Showing posts with label open access. Show all posts
Showing posts with label open access. Show all posts

Tuesday, April 28, 2009

Tyrannosaurus rex, The Tyrant King--Reviewed


For those who are interested, I have a book review of Tyrannosaurus rex, The Tyrant King, (edited by Peter Larson and Ken Carpenter), in the latest issue of the on-line, open access journal Palaeontologia Electronica. Go check it out (both the book and the review), and let me know what you think!

The latest issue of PE also features articles on Jurassic ammonites, ?Paleocene dinosaurs, and special photography techniques, along with book reviews (including one by Laelaps blogger Brian Switek) and an editorial.

Reference
Farke, A. A. 2009. Review of Larson, Peter L., and Carpenter, K., eds. Tyrannosaurus rex, The Tyrant
King. Palaeontologia Electronica 12, Issue 1, R2:2 pp.

Open Access Paleontology Journals - Community Opinions

We're almost to the end of the series on the 2009 Open Access Paleontology Journal Rankings (see other posts in the series here, here, and here)! Citations and number of papers are all well-and-good, but one thing that's often omitted in journal comparisons is community opinion. In other words, what do paleontologists think of this or that journal? Have they even heard of the journal?

In order to see how open access journals have fared within the paleontology community, I ran an informal survey. It provided a list of open access journals in paleontology, and asked respondents to rank each publication as "excellent," "good," "fair," "poor," or "I've never heard of it." This survey was advertised on this blog, Facebook, the Dinosaur Mailing List, VRTPALEO Mailing List, and Laelaps. Ninety-two people responded, but not everyone answered every question. I have no idea (for the most part) who filled out the survey, but given the scope of advertising and the bits of feedback I received, I suspect respondents were primarily professional paleontologists and students of paleontology. Given the distribution of results, I have no reason to suspect poll crashing, but would also caution that this is not a scientifically sampled survey, either.

The results were then tallied, and an average rating was assigned to each. An excellent counted as 1 point, good as 2, fair as 3, poor as 4, and "never heard of it" as 5 points. So, here's the list from highest to lowest rating; the results are presented as "Journal Name, Average Score, (# Excellent Ratings, # Good Ratings, # Fair Ratings, # Poor Ratings, # Never Heard of It, Total Responses)." Journals with immediate open access are listed in bold.

Community Opinions of Open Access Paleontological Journals, 2009
  1. Proceedings of the National Academy of Sciences, 1.45 (53, 19, 7, 1, 0; 80 total)
  2. Proceedings of the Royal Society B, 1.52 (59, 20, 3, 1, 4; 87 total)
  3. Bulletin of the American Museum of Natural History, 1.56 (53, 28, 5, 0, 3; 89 total)
  4. American Museum Novitates, 1.57 (51, 33, 3, 0, 3; 90 total)
  5. Acta Palaeontologica Polonica, 1.64 (51, 30, 6, 0, 4; 91 total)
  6. PLoS ONE, 1.79 (44, 27, 8, 3, 4; 86 total)
  7. Palaeontologia Electronica, 1.94 (30, 38, 16, 0, 3; 87 total)
  8. PLoS Biology, 1.99 (36, 32, 4, 2, 9; 83 total)
  9. Biology Letters, 2.36 (23, 33, 11, 1, 13; 81 total)
  10. Smithsonian Contributions to Paleobiology, 2.58 (18, 32, 11, 4, 15; 80 total)
  11. Bulletin of the Museum of Comparative Zoology, 2.62 (19, 28, 17, 1, 17; 82 total)
  12. Paläontologische Zeitschrift, 2.64 (17, 30, 20, 3, 15; 85 total)
  13. Ameghiniana, 2.87 (12, 27, 23, 4, 18; 84 total)
  14. Contributions in Science from the Natural History Museum of Los Angeles County, 2.92 (14, 27, 15, 6, 21; 83 total)
  15. Vertebrata PalAsiatica, 3.01 (10, 22, 26, 9, 17; 84 total)
  16. Geodiversitas, 3.08 (9, 29, 17, 4, 25; 84 total)
  17. Contributions from the Museum of Paleontology, 3.31 (11, 20, 14, 3, 32; 80 total)
  18. Revue de Paléobiologie, 3.48 (5, 23, 15, 3, 34; 80 total)
  19. PalArch, 3.55 (4, 13, 28, 9, 29; 83 total)
  20. Palaeodiversity, 3.71 (3, 22, 13, 3, 42; 83 total)
  21. Memoir of the Fukui Prefectural Dinosaur Museum, 3.94 (3, 8, 19, 10, 39; 79 total)
  22. The Open Paleontology Journal, 4.01 (4, 14, 9, 5, 50; 82 total)
  23. Journal of Paleontological Techniques, 4.04 (5, 7, 14, 8, 46; 80 total)
  24. Geologica Acta, 4.05 (1, 13, 15, 2, 48; 79 total)
  25. Estudios Geológicos, 4.12 (1, 12, 14, 5, 51; 83 total)
  26. Coloquios de Paleontología, 4.24 (2, 8, 14, 3, 56; 83 total)
  27. Geogaceta, 4.43 (0, 7, 10, 5, 59; 81 total)
  28. Natura Nascosta, 4.49 (0, 6, 8, 7, 60; 81 total)
  29. Joannea - Geologie und Paläontologie, 4.51 (2, 5, 5, 7, 62; 81 total)
Notes
A low rating does not necessarily mean a journal for which paleontologists have a low opinion. In at least some cases (e.g., Palaeodiversity), low scores result largely from poor "brand recognition." As the crop of new journals matures, and as the internet allows broader distribution of work, this situation is likely to change.

