Friday, December 31, 2010

Last Day of the Paleo Project Challenge!

As 2010 draws to a close, so does the 2010 Paleo Project Challenge (PPC). It sounds like some folks are doing well, others haven't made much progress, and others have made some. We'll have the final check-in next week!

Sunday, December 26, 2010

Common Mistakes in Scientific Writing [or, A Pedant's Paradise]

In scientific writing, proper terminology is everything. I learned early on that many of my favorite turns of phrase were technically incorrect - and I have been working to improve my writing and editing ever since. Below, I've included some of my "favorite" stylistic oddities. . .hopefully this is useful for at least a few readers! This may be old hat for some of you - in that case, please post a comment with your own grammatical grumblings.

"Outcrops" as a verb
Despite rampant misuse, there is no verb form of "outcrop."
Incorrect: "The Barstow Formation outcrops in southern California."
Correct: "The Barstow Formation crops out in southern California."

"Monophyletic clade"
A clade is, by definition, monophyletic. So, save your space and only use one of the two words!
Incorrect: "Dinosauria is a monophyletic clade."
Correct 1: "Dinosauria is monophyletic."
Correct 2: "Dinosauria is a clade."

"Data is. . ."
The word "data" is plural; "datum" is the singular. You're bucking against popular culture, but think of how delightfully smug you can feel whenever you use the words correctly.
Incorrect: "The data is overwhelming."
Correct 1: "The data are overwhelming."
Correct 2: "The datum is overwhelming, which is odd because it's only a single measurement."

"e.g." and "i.e."
"E.g." is an abbreviation from the Latin "exempli gratia", basically translating as "for example." "I.e." is the abbreviated form of the Latin "id est", translating as "that is." The meaning for the former should be pretty clear; the latter is used when one wishes to provide further clarification of a point.
Incorrect 1: "Many dinosaurs are found in the Hell Creek Formation (i.e., Triceratops and Tyrannosaurus)."
Correct 1: "Many dinosaurs are found in the Hell Creek Formation (e.g., Triceratops and Tyrannosaurus).
Incorrect 2: "Bird skeletons are pneumatized; e.g., they are filled with air sacs."
Correct 2: "Bird skeletons are pneumatized; i.e., they are filled with air sacs."

Lower/Upper vs. Early/Late
Unless you have had a solid introduction to geology (and even then, it's easy to forget), most people probably don't know that there is a major nitpicky difference between Upper Cretaceous and Late Cretaceous. The Upper/Lower designation refers to lithostratigraphic divisions of rocks; they are not the same as the geochronologic ages of the rocks. In other words - Upper Cretaceous refers to a physical lump of sedimentary rocks; Late Cretaceous refers to the age of these rocks. Whenever I try to figure out which word to use, I concentrate on whether I'm talking about time (Early/Late) or position in the rock column (Lower/Upper).
Incorrect 1: These Early Cretaceous rocks are full of fossils.
Correct 1: These Lower Cretaceous rocks are full of fossils.
Incorrect 2: Tyrannosaurus is Upper Cretaceous in age.
Correct 2: Tyrannosaurus is Late Cretaceous in age.

Want some more? The style guide for Journal of Vertebrate Paleontology (available in PDF format) has lots more great hints and tips!

Monday, December 13, 2010

Back to the Late Jurassic, With Chris Noto

ResearchBlogging.orgIf you ask the average person to imagine the Age of Dinosaurs, odds are quite good that they might envision a scene from the Morrison Formation. This Late Jurassic-aged (156 - 147 million year old) rock unit of the western United States has given us such dinosaur greats as Stegosaurus, Apatosaurus, Allosaurus, and more. Many of these animals are known from exquisitely-preserved, complete skeletons - and thus their anatomy has been described in pretty ridiculous detail. The functional morphology (how these animals moved, breathed, ate, and fought) has also gotten a lot of attention. But, this only tells us about the individual lives of the organisms. To really understand their world, we need to think bigger.

Chris Noto, my friend and academic brother (we had the same Ph.D. advisor), has devoted his scientific career to a big-picture understanding of dinosaur ecology. He has a special place in his heart for the dinosaurs of the Morrison Formation, and has been chipping away at their ecology for quite awhile now. Thus, it was really exciting to see his recent co-authored paper in PLoS ONE, about that very topic. Also of note was that this paper served as Chris's contribution to the 2009 Paleo Project Challenge!

