How do you read the literature? Thoughts on academic maturation

How much should you trust the scientific literature? Reflecting on my own academic maturation, as well as observing on-line discussions of dinosaur paleontology for over 15 years (yikes, I'm getting old!), I have concluded that most of us pass through three stages: 1) Credulity; 2) Cynicism; and 3) Maturity.

Credulity
This is inevitably one's first stop on the journey through the scientific literature: accepting everything that's published at face value. Credulity is also paired with the assumption that the most recent publication must be the most conclusive. For instance, let's say Dr. X described a new species in 2001. Dr. Y published a new paper in 2010, saying that the new species is invalid. Dr. Y must be correct, because she had the last word, right?

Another symptom of this stage is fanboy(girl)-ism. Anything published by Dr. Glamour is the bee's knees (it's widely featured in the news media, so it must be true)! Wow, Dr. Glamour published a new theory on the dinosaur extinction - it will revolutionize the science! Any nay-sayers are just jealous, or afraid of change.

I hit this stage during high school and college.

Cynicism
Suddenly, everything comes crashing down. You talk to another paleontologist, who tells you that Dr. Glamour's work isn't actually that highly regarded. Maybe he has a reputation for massaging his data just a little too much, or conveniently omits contradictory evidence in his papers. Then you find out that Dr. Z has just published a paper saying that Dr. X was actually correct in the first place, and Dr. Y's synonymization was a little too hasty. Your obvious conclusion: the scientific literature is untrustworthy. Everything ever written is a steaming pile of unreliable ramblings.

Most people don't go through a full-blown case of cynicism, of course. Usually we just get an incomplete case. Everything written by Dr. Glamour (but only some of the stuff by Dr. Y) is untrustworthy, etc. A related syndrome focuses on the methodology; a paper is considered horrible because it used or didn't use a particular technique.

I hit this stage between the end of my undergrad and the early to middle parts of my graduate career.

Maturity
Most of us reach this stage only after a lengthy amount of time in the field (or the end of our graduate student career). Our BS detectors are honed to an appropriate level, and we accept that many of the papers out there aren't half-bad, and a minor mistake or two isn't enough to relegate research to the dustbin.

For my part, I still occasionally waver between cynicism and maturity; I might cast an exceptionally suspicious eye on research coming from certain researchers or using certain techniques (even if it's not necessarily warranted). Maybe I even have a little credulity at first, if it's a technique or area of science I'm not yet completely familiar with. At the same time, having been around the block a few times as a scientist, I am a little more understanding when it comes to the perceived shortcomings of a paper. As long as the basic science is still good, live and let live. A paper can have a fantastic morphological description, but a pretty weak discussion. With a little practice reading the literature, it's becoming easier and easier to pick up on the high and low points of a publication.

Summing it up
We all relate to the academic literature in different ways, depending on our life experience, scientific goals, and "academic maturity." It's up to us - with the help of trusted friends and colleagues - to continually work to improve our own approaches.

Nedoceratops - Random Thoughts

The last two posts here have focused on my most recently published paper, fully describing the skull of the horned dinosaur known as Nedoceratops hatcheri and critiquing the hypothesis that it, along with Torosaurus latus, is simply an older individual of what we call Triceratops. Because I've already talked about the science of the paper, and some collegial interactions, I'm going to spend this final post in the series talking about a few odds-and-ends that just didn't fit anywhere else. Most of these are little windows into the process behind the paper - from writing to review to revision. And we'll start with. . .

Open Source Composition

I'm proud to say that every single step of the authoring process for my paper happened in open source software. I wrote the manuscript in OpenOffice.org Writer, formatted most of the references in Zotero, did initial image editing (contrast adjustment and background removal) in GIMP, assembled the figures in Inkscape, and submitted the manuscript through the journal website on the browser Firefox, all of which were running on various releases of Ubuntu. Score one for open source software (and open access publishing)!

On Organizing the Paper

I'm under no illusion that everyone (?anyone?) will agree with my conclusion that Nedoceratops is a valid taxon. In fact, I'm quite accepting of the possibility that I may be wrong. But even if this is the case, I still want my paper to be useful. So, I made my best effort to separate data from interpretation in the description section of the paper. Of course, I couldn't be completely successful on this point - after all, I had to compare Nedoceratops with Triceratops and Torosaurus (the most likely candidates for synonymy) - but I like to think that I mostly achieved my goal. If nothing else, I have pretty pictures. And. . .