The journals Revista Brasileira de Paleontologia, Science, and Journal of Paleontological Sciences were inadvertently omitted from the poll.

Final Thoughts
In hindsight, there are a few more things I'm curious about. How do major closed access journals such as JVP stack up against their open access brethern? Who responded to the survey, and how do different types of paleontologists (students, early career and late career professionals, etc.) consider open access journals versus their closed access counterparts? What are general attitudes amongst paleontologists towards open access?

Coming Up. . .A Final Post With Raw Scores

Monday, April 27, 2009

Open Access Paleontology Rankings - Part III

This post continues the series on the 2009 Open Access Paleontology Journal Rankings. Previously, I posted the rankings for Immediate Open Access Journals for General Submission and All Immediate Open Access Journals (including those museum publications with more restrictive submission requirements). Here, I'll release the final set of rankings, including both immediate open access and delayed open access journals. A number of notable journals (such as Science) now allow open access after a period of one year, so it only seemed fair to address them too.

As always, the ratings are based on a combination of journal citations, recent citations, number of articles, and community opinion (outlined previously). At the end of this series, I will post the raw data underlying the ratings.

Don't Forget The Caveats
Remember, these rankings are only one method for measuring the efficacy, quality, and impact of a journal, and you will probably disagree with one or more of the placements on the list. Especially for relatively young journals, rankings may change rapidly in the coming years.

Top Open Access Journals for Paleontology 2009
(General Results, Immediate and Delayed OA)
  1. Science*
  2. Proceedings of the National Academy of Sciences
  3. Proceedings of the Royal Society B
  4. PLoS Biology
  5. Acta Palaeontologica Polonica, Bulletin of the American Museum of Natural History [tie]
  6. [tie]
  7. American Museum Novitates
  8. Biology Letters
  9. Ameghiniana
  10. Paläontologische Zeitschrift
  11. PLoS ONE
  12. Palaeontologia Electronica
  13. Geologica Acta
  14. Vertebrata PalAsiatica
  15. Bulletin of the Museum of Comparative Zoology, Geodiversitas [tie]
  16. [tie]
  17. Geogaceta
  18. Estudios Geológicos
  19. Smithsonian Contributions to Paleobiology
  20. Revue de Paléobiologie
  21. Memoir of the Fukui Prefectural Dinosaur Museum
  22. Contributions in Science from the Natural History Museum of Los Angeles County, Contributions from the Museum of Paleontology [tie]
  23. [tie]
  24. Journal of Paleontological Sciences*
  25. Coloquios de Paleontología
  26. PalArch
  27. Joannea - Geologie und Paläontologie
  28. Natura Nascosta
  29. The Open Paleontology Journal
  30. Palaeodiversity
  31. Journal of Paleontological Techniques
*not included in the community ranking survey

Note
It should be noted that some very fine journals (e.g., PaleoBios) have open access archives for older issues (five years or older), but these publications were not included on the general list. I made the somewhat arbitrary decision to exclude journals with lag times of greater than one year.

Up Next. . .Community Rankings of Journals

Sunday, April 26, 2009

Open Access Paleontology Rankings - Part II

This post continues the series on the 2009 Open Access Paleontology Journal Rankings. Previously, I posted the rankings for Immediate Open Access Journals for General Submission. Here, I'll release the general results for Immediate Open Access Journals. As mentioned previously, this category includes both journals to which anyone can submit a manuscript, as well as those with more restrictive authorship requirements. This latter category includes several museum publications, such as American Museum Novitates [see their submission policies here]. For journals such as these, authors usually must be an employee or research associate of the publishing institution, or receive special invitation. Journals with delayed open access (such as Science) are not included on the present list.

As always, the ratings are based on a combination of journal citations, recent citations, number of articles, and community opinion (outlined in my previous post). At the end of this series, I will post the raw data underlying the ratings.

Yet Again With the Caveats
Remember, these rankings are only one method for measuring the efficacy, quality, and impact of a journal, and you will probably disagree with one or more of the placements on the list. Especially for relatively young journals, rankings may change rapidly in the coming years.

