they can be made available to anyone who is working on the project. We’ll probably do a post specifically on this in the near future, but there’s no reason not to be pulling things together in the meantime.
  • Look at the outline of the paper, suggest improvements, and–if you are so inclined–start writing those bits that can be written right now. For now, feel free to post chunks in comments or send them to us. Jay Fitzsimmons’s paragraph on citizen science and the ODP is a good model to follow. We’ll definitely be posting more on the actual writing of the paper soon, but, as with boning up on the relevant references, there’s no reason to hold off if this is something you’re interested in working on.
  • Analyze data. Obviously there are limits to what we can do until we really finalize the database once and for all, but this is a good time for exploring the data and for test-driving analyses to be done on the finalized database. We have enough data that overall trends are not likely to change much, so anything that looks interesting now will probably still be interesting in the final version.
  • Work on a time-calibrated phylogeny for the dataset. This is a big one, again probably deserving of a post of its own. We’ll also need to update the “master tree” to include the most current phylogenetic trees for the included taxa. If you’re into trees, timelines, or both, the mothership is calling you home.
  • Figure out how to do disparity analyses. This is one of those things that we project organizers have never done before. We’re reading up on it right now, but if you know anything about it, let us know. Even when we get up to speed, we’ll still need your input. Like Project Mayhem, you can determine your own level of involvement.
  • Other stuff? The project is probably at its maximum breadth in terms of types of work to be done. Up until now we’ve focused mainly on building the database and outlining where we want to go, and in a few weeks we’ll have the database finalized and our efforts will narrow as we focus on running the analyses and writing the paper. So whether you’re brand new and want to get involved for the first time, or an old hand who wants to do something different, there is something around here that needs doing. Have a look at the tasks list, go back through the last few posts, and see what appeals to you. If in doubt, give us a shout.

That’s all for now. Stay tuned for more posts very soon. But don’t just stay tuned–keep posting ideas, data, references, bits of text, and whatever else you want to contribute. We’ll do likewise.

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Categories: Housekeeping, To-Do List
  1. May 26, 2011 at 2:45 pm

    This is great news! I’m excited to see this project come to completion.

  2. May 26, 2011 at 2:53 pm

    I’m very pleased to see the project approaching this milestone!

  3. Christian Foth
    May 30, 2011 at 8:44 pm

    hi everybody,

    cool that the project goes in the next and hopefully final round. I like to do the supertree and timescale stuff. In this context I can also do the the parsimony analyses with mesquite. However, if you really want to update the data set (after a year of abstinence it might be good to udo that) I would wait till the final version is ready.

    So let’s get it on.

  4. Sin Wei
    June 1, 2011 at 1:48 pm

    Hi everybody,

    Would editorial work be appreciated? Like editing of paper drafts etc.

  5. June 1, 2011 at 2:02 pm

    Sin Wei,

    Proofreading, certainly! As far as actually editing the document goes, we think that having three sets of fingers on it (Andy’s, Matt’s and mine) is enough. But we’ll happily accept submissions of text and lists of corrections.

  6. 220mya
    June 5, 2011 at 8:19 pm

    Reading assignments below:

    Phylogenetic methods for understanding character evolution
    Pagel M (2006) BayesTraits. v1.0: University of Reading; http://www.evolution.rdg.ac.uk/BayesTraits.html. [Read the manual for this, which is at http://www.evolution.reading.ac.uk/Files/BayesTraits-V1.0-Manual.pdf]

    Pagel M (1997) Inferring evolutionary processes from phylogenies. Zoologica Scripta 26: 331-348.

    Pagel M (1999) The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology 48: 612-622.

    Felsenstein J (1985) Phylogenies and the comparative method. American Naturalist 125: 1-15. [The classic path-breaking paper, but a little hard to digest, so read Garland et al 1992 for an easier explanation]

    Garland T, Jr., Harvey PH, Ives AR (1992) Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41: 18-32.