Speaking of Pictures

My figures went through some pretty drastic changes during the evolution of this paper. In the first round of reviews, it was pointed out that in the text I kept referring to various structures illustrated in the figures, but only a ceratopsian geek could figure out what I was talking about.

For example, we have this lovely sentence:

The narial strut is inclined rostrally towards the dorsal end of the element, and enough original bone surface is preserved to indicate that a posterior internarial flange did not project from the caudal surface of this structure (Figure 4).

My original Figure 4 looked like this:

The photo is relatively pretty, but only a die-hard ceratopsian nerd could locate the narial strut or know where to look for a posterior internarial flange if such a thing even existed in this animal. So, for my next iteration I added some labeling:

Of course, all of the abbreviations are explained in the caption (not shown here). "ns" refers to the narial strut I was talking about above. Finally, the editor mentioned that I should do a better job of indicating the "cpf" (canal at the edge of the premaxillary fossa). It wasn't just at the tip of the arrow, but over a somewhat broader area. Thus, that brings us to version 3:

This, with the extra arrows showing the position of the canal, was the version that appeared in the paper.

If I learned anything from this experience, it was about the importance of good labeling and interpretive drawings for non-expert readers. Most of the labeled interpretive drawings alongside photographs (with the exception of parts B and D in Figure 1) were added at the direct request of the editor. Looking at the end product, this addition was a major improvement to the paper. Of course, I must also admit that having relatively unlimited space in an online journal allows this luxury!

Editorial Ethics

It's probably not a surprise to many of you that I am a volunteer academic editor at PLoS ONE. And those of you who have been paying attention probably noticed that the Nedoceratops paper was just published in that very same journal. This sounds pretty problematic on the face of it.

Thankfully, PLoS ONE has pretty strict editorial controls when one of their own editors submits a paper (in addition to a competing interests policy that covers this and similar situations). My experience as a submitting author was exactly the same as for any other author. Once the "submit" button was pressed, I had to wait just like everyone else. I couldn't control which editors handled it, who reviewed it, or even have a sneak peek at the reviews on-line. In other words, the system functioned exactly as it should.

My authorial feet were held to the fire by Leon Claessens, the handling editor for my submission. Leon, in my opinion, did a very professional job and didn't let me get away with anything (even sending the manuscript back to me a second time for a few last corrections and improvements). The reviewers - Michael Ryan and Peter Dodson - also did their jobs (in my opinion). And, as mentioned in my last post, comments by John Scannella and Jack Horner offered additional constructive feedback.

One thing I really like about PLoS ONE is that my competing interest - as an editor at the journal - is stated up-front in the paper. Although it's somewhat scary seeing it there, I think such notices are certainly appropriate.

Final Thoughts

It's nice to finally have this paper out there - these ideas have been floating around in my head for awhile, and I've always had a secret desire to be the person to describe Nedoceratops. I'm relatively pleased with the final product (of course, there are always one or two typos that slip through, and why couldn't some of the figures in the PDF have been bigger?), and look forward to the discussion that this paper generates. Thank you to all who helped out (see the acknowledgments for a comprehensive list)!

Return to the Blogosphere

I'm back! Let's just say that a global circumnavigation, two months away from home, and a move in the middle, don't leave a lot of time for blogging. It was a fun and productive summer, but now it's time to settle back in for the fall.

For this re-inaugural post, I wanted to touch on a few highlights from the past few months, particularly in the world of open access and paleo research. I'll cover a variety of topics in more detail in future posts, hopefully.

Big Happenings at PLoS ONE

The online, freely accessible journal PLoS ONE hit a variety of important milestones this summer, including:

• For the first time, the journal received an official impact factor from Thompson-Reuters. The result: a respectable 4.351. Although this value certainly exceeds that for your typical paleontology journal (e.g., Paleobiology has an IF of 2.985, and JVP has an IF of 2.536), it is more properly compared to other general interest journals. For instance, Naturwissenschaften has an IF of 2.126 and Proceedings B an IF of 4.857. Thus, PLoS ONE is doing pretty well in the whole impact factor "game." Although impact factor has come under a lot of fire lately, we still face the reality that many scientists need to publish in journals that have an IF. Thus, the assignment of an official IF is a big step forward for the journal.
  
• PLoS ONE launched a new (and hopefully more user friendly) manuscript submission system. Read all about it here.
• PLoS launched a new blog network.
• Full disclosure: I am a section editor at PLoS ONE.