Top Immediate Open Access Journals for Paleontology 2009
(General Results)
  1. Acta Palaeontologica Polonica, American Museum Novitates, PLoS Biology [tie]
  2. [tie]
  3. [tie]
  4. Bulletin of the American Museum of Natural History
  5. Ameghiniana
  6. Paläontologische Zeitschrift
  7. PLoS ONE
  8. Palaeontologia Electronica
  9. Geologica Acta
  10. Vertebrata PalAsiatica
  11. Bulletin of the Museum of Comparative Zoology, Geodiversitas [tie]
  12. [tie]
  13. Geogaceta
  14. Estudios Geológicos
  15. Smithsonian Contributions to Paleobiology
  16. Contributions from the Museum of Paleontology
  17. Revue de Paléobiologie
  18. Memoir of the Fukui Prefectural Dinosaur Museum
  19. Contributions in Science from the Natural History Museum of Los Angeles County
  20. Journal of Paleontological Sciences*
  21. Coloquios de Paleontología
  22. PalArch
  23. Joannea - Geologie und Paläontologie
  24. Natura Nascosta
  25. The Open Paleontology Journal
  26. Palaeodiversity
  27. Journal of Paleontological Techniques
*not included in the community ranking survey

Notes
In some cases, relative ranks of journals may differ in this list from the previous category. This is because journals are ranked relative to all entries in a single category. For instance, PLoS ONE and PLoS Biology were tied in the last list, but are separated in the present one. Let's consider the number of article citations - relative to all immediate open access journals, PLoS ONE is ranked fifteenth and PLoS Biology is ranked second. When we exclude museum journals, the ratings move to ninth and second, respectively. When you add up all the rankings, little changes like this can jostle a journal's position; such behavior is particularly common near the top of the list. Later, I'll be releasing the underlying data and you can see for yourself.

Up Next. . .All Open Access Journals

Saturday, April 25, 2009

Open Access Paleontology Rankings - Part I

Over the next few days, I'll be posting results of the 2009 Open Access Paleontology Journal Rankings. These results will be divided into several categories, including:
  • Immediate Open Access Journals for General Submission (journals to which anyone can submit [excluding most museum publications with more exclusive author criteria], and which provide open access immediately upon publication)
  • Immediate Open Access Journals (same as above, with museum publications included)
  • All Open Access Journals (includes those journals with delayed open access)
  • Community Ranked Open Access Journals (journals as ranked by the opinions from the survey)
In this post, I'll just be covering Immediate Open Access Journals for General Submission. As described above, this includes only journals with immediate open access (versus open access after a set delay) and excludes those with restrictive authorship criteria (e.g., museum publications which usually require employment, association, or invitation to submit). The ratings are based on a combination of journal citations, recent citations, and community opinion (outlined in my previous post). At the end of this series, I will post the raw data underlying the ratings.

Again With the Caveats
Remember, these rankings are only one method for measuring the efficacy, quality, and impact of a journal, and you will probably disagree with one or more of the placements on the list. Especially for relatively young journals, rankings may change rapidly in the coming years.

Top Immediate Open Access Journals for Paleontology 2009
(General Submission)
  1. Ameghiniana
  2. Acta Palaeontologica Polonica
  3. PLoS ONE, PLoS Biology [tie]
  4. [tied for 3]
  5. Paläontologische Zeitschrift
  6. Geologica Acta
  7. Palaeontologia Electronica
  8. Vertebrata PalAsiatica
  9. Geodiversitas
  10. Geogaceta
  11. Estudios Geológicos
  12. Revue de Paléobiologie
  13. Journal of Paleontological Sciences*
  14. Coloquios de Paleontología
  15. PalArch
  16. Joannea - Geologie und Paläontologie
  17. Natura Nascosta
  18. The Open Paleontology Journal
  19. Palaeodiversity
  20. Journal of Paleontological Techniques
*not included in the community ranking survey

Notes
While compiling the results, I noted that sometimes community opinions of a journal varied from the rankings by sheer number of articles or citations. This will be highlighted in a future post. So, if you're worried because your favorite journal is lower than you thought, or your least favorite journal is higher than you thought, you'll probably be interested to see those results.

Unlike the widely-known Science Citation Index, these rankings include very new journals as well as more established journals. Thus, some rankings may change in the coming years are the new kids on the block accumulate more citations, more papers, and more exposure. Still, it is very interesting to note how some quite new journals (such as PLoS ONE) still have a high position within the list.

It is interesting to note how truly global this list is - a healthy mix of journals from South America, Europe, Asia, and North America round out the top 10. What does this mean, if anything, for the future of paleontology?

Up Next. . .All Immediate Open Access Journals

Friday, April 24, 2009

About the Ratings

In a series of posts over the next several days, I will be releasing the long-awaited(?) rankings of open access journals. This post will provide some background on the journals, the ratings, and my methodology.

What Are Open Access Journals?
If you are not familiar with the concept of open access publication, I recommend checking out my post, "Open Access Publishing and the Paleontologist."

Why Rate Journals?
Lots of open access journals are out there now--but not all are made equally. Some are widely read, others are ignored. Some publish high impact articles of general interest, and others are more focused in their scope. How is one to decide which publication to follow or submit research to? I've developed these ratings primarily as a service to those of us who are looking for open access journals in which to publish. Rankings that incorporate citation counts, numbers of articles published, and community opinion may be useful as one part of this decision-making progress.