Chris was kind enough to offer a little behind-the-scenes look at his project and the research results. I hope you'll find it enlightening!

How did you get the idea for your project?
Well, this involves going back a ways. I have always been fascinated by extinct organisms, particularly what they were like as living, breathing individuals in their environment. As an undergraduate at the University of Chicago I had the privilege of working with two really great scientists: Paul Sereno and Fred Ziegler. Paul is a well known paleontologist who has worked all over the world. Fred’s work was responsible for many of the paleogeographic and paleoclimate maps used today. Working with Paul got me thinking about how dinosaurs varied over space and time; working with Fred introduced me to global climate patterns and changes in continental arrangement.

Once I got to graduate school at Stony Brook University I was taught the fundamentals of ecological theory. I started formulating an idea for looking at variation in dinosaur communities (the collection of all the different types of organisms that live in an area) and how those differences may be related to climate, but wasn’t sure how to approach it. Enter my good friend (and coauthor) Ari Grossman, who suggested applying this method, called Ecological Structure Analysis, commonly used in the study of fossil mammals. After some discussion on the appropriate way to adapt this method to the type of information available for dinosaur fossils, we agreed to work together on this project.

What was the most challenging part of writing the manuscript?
Like many papers, this one languished half done for many years. This was a side project of ours, and unfortunately our dissertation research had to come first. Every time I started working on it again I would realize that the data needed to be changed or updated, and this would sometimes change the results and our interpretation. I am a stickler for details and want to make sure all the data are as accurate as possible. But this project was simply too cool to let go. Once I graduated I decided to finish this manuscript as a first priority. It actually didn’t take too long after that once I put my mind to it; in the end I think that the paper was all the better for it. I learned a lot in the meantime, which contributed to making it a stronger manuscript. The hardest part by far though was actually submitting it to PLoS ONE for consideration. No one likes to be rejected, especially after putting so much work into a project! But this is the way the peer-review system works.

I noticed that you used the program PAST for your statistical analyses - how did you decide on that program? Were there any particular challenges to using this software?
I was attracted to PAST because it could perform the analyses I needed to do without a lot of unnecessary complication. Best of all, it was free, and I was a poor graduate student at the time. Most commercial statistics programs are expensive and difficult to use. PAST has a relatively simple interface and the results are easy to interpret, which is important. The major challenge with using PAST is in data management. If the data are not arranged in exactly the right way the analysis will not work correctly. Therefore it requires arranging the data first in a program like Microsoft Excel, and then copying and pasting it into PAST.

What was the most interesting thing you learned while doing your research?
First of all, I wasn’t sure what to expect when I started doing this research. No one has looked for large-scale patterns like this in dinosaurs before. One interesting thing I learned is that such patterns exist in the fossil record and are preserved over the immense spans of time between when these communities existed and when they were recovered. The most exciting result for me has to be the fact that the proportion of different “ecomorphs”, such as high-browsing herbivores vs. low-browsing herbivores or bipeds vs. quadrupeds, varies with climate. So, we can draw a connection between the climate, environment, and adaptations of organisms living in an area (see figure below). This is no surprise for any ecologist working today, but has not been shown in a terrestrial ecosystem as ancient as the Jurassic (~155 million years ago). This opens up new areas of research into the role climate change plays on the structure of ecosystems over time.

Cartoon showing variation of environment and dinosaur ecomorphs. Drier conditions are on the left, where very large herbivores dominated among relatively sparse plant life. Communities under seasonal conditions are towards the center, and include a greater diversity of feeding modes among increased ground cover. To the right are moister conditions, where smaller herbivores are more prevalent within a more densely vegetated environment. Green=high browser, orange=intermediate browser, blue=low browser, red=ground forager. After Noto and Grossman 2010.

Thanks, Chris! For more about his research, check out his web site.

[Disclaimer: Although I am an editor at PLoS ONE, I had no role in the handling of this paper]

Noto, C., & Grossman, A. (2010). Broad-scale patterns of Late Jurassic dinosaur paleoecology PLoS ONE, 5 (9) DOI: 10.1371/journal.pone.0012553

Thursday, December 9, 2010

The Curse of the Nonexistent Dinosaurs

You all probably remember Darwinius, that little extinct primate that caused such a huge fuss last year (the image at left is from the original paper). In addition to the massive hyperbole surrounding the specimen (much of which has now been tempered by additional analyses from other researchers), an early issue concerned the validity of the name Darwinius itself.