Happenings Around the Blogosphere

• The venerable ScienceBlogs had a major sea change, with a number of respected bloggers jumping ship. I'm still working on updating my personal blog feeds. But, don't forget that notables such as Tetrapod Zoology remain!
• WitmerLab launched a great new blog, chock full of goodies from all of the folks there.
• The spam filters at Blogger are horrible. I'm seriously considering transferring over to WordPress.
  

Research Happenings

• The long-awaited proceedings volume of the Tyrrell ceratopsian symposium is finally out. The first review, by Hans-Dieter Sues, is available here. Seriously, if you are a dinosaur enthusiast or researcher, you need to get a copy of this book (and no, I don't get royalties).
  
• The final unpublished chapter of my dissertation (on ceratopsian sinuses) is now officially in press - look for it to come out in JVP within the next few weeks!
• Another major paper should be out in two weeks. Stay tuned for details.
• I had my first publishing experience with PalArch's Journal of Vertebrate Paleontology, with a paper on dinosaur skin from Utah. Brian Switek had a nice write-up of this over at Dinosaur Tracking. Hopefully I'll have a chance to blog more about this later - for now, I'll just say that you should consider the journal as a publishing venue! In the meantime, you can learn more about the journal in this two-part interview with editor Brian Beatty.
  
• And much more. . .too much to mention here, in fact!

That is all for now.

New issue of Palaeontologia Electronica

Sorry for the slow posts lately. . .it's that end of the year crunch!

To keep you busy in the meantime, there is a new issue of the on-line, open access paleontology journal Palaeontologia Electronica. This has lots of interest, with an editorial for new faculty by new faculty, a review of the current state of bovid systematics and paleontology, digital dinosaurs, and much more.

And, a belated congrats to Sterling Nesbitt and colleagues on the publication of Tawa hallae!

Big News on the Way

Research of catastrophic proportions. Another piece of the Shiny Digital Future. An unholy union between members of SV-POW! and The Open Source Paleontologist. Bigger than Ida. A cast of dozens. . .hundreds. . .thousands! Visit here on Tuesday morning to find out what the hyperbole is all about!

A Few Quick Peeks Before Fieldwork Hiatus

Sorry for the massive delay in posting - as many of my readers probably experience, summer is a busy time for fieldwork, catching up on research projects, and the like. In the morning, I'm heading into the field for the next three weeks. Upon my return, you can look forward to the following posts:

• A full review of the Asus Eee PC 901 as an option for field paleontologists. I bought one a few months ago as an ultra-light travel laptop as well as a machine for the field. Its extended battery life (up to 8 hours under the most ideal conditions, allegedly) is particularly intriguing to me. . .will it hold up to the hype?
• A look at how to use ImageJ for basic measurements from digital photographs, including lengths and angles.
• More open source journal goodness, with a focus on one or two publications in particular.
• And, much more!

And finally, a link. . ."Does publication in top-tier journals affect reviewer behavior?" This study, published recently in PLoS ONE, asks an interesting question with direct relevance to all of us who publish.

And another link. . .an interesting piece of free software called paleoPhylo was just published in the latest issue of Paleobiology. It slices! It dices! It draws temporally-calibrated phylogenies using R!

See all of you in a few weeks.

Advice from a Nobel Laureate

This evening I attended a talk by Eric Cornell, who shared the Nobel prize in physics in 2001 for his work on the creation of the first Bose-Einstein condensate. The talk was accessible, entertaining, and engaging--a rarity in any field of science, let alone condensed matter physics.

During the question and answer period, a young woman in the front row (probably no more than 12 or 13 years old) asked what she should study if she wants to be a successful scientist. Dr. Cornell mentioned the usual suspects - take courses in math and science. And then he added - work on your writing! This is an important word of wisdom, and one that is often neglected.

Good communication skills are a foundation of science - if we can't share our work with friends and colleagues, and have them understand the research, what's the point? So, to all of you students out there, work on your writing skills! Practice writing, get honest critiques from someone who has the time and honesty to really hammer your work, and then learn from the experience. And, practice communicating your research through other methods--oral presentations, posters, email, and the Internet. Even today, after completing a Ph.D., I am still working on my communication skills--I suspect it will be a lifelong task!

One Velociraptor Per Child

If you follow the open source/open access movement at all, you're probably familiar with the "One Laptop Per Child" initiative. Well. . .now there is a movement that combines the open access aesthetic with paleontology:

One Velociraptor Per Child

(I promise a real post after this week is done!)

SVP and Research Hiatus

I'm writing from the airport, as we move from SVP directly into a museum trip. The meeting was a great time (as usual), with a fantastic bloggers' luncheon, some stimulating talks, and lots of networking. Now to get some sleep. . .