How Were the Journals Chosen?
Basically, I combed the internet, dredged up my own knowledge of the literature, used the list on SV-POW!, and incorporated comments from readers. I have quite probably omitted one or two journals by accident, and I can assure you that this was unintentional. I adopted four criteria for selecting journals:
  1. The journal must regularly publish articles on the topic of paleontology (a single article every two years is not sufficient).
  2. Entire issues must be open access, not just selected articles.
  3. The journal must be active, with at least one issue in 2008 (exceptions may be made for irregular museum publications that are not intended to be released on a set schedule).
  4. The journal may have either immediate or delayed open access (a year is the cut-off point).
How Were the Journals Rated?
Journals were evaluated in five general areas:
  1. Number of journal hits. This was calculated by searching for all articles within a given journal on Google Scholar, and recording the number of hits. [example]
  2. Number of paleontology hits. This was calculated by searching for all articles within a given journal on Google Scholar that included the words "paleontology" or "fossil," and recording the number of hits. [example]
  3. Number of article citations. This was calculated by searching for all articles within a given journal on Google Scholar that included the words "paleontology" or "fossil," and recording the number of citations for the top 10 search results. [example]
  4. Number of citations of recent articles. This was calculated by searching for all articles within a given journal on Google Scholar that included the words "paleontology" or "fossil," published in 2007 or 2008, and recording the number of citations for the top 10 search results. [example]
  5. Community rating. A survey was posted with a list of all journals, and respondents were invited to rate each journal as "excellent," "good," "fair," "poor," or "never heard of it." A notice of the survey was posted on this blog, Facebook, the Dinosaur Mailing List, VRTPALEO Mailing List, and Laelaps. Each journal was then given an overall rating, by weighting the number of responses in each category.
The journals were ranked in each category, and then an overall ranking incorporating all categories was calculated.

A Disclaimer
These are informal ratings, compiled in a manner that is probably non-scientific and flawed in one or more ways. No ranking system is perfect! Regardless of any imperfections, I think that these rankings may provide some useful information. Just take it with a grain of salt.

Coming up next. . .rankings for Immediate Open Access Only Journals.

Thursday, April 23, 2009

Science - Now With Open Access Archives

Another high profile journal has made its first steps towards open access! I learned earlier today that Science now has free access to its archives, for articles older than one year and published on or after January 1997. Registration (free) is required, but this is quick and relatively painless.

Unfortunately, it is too late to add Science to the survey, but it will be included in other ranking methods. If you haven't already, don't forget to fill out the open access journal poll! It closes Friday night, 23 April.

[Note: I also learned that the journal has actually had open archives for since 2001 - wow, am I out of the loop!]

Saturday, April 18, 2009

What Are the Best Open Access Journals for Paleontologists?

The number of open access journals available for paleontologists is growing rapidly (see both my previous post as well as a more comprehensive post over at SV-POW!). When it comes time to submit something for publication, the options can be quite disconcerting. What journal will best get that paper out there? Search engines are great for finding specific papers on a specific topic, but it's nice to know that the casual journal reader might also happen across your paper. So, which journals do my colleagues pay attention to? Which journals do my colleagues respect most?

Although inherently flawed in some respects, ranking systems provide a first pass at trying to evaluate publications. So, I've been working on developing a rudimentary ranking system for today's open access paleontology journals. And, I'd like your help! I'll be incorporating citation counts, page rankings, and other metrics, but would also like to consider reader opinion. So, I have developed a highly unscientific survey as part of this effort. Please take a few minutes to fill in your opinions.

As a preview, the survey provides a list of open access journals in paleontology, and asks you to rank them as "excellent," "good," "fair," "poor," or "I've never heard of it." The form will be open until next Friday evening at 11:45 (Pacific time). Results will be published here soon thereafter.

Coming Up, After Your Hard Work on the Poll: The Top Open Access Journals for Paleontology 2009.

Thursday, April 16, 2009

Open Access Journals in Paleontology

As part of a larger upcoming post (by the weekend, I hope), I am compiling a list of open access journals that regularly publish articles in paleontology. So far, the journals have been selected using the following criteria:

1) The journal must regularly publish articles on the topic of paleontology (a single article every two years is not sufficient).
2) Entire issues must be open access, not just selected articles.
3) The journal must be active, with at least one issue in 2008 (exceptions may be made for irregular museum publications that are not intended to be released on a set schedule).
4) The journal may have either immediate or delayed open access (a year is the cut-off point).

Here's what I have so far. . .any suggestions for additions or corrections? At this point, I am not making statements one way or another on the quality of the journals. . .just assembling a list!

Acta Palaeontologica Polonica
Ameghiniana
American Journal of Science
American Museum Novitates
Biology Letters
Bulletin of the American Museum of Natural History
Bulletin of the Museum of Comparative Zoology
Coloquios de Paleontología
Contributions from the Museum of Paleontology
Contributions in Science from the Natural History Museum of Los Angeles County
Estudios Geológicos
Geodiversitas
Geogaceta
Geologica Acta
Joannea - Geologie und Paläontologie
Journal of Paleontological Techniques
Memoir of the Fukui Prefectural Dinosaur Museum
Natura Nascosta
Palaeodiversity
Palaeontologia Electronica
Paläontologische Zeitschrift
PalArch
PLoS Biology
PLoS ONE
Proceedings of the National Academy of Sciences
Proceedings of the Royal Society B
Revue de Paléobiologie
Smithsonian Contributions to Paleobiology
The Open Paleontology Journal
Vertebrata PalAsiatica

Thursday, March 12, 2009

Two Items

First, congratulations to Dr. Mark Loewen, who successfully completed his dissertation defense on Tuesday afternoon. His dissertation focused on variation in Allosaurus, and was truly an epic piece of work.