Scientific names for new animals, living or extinct, are governed by a set of rules from the International Commission on Zoological Nomenclature (ICZN). This body - which has no real authority, other than that granted it by us scientists - is by its nature a rather conservative entity. This isn't necessarily a bad thing, particularly because stability in our naming system is so critically important. When I say Kosmoceratops richardsoni, everyone else should know I'm talking about. But, this conservatism also means that the ICZN has been very, very slow to react to electronic publishing. Right now, names published in electronic-only form are not valid! A paper version, even if it is otherwise identical to the electronic version, must be created (although the ICZN is working to change this).

So back to Darwinius. . .when the name was initially published, it was only in electronic form, and thus not "real" in the eyes of the ICZN. Vigilant eyes noted this, and the problem was rapidly broadcast in the blogosphere. Some wags suggested naming Darwinius out from under the authors, but thankfully cooler heads prevailed. PLoS ONE, the journal in which Darwinius was published, was able to produce a paper copy of the article in order to satisfy the ICZN. It took a few days, but finally Darwinius was "real"!

Thankfully, PLoS ONE learned its lesson. Their publication policies (full disclosure: I am an editor there) have been revised to accommodate the needs of the ICZN, and all is happy now. Or is it?

It turns out that other journals haven't necessarily learned this tough lesson. Time and again, scientific names invalid in the eyes of the ICZN are being published by some pretty major journals. This "zombie nomenclature" walks among us, even today. Here are just two examples.

On September 17, 2009, Science posted a preprint of a paper naming a new small tyrannosaur, Raptorex kriegsteini. As near as I can tell, this name existed only in electronic form at the time, and thus was not yet valid in the eyes of the ICZN. Raptorex was very well publicized (and rightfully so - it's a neat specimen), yet no paper edition appeared until October 16, 2009 - a month later. For four weeks, the name Raptorex was in taxonomic limbo.

Koreaceratops (image by Nobu Tamura)
This early horned dinosaur is hot off the digital presses. As you can probably guess, it hails from South Korea, and the authors hypothesize that it may have been aquatic. Koreaceratops appeared on November 17, 2010, as an online preprint at Naturwissenschaften, and some media attention started popping up earlier this week. Yet. . .the name is not yet valid in the eyes of the ICZN! Until Koreaceratops appears on the printed pages of that journal, the name has no real weight. Hopefully this will get resolved soon!

Cryptovenator (image by Charles R. Knight)
Dinosaurs (and Darwinius) aren't the only organisms afflicted by digital naming issues. On September 16, 2010, the genus Cryptovenator appeared on the website for Acta Palaeontologica Polonica, as a new kind of early synapsid (closely related to the fin-backed Dimetrodon, depicted at right). It hasn't yet appeared in print - so remains "undead" according to the ICZN.

Some Thoughts
The rise of online pre-prints is a Good Thing. It speeds the flow of scientific information in a way that just wasn't possible before. Yet, it also creates a bit of a headache for authors. The window of time between pre-printing and real-printing is a dangerous place for a new scientific name. Although the threat is slight, there is nothing to stop someone from accidentally or intentionally "scooping" the rightful authors. As near as I can tell, the proposed ICZN rules won't do anything to fix the situation, either.

So, what solutions are there?
  1. Don't publish pre-prints of papers with nomenclatural acts. This is the simplest solution in some ways, but also produces the undesirable effect of slowing down scientific communication. Canadian Journal of Earth Sciences has adopted this strategy (hat-tip to Hans-Dieter Sues for the reminder on this one).
  2. Petition the ICZN to give priority to the first appearance of the name in the first widely disseminated pre-print of a paper. This would be a nightmare on multiple levels - an addendum to the Code could take years, and how would one decide which version of a paper containing a name is the authoritative one?
  3. Continue to publish pre-prints, assume that all is going to be well, and worry about it when something bad happens (taxonomic scooping, perhaps?). Highly undesirable, but basically the course of action that we're on now.
  4. Expunge the names from the paper in its pre-print form (suggested by Martin Brazeau at another venue). This does solve the problem, but it requires someone to go through the paper and remove all mentions of the taxon. Despite all of the talk from commercial publishers about "value added", I suspect it's either the unpaid editorial volunteers or unpaid authors who would get stuck doing this. Removing names is not so tough in the text, but figures (such as phylogenies) would be a bear. Also, we're left with multiple versions of the same paper floating around.
What thoughts do you have on the matter? Is it really an issue? Or am I making a mountain out of a molehill? Speak up in the comments section!