    Garland T, Jr., Ives AR (2000) Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155: 346-364.

    Martins EP, Hansen TF (1997) Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. American Naturalist 149: 646-667.

    Kilbourne BM, Makovicky PJ (2010) Limb bone allometry during postnatal ontogeny in non-avian dinosaurs. Journal of Anatomy 217: 135-152. [This is a good recent example of how to treat our types of data]

    Disparity
    Briggs DEG, Fortey RA, Wills MA (1992) Morphological disparity in the Cambrian. Science 256: 1670-1673.

    Foote M, Gould SJ, Lee MSY, Briggs DEG, Fortey RA, et al. (1992) Cambrian and recent morphological disparity. Science 258: 1816-1818.

    Wills MA, Briggs DEG, Fortey RA (1994) Disparity as an evolutionary index: a comparison of Cambrian and Recent arthropods. Paleobiology 20: 93-130.

    Villier L, Korn D (2004) Morphological disparity of ammonoids and the mark of Permian mass extinctions. Science 306: 264-266.

    Gatesy SM, Middleton KM (1997) Bipedalism, flight, and the evolution of theropod locomotor diversity. Journal of Vertebrate Paleontology 17: 308-329.

    Carrano MT, Sidor CA (1999) Theropod hind limb disparity revisited: comments on Gatesy and Middleton (1997). Journal of Vertebrate Paleontology 19: 602-605.

    Gatesy SM, Middleton KM (1999) Theropod hind limb disparity revisited: a response. Journal of Vertebrate Paleontology 19: 606.

    Ruta M, Wagner PJ, Coates MI (2006) Evolutionary patterns in early tetrapods. I. rapid initial diversification followed by decrease in rates of character change. Proceedings of the Royal Society of London, Biological Sciences 273: 2107-2111.

    Wagner PJ, Ruta M, Coates MI (2006) Evolutionary patterns in early tetrapods. II. differing constraints on available character space among clades. Proceedings of the Royal Society of London, Biological Sciences 273: 2113-2118.

    Brusatte SL, Benton MJ, Ruta M, Lloyd GT (2008) Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs. Science 321: 1485-1488.

    Brusatte SL, Benton MJ, Ruta M, Lloyd GT (2008) The first 50 myr of dinosaur evolution: macroevolutionary pattern and morphological disparity. Biology Letters 4: 733-736.

    Brusatte SL, Benton MJ, Lloyd GT, Ruta M, Wang SC (2011) Macroevolutionary patterns in the evolutionary radiation of archosaurs (Tetrapoda: Diapsida). Earth and Environmental Science Transactions of the Royal Society of Edinburgh 101: 367-382.

    Brusatte SL, Montanari S, Yi H-y, Norell MA (2011) Phylogenetic corrections for morphological disparity analysis: new methodology and case studies. Paleobiology 37: 1-22. [important new methodological advance for correcting the phylogenetic non-independence of datapoints]

    Time-calibration of trees (most have the relevant details in the Suppl Info)
    Ruta M, Wagner PJ, Coates MI (2006) Evolutionary patterns in early tetrapods. I. rapid initial diversification followed by decrease in rates of character change. Proceedings of the Royal Society of London, Biological Sciences 273: 2107-2111.

    Lloyd GT, Davis KE, Pisani D, Tarver JE, Ruta M, et al. (2008) Dinosaurs and the Cretaceous terrestrial revolution. Proceedings of the Royal Society of London, Biological Sciences 275: 2483-2490.

    Nesbitt SJ, Smith ND, Irmis RB, Turner AH, Downs A, et al. (2009) A complete skeleton of a Late Triassic saurischian and the early evolution of dinosaurs. Science 326: 1530-1533.

    Irmis RB (2011) Evaluating hypotheses for the early diversification of dinosaurs. Earth and Environmental Science Transactions of the Royal Society of Edinburgh 101: 397-426.

  1. June 21, 2011 at 4:14 am

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