Second, check out this paper that just came out in PLoS ONE. The paper covers some interesting aspects of limb bone allometry (shape changes with size), and provides open source macros for ImageJ, so you could do similar analyses on your own dataset. In the next day or two, I should have more to say, but for the time being check out the link. . .as always, the papers are free to download, and please take advantage of the commenting/note-making/rating features on the PLoS website.

Doube M, Conroy AW, Christiansen P, Hutchinson JR, Shefelbine S (2009) Three-Dimensional Geometric Analysis of Felid Limb Bone Allometry. PLoS ONE 4(3): e4742. doi:10.1371/journal.pone.0004742

Wednesday, March 4, 2009

PLoS ONE's newest editor

It's official. . .I have just accepted an invitation to join the editorial board for the on-line, open access journal PLoS ONE. With its recent burst of vertebrate paleontology articles (featured prominently in their Paleontology Collection), the future is looking quite bright. I am very eager to assist the open access movement in a more concrete way, for a journal that is making many positive changes to the way research is communicated. Other vertebrate paleontologists on the editorial board include Tom Kemp, Paul Sereno, and David Unwin (and my apologies to anyone else I neglected to mention).

So. . .bring on the manuscripts!

Friday, February 27, 2009

PLoS ONE's Paleontology Collection

As many of my posts over the past month have emphasized, the online open access journal PLoS ONE has been a hotbed of interesting papers relevant to paleontologists. Pterosaurs, Triceratops, whales, stromatolites, rodents and friends have been featured on the digital pages of this publication. Of course, the journal covers many other topics, too. So how is a paleontologist to find those papers immediately relevant to his or her research, among all of the other interesting papers on topics ranging from genetics to mathematics?

Enter PLoS ONE's Paleontology Collection. This is an open collection of articles--meaning that it is continually updated and augmented as new research is published in the journal. Everything the journal has ever published on paleontology is there! Right now, this includes a grand total of 26 articles, six of these in the first two months of 2009 alone. Contrast this a closed collection at PLoS ONE, which is a one-time conference proceedings or similar compendium of research.

Why should we care? Speaking selfishly, this will allow us to easily access all articles in our field. All future articles are automatically added to the collection. This means that if you don't want to wade through all of the other contributions on the PLoS ONE list (although there are some very interesting ones!), you can just keep an eye on the paleontology collection for any and all exciting developments. In a broader sense, this collection will help paleontologists to reach an even broader audience.

And once again--take advantage of the comment, note, and rating features at PLoS ONE (as outlined in my previous post). It's really a unique opportunity to interact with authors, make your thoughts known, and help science march onward. If you have that really cool piece of research, submit your manuscript!

To see what PLoS ONE has to say about the collection, point your browser here.

Image Credit: Mark P. Witton (see Witton and Naish, doi:10.1371/journal.pone.0002271)

Saturday, February 21, 2009

Using the Comment, Note, and Rating Features at PLoS One

In my previous post, I highlighted some new articles from the online, open access journal PLoS ONE, and noted that the commenting feature at this journal is relatively unused for most articles. Some interesting discussion ensued on why this might be (among other issues). . .Mike Keesey suggested that maybe folks just aren't used to commenting in this format. Well then, let's do something about it!

Your Assignment:
  • If you haven't already, create a user account on the PLoS website. This will allow you to post notes, make comments, and rate articles.
  • Read an article that interests you on PLoS ONE (consider it part of your academic duty to keep on top of the recent literature), and make a substantive comment or note about something in the article. If you don't feel like making a specific comment (or if the article is so incredibly good as to not need comment), just rate the article.
  • Feel good about contributing to a scientific discussion!
How It Works
Notes are for comments on specific portions of an article. For instance, maybe you think a particular sentence is well said, or relates to a very specific point that you have in mind. In this case, a note is most appropriate.

Comments are for more general thoughts on a paper--is there something particularly good, bad, or ugly? Might you have suggestions for an interesting follow-up study? Is there just something you're wondering about that you'd like the author(s) to answer?

Finally, ratings are a chance to tell folks what you really think about the paper. PLoS has three categories in which you rate an article--insight, reliability, and style. These categories are unfortunately vague in their names, but the PLoS website provides a succinct explanation of what is meant by each. Essentially, the categories rate the "importance" or "thought-provokingness" of an article, solidness of the conclusions, and technical execution and presentation of the whole package.

My First Notes, Comments, and Ratings
To check out an example, see another new paper in vertebrate paleontology published by Bates et. al:

Bates KT, Manning PL, Hodgetts D, Sellers WI (2009) Estimating Mass Properties of Dinosaurs Using Laser Imaging and 3D Computer Modelling. PLoS ONE 4(2): e4532. doi:10.1371/journal.pone.0004532

I just finished some notes, comments, and a rating of the article. (no, I did not do this just for the purpose of the blog--the topic genuinely interests me!) It's easy! Science marches on.

What are you waiting for? Go try it for yourself!

Tuesday, February 17, 2009

PLoS ONE strikes again!