Disclaimer: Mention of the "invalid" names above is not, not, not an invitation for paleontological wannabes, ethical miscreants, or rabblerousers to wreak havoc on paleontological nomenclature. Although I hesitate to draw attention to particular instances, I feel that without some concrete examples, my arguments would be less effective. Furthermore, the names are already out there in some very widely read venues! Leave the names for the authors; the situation is not their fault.

Update December 31 2010: Bill Parker over at Chinleana has a great post relevant to this issue.

Saturday, December 4, 2010

Paleo Project Challenge: 27 Days to Go!

We're now about three months into the 2010 Paleo Project Challenge (PPC), an annual "contest" co-sponsored by Dave Hone's Archosaur Musings and The Open Source Paleontologist. As a quick recap, this event is for anyone (vocational or avocational paleontologist, researchers, preparators, artists, etc.) who has that nagging project that just needs a final kick in the pants. In exchange for signing up, we list your name publicly as an extra bit of. . .incentive. . .to finish the project.

So, how have you done? Out of my two goals, I got one (the paper on anatomy of a certain ceratopsian) submitted this past week, and the other one (for the ODP) is moving along nicely. I'm not sure if the latter will make the December 31 deadline imposed by the PPC, but significant progress is still happening. And that's the point of this whole Challenge, isn't it?!

In case you need your memory jogged, the participants are listed below. Tell us how you're doing in the comments! If you finished a project and I missed you, let me know and I'll update your status.

Participants in the Paleo Project Challenge
Andy the Micropaleontologist - submit foram macroevolution paper; write draft of clade shape paper
Anonymous - find job; paper for Paleobiology; prep alligator fossil
Brian Beatty - paper on meningeal ossification in cetaceans
Robert Boessenecker
- finish first draft of master's thesis
Martin Brazeau -
finish redescription Ptomacanthus anglicus and include updated matrix
Andrea Cau
- describe new theropod remains from north Africa
John Conway
- finish Heterodontosaurus painting
- restoration of Dryptosaurus [finished]
Andy Farke
- finish paper for ODP; finish paper on ceratopsian anatomy [finished!]
Nick Gardner
- submit grant for Youngina part II
Casey Holliday
- either a new croc species description or paper related to frontoparietal fossae
Dave Hone
- the necks paper [finished]
- finish descriptions for Katian graptolite systematic paper.
David Maas
- Illustrating Mallison's Kentrosaurus
Heinrich Mallison -
finish Plateosaurus CAE paper; sauropod rearing paper; sauropodomorph rapid locomotion paper
Jay - finish sauropod description
Jordan Mallon - Anchiceratops manuscript
Anthony Maltese - sharks scavenging on mosasaur paper; Niobrara ammonite paper
Paleochick - Cloverly paleobotany paper
Patty Ralrick - paper on subfossil mass mortality site
Julie Reizner - submit Einiosaurus histology paper
Manabu Sakamoto - finish Pachyrhinosaurus drawing; finish and submit theropod bite force paper
John Scanlon - write up Oligocene lizards from Riversleigh; process and sort samples from Miocene microsite
Leo Sham - illustrate Raptorex; write cosmetic surgery review paper
Mark Spencer - finish paper critiquing model-based approaches to phylogeny reconstruction
Brian Switek - finish book proposal; polish and submit paper on Alabamornis; paper on Thoracosaurus specimen
David Tana - sign up for GRE; submit 9 pieces to Art Evolved time capsules; overhaul blog
Darren Tanke - finish biography of Oscar Erdman [finished]; finish paper on first helicopter lift of a dinosaur specimen; finish extended abstract on Hope Johnson
Mike Taylor - finally finish the Archbishop sauropod description
Matt van Rooijen - finish up Tarbosaurus bite pattern illustrations
Bruce Woolatt - 1/10 scale Quetzalcoatlus northropi flesh restoration