So far, 2009 has been a banner year for vertebrate paleontology in the open access journal PLoS ONE. First there was the fighting Triceratops paper, followed by the Maiacetus announcement. This week brings two more offerings of the archosaurian persuasion:

Claessens LPAM, O'Connor PM, Unwin DM (2009) Respiratory Evolution Facilitated the Origin of Pterosaur Flight and Aerial Gigantism. PLoS ONE 4(2): e4497. doi:10.1371/journal.pone.0004497

Martinez RN, Alcober OA (2009) A Basal Sauropodomorph (Dinosauria: Saurischia) from the Ischigualasto Formation (Triassic, Carnian) and the Early Evolution of Sauropodomorpha. PLoS ONE 4(2): e4397. doi:10.1371/journal.pone.0004397

I don't have time right now to blog these articles (and I really, really need to get that Slicer series finished!), but do have the following thoughts:
  • Is this string of papers a fluke, or is PLoS ONE becoming a more accepted, high-profile journal along the line of Science and Nature?
  • PLoS ONE offers the opportunity to post comments about the article (ostensibly for "post publication peer review"). Yet, this feature really hasn't been utilized much for many of the paleontological articles. Is it that the articles are just that good? Or are paleontologists shy about posting their thoughts on this sort of thing, and saving it instead for the peer reviewed literature? Or, are the papers just not worth commenting on? Or, do paleontologists have better things to do with their time?

Wednesday, February 4, 2009

New Paleo Paper in PLoS ONE

If you haven't seen already, the past two weeks have been great for paleontology on the pages of PLoS ONE, a high-profile open access journal. Phil Gingerich and colleagues have just published a paper on Maiacetus, a new fossil whale from Pakistan. Other bloggers have done a much more thorough job than I could of presenting the work and its importance for understanding whale evolution, so I'll just link to them and the original article.

It is good to see more paleo papers taking the open access route!

Gingerich PD, ul-Haq M, von Koenigswald W, Sanders WJ, Smith BH, Zalmout IS. (2009) New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism. PLoS ONE 4(2): e4366. doi:10.1371/journal.pone.0004366

Read about it at Laelaps, Not Exactly Rocket Science, A Blog Around the Clock, The Loom, and elsewhere.

Saturday, January 31, 2009

The Open Source Triceratops Paper

Wow! The past few days have been a real whirlwind. As mentioned in my last post, our long-awaited paper (well, long-awaited by my co-authors and me) on Triceratops horn use and paleopathology was unleashed by PLoS ONE on Tuesday evening. We've received some wonderful feedback through this blog and email, and are very ready to move on to the next research project.

Because this blog focuses partly on open access and open source software, I wanted to write briefly about how these issues factored into our research. This is one of the most "open" projects I've attempted to date, from start to finish. Here are the details:
  • The data collection and statistical analysis were completed in OpenOffice.org Calc, with the calculations based on a spreadsheet file I found (and tested against known examples) from somewhere on the internet (but can't remember where, now!). R will also do the appropriate calculations, but I stuck with the spreadsheet because my data files were so small and straight-forward.
  • The manuscript was written in OpenOffice.org Writer, but my co-authors and I batted it back and forth in Word format (because Darren and Ewan are using the latter program). We had no problems with this strategy, and the format conversions were a snap for the relatively simple documents we were using.
  • The bibliography was compiled and formatted using Zotero. Zotero even has a readily available style file for PLoS, so this made my life very easy.
  • The figures were edited for contrast and brightness in GIMP (no other manipulation was performed on the images) and assembled in Inkscape.
  • The journal, PLoS ONE, was selected because of its high profile, high impact, and open access. Thanks to the open access policy, our article is readable by anyone who wishes to see it. I hope that the broader exposure will facilitate debate and further research on the topic--only time will tell. If I have any future articles of potentially broad interest, PLoS ONE will definitely be on my list of candidate journals.
  • The popularization of the article was initiated by PLoS ONE, with follow-ups by numerous journalists and bloggers. Thanks to the wonders of the internet, many of the articles are available for free. And, I am happy to say, most of them are pretty well-done.

Saturday, January 24, 2009

Open Access Publishing and the Paleontologist

Open access publishing provides free and unrestricted access to scientific works. This contrasts with the traditional model of publishing, in which an interested reader either needed to purchase a personal copy of the publication or access to a library with a subscription. The rise of the internet has made open access a reality--and a thorny issue for the paleontologist looking to get published.

In this post, I'll talk about some of the benefits and drawbacks of open access publishing from the perspective of a paleontologist. I'll also discuss how to choose an open access journal.

Kinds of Open Access
Open access comes in many different flavors. From least to most restrictive, they are:
  • Open Access Immediately. Your paper is available, for free to the reader, from the instant of publication. Palaeontologia Electronica and PLoS One are widely known examples.
  • Open Access After Awhile. The paper is available to paid subscribers for a set length of time (perhaps six months or a year), and then becomes freely available. Journal of Experimental Biology, as one example, uses this method.
  • Hybrid Access. The article is in a normally closed-access journal, but the author pays a fee to allow open access for all readers. Journal of Systematic Palaeontology allows this option.
  • Author's Choice Access. The author pays a fee to a closed-access journal for the privilege of posting a PDF of the said article on a personal website. Journal of Vertebrate Paleontology is a well-known example of this mode.
  • Author's Email Access. The author pays to get a PDF file that they can then distribute (legally) via email only. JVP also allows this mode.

Benefits of Open Access
The most striking benefit of open access is availability--the article is free to download for anyone who has an internet connection. The paper is picked up by Google and other search engines pretty much automatically, and people who are looking for that sort of research will usually find it.

From the author's standpoint, open access publishing is also usually faster than the standard model. Everything is done electronically, including the final publication. There is no lag time to mail the journals out, and some open access journals have a "rolling" publication schedule (meaning that once your article is approved, it's out there). Because many of the journals aren't bound by page constraints, they can place as many articles in a single issue as are available. There's no waiting 14 months for space to be available in the journal (a frighteningly common problem in many journals - if you've published papers, you've probably experienced this at least once).

Finally, the electronic-only mode of many open access journals allows some creativity in presentation. Need to have a movie as Figure 1 in your paper (rather than just a supplement)? Go right ahead (in some cases)!

The Costs of Open Access
Like many "regular" publications, some (but not all) open access journals have page charges. Depending on the journal, these can run up to $3,000 for a single article. A partial list of typical fee schedules is available here (thanks to Dr. Randy Irmis for passing along this link).

What is a poor paleontologist to do? In some cases, universities (that is, if you're based at a university) will partially subsidize the cost. In other cases, the journals (such as PLoS One) may partially or completely waive the open access fee for those with financial need. Finally, you can always find an open access journal with no fees (and they are numerous!). The most ethical of open access journals will not consider ability to pay in making decisions on publication.

A more critical concern, from the standpoint of relatively unestablished authors, is that some in the scientific community don't consider open access journals "real" or as good as their closed access counterparts. Yes, there are some open access journals out there with questionable editorial practices (they are in the minority, fortunately) --but there are also printed journals with loose standards (and these are also in the minority). And, there are many quite excellent open access journals, which are widely cited and recognized as such! So, the "quality" argument doesn't hold a lot of water in my view. Unfortunately, this reality doesn't necessarily hold up to the perception of the search, award, or tenure committee (rightly or wrongly).

Hope for the Future
How does a researcher support open access and circumvent this last concern? As a compromise, I might recommend using open access journals as one part of a publishing portfolio. After all, there are some really good closed-access publications out there (e.g., Journal of Vertebrate Paleontology, etc.) that do well at getting research into the hands (and minds) of the right audience. Some open access journals (Acta Palaeontologica Polonica, PLoS One, etc.) also do a good job at this. Choose the right journal for your paper--and an open access journal if that will get the research to the right people. Out of all the papers I have published, the one that gets cited the most was in Palaeontologia Electronica. I submitted it there on a whim, and have been pleasantly surprised by just how widely read it has been. Finally, just write good papers! A good paper is recognized as one no matter what, regardless of the journal.

Time will be the most important factor in changing attitudes. As open access publishing becomes more common, it will be seen as less freaky by the powers-that-be. And, this is a very, very good thing.

Tuesday, September 23, 2008

Head Butting Goats and FEM: Teaser

Finally! The first paper from my dissertation has made it into press:

Farke, A. A. 2008. Frontal sinuses and head butting in goats: a finite element analysis. Journal of Experimental Biology 211: 3085-3094. doi: 10.1242/jeb.019042

Abstract: Frontal sinuses in goats and other mammals have been hypothesized to function as shock absorbers, protecting the brain from blows during intraspecific combat. Furthermore, sinuses are thought to form through removal of `structurally unnecessary' bone. These hypotheses were tested using finite element modeling. Three-dimensional models of domesticated goat (Capra hircus) skulls were constructed, with variable frontal bone and frontal sinus morphology, and loaded to simulate various head-butting behaviors. In general, models with sinuses experienced higher strain energy values (a proxy for shock absorption) than did models with unvaulted frontal bones, and the latter often had higher magnitudes than models with solid vaulted frontal bones. Furthermore, vaulted frontal bones did not reduce magnitudes of principal strain on the surface of the endocranial cavity relative to models with unvaulted frontal bones under most loading conditions. Thus, these results were only partially consistent with sinuses, or the bone that walls the sinuses, acting as shock absorbers. It is hypothesized that the keratinous horn sheaths and cranial sutures are probably more important for absorbing blows to the head. Models with sinuses did exhibit a more `efficient' distribution of stresses, as visualized by histograms in which models with solid frontal bones had numerous unloaded elements. This is consistent with the hypothesis that sinuses result at least in part from the removal of mechanically unnecessary bone.

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To get a PDF of this paper, try this link first. If you don't have institutional access via the link, email me at andyfarke [at] hotmail [dot] com, and I'll send you a (legal) link for a free download (more on this below).

Within the next few days, I'll have a post summarizing this research. For now, I'll just talk a little about. . .

JEB and Open Access
Journal of Experimental Biology is not an open access journal - although it does allow that option for a healthy (unaffordable, in my case) fee. But, they present an admirable compromise - all papers become freely available 6 months after initial publication. Although a full open access model would be ideal, I think the publishers have found a good middle ground. The publishers get their due priority, and folks who are willing to wait a few months will get full access to all papers (or can email the authors for a reprint). If only more upper tier journals were to follow this route!

Authors get a link that allows up to 50 free downloads of the PDF (for use before the PDF goes free in six months). As mentioned above, anyone who would like this link should email me at andyfarke [at] hotmail [dot] com. Out of respect for JEB (because I think they're one of the few commercial journals that might have researchers' interests at heart), I won't be posting the PDF outright at this time. But, don't be afraid to email me if you want a copy!

Wednesday, May 28, 2008

Aetosaurs and the Open Access Dissertation

It's done. The Society of Vertebrate Paleontology has weighed in on allegations of plagiarism and claim-jumping centered on those spiny aetosaurs. The end verdict is "not guilty" on one charge and "inconclusive" on the other (but please read it for yourself), and I won't comment here where others have already (summarized here). I do wish to discuss, however, one point from the official SVP document that has not been addressed elsewhere.

"Sixth, the expectation that theses and dissertations that have not been republished in widely read periodicals will be read by most workers or manuscript reviewers is unlikely to be realized. If students publish material in theses or dissertations that they intend to republish in other venues, they should be wary about circulating their work until publication is well under way, if they are concerned that their work is topical enough that other workers might want to draw immediately from their findings." [p. 3 of SVP executive committee statement; italics are my own]

My main concern here is with the statement that it's unlikely that dissertations and theses will be read by other workers. This may have been true 20 years ago - today, this is changing very rapidly. You can find dissertations on Google Scholar, Dissertation Express, Theses Canada Portal, and DATRIX, just to name a few (although it's admittedly easier on some of these options than others). UMI now offers the option to distribute your dissertation under an open access scheme (with options for an embargo, for those concerned about such things). I have chosen to release my dissertation on open access (and will update here when my dissertation is readily available). Searching for dissertations and theses on a research topic should be part of any basic literature search (although whether or not this would have avoided the problems leading to the ethics investigation is certainly debatable).

The responsibility runs both ways. Students have an obligation to ensure that their thesis or dissertation is available and accessible via the information superhighway. This means making it available through relevant databases (and UMI's dissertations and theses have been crawled by search engines since 2006, apparently, with more complete access since 2007), and in most cases could [?should?] probably entail open access (with or without embargo). All paleontologists have a responsibility, too - to keep on top of the literature and other researchers' work. Even without a search engine, it wouldn't take a genius to figure out that a student who has had one or more conference presentations on thesis-y sounding research may have a thesis in his or her name on that topic. And with a search engine, there really is less of an excuse now. Sure, there will still be dissertations that slip through the cracks - but is this any different from not finding a peer-reviewed article just because it was in a journal outside your normal reading list? So--make those dissertations and theses available, and spend a few minutes on Google!

[This discussion is not intended to comment on the correctness or incorrectness of the SVP's general ruling about the charges. As Kevin Padian said, "There’s something for everyone to like – and dislike – about the statement. . ." I'm just calling attention to an area that fits in nicely with the mission of this blog.]

Tuesday, May 20, 2008

Data and the Open Source Paleontologist 2

The previous post on this topic outlined some resources for the posting and dissemination of primary paleontological data on the internet. In this post, I'll take a look at why more people don't do so, and what we can do about it.

Why Aren't More Data Posted?
Myriad factors contribute to this issue - some of them are genuine roadblocks, and others are simply opportunities to change attitudes and common practice.

Laziness
Sometimes it's a lot of work to get your data posted online. You may have to reformat everything, or re-enter the data, or engage in digital gymnastics that take longer than the research itself took. In other cases, it's just one more thing to do on an already crowded research schedule. How to counter this? Perhaps my best suggestion is better awareness of the importance of these data being available - if people demand it, it will be viewed as an item of high importance, just as needed as the peer-reviewed publication itself. Some repositories, such as MorphoBank, also allow you to enter the data as you collect them, rather than doing the whole thing at the very end. This might also be a good talisman against the rush to upload a whole bunch of data files at the end of a program.

Museum Policies
In the case of posting photographs of specimens, many museums have policies that are unclear or seem to prohibit general dissemination of photographs. These policies are in place for good reason in some cases - this discourages commercial concerns from profiting off of images of specimens without a museum's knowledge. Although it's my understanding that most museums don't have a problem with posting things into scientific databases, it's probably best to check. Does anyone out there have experience with this issue?

Priority of Publication
If your data are online, this means other people have access. This can lead to productive collaborations - or, it could potentially lead to being "scooped." Here, the safest thing is to delay uploading of data until after the major resulting publication. The important thing is to get those data out there! And, if you use data from an online database, you have a responsibility to credit the person who did the primary work. Anything less just isn't very nice. There are always going to be people who are stingy with sharing already-published data, even when it isn't warranted (or in the case of CT scan data, even when the museum requests that a publicly-available copy be reposited with the institution!). The most important thing is to work to change attitudes and foster a culture of openness. Recent events in paleontology have perhaps made this a little more difficult, but I like to think that things will work out in the long run.

What Can Be Done?
Above, I've outlined a few solutions to some of the problems. In addition to the suggestions given above (some of which are more practical than others), I think we really need more databases. And more encouragement to use these new (and existing) databases. Gene squeezers have GenBank, but why aren't there more Paleobiology Databases out there? Advisors - make your students reposit their data online. Students - get your data out there, even if your advisors don't encourage it! And paleontologists in general - welcome to the 21st century! I hope that time and a new generation of tech-savvy paleontologists will change all of this for the better.