Cretaceous African ant in amber (Courtesy of Vincent Perrichot via http://myrmecos.wordpress.com)

1. A peer-review paper gets published;
2. The media gets hold on the story;
3. The blogs react: scientists and general public fill the comments section (in the genuine tone of the internets);
4. The authors of the original paper join in the discussion.

Discussion may get heated, comments may get bitter, but the results are always rewarding for all.

To clarify, I don’t have an opinion on the issue of publication policies used by the National Academy of Sciences.

PNAS will eliminate Communicated submissions in July 2010

1. Randy Schekman, Editor-in-Chief

As of July 1, 2010, PNAS will no longer allow the submission of papers “Communicated” to the journal by NAS members and will instead handle these papers as Direct Submissions. Authors are free to ask an NAS member to edit their paper as a “Prearranged Editor” prior to submission to PNAS. Assignments are handled by the Editorial Board, and members who agree in principle to edit a paper are given special consideration by the board. NAS member contributions are not affected by this policy change.

You can read the full text at PNAS’ site.

Most people in academia will cringe at the thought of formally citing a page that exists only on the internets. One main objection is that the electronic information could not be there the next time one tries to access it. This is what has kept the ICZN from allowing publication of new species names in online peer-reviewed journals, even well established ones.

In reality formal citation of electronic media has become more common than scientists realize. In systematics, for example, many of the specialized software we use is distributed directly by the authors (who are research biologists themselves), and URLs to the pages where these applications can be downloaded are included as part of the citation. Many electronic databases accessible through the web, like antbase.org and antweb.org for myrmecology, have accumulated multiple formal citations in recent years. And if that doesn’t convince you just think about the ubiquity of GenBank– after all, a list of GenBank accession numbers is nothing but the digital identifiers of information about particular pieces of genetic information stored on an database that is accessible online.

Pers. comm. to me is the right comparison for a blog post (at least the type of posts I write): part of the content is original unpublished information; part is word of mouth circulating within the scientific community; part is published information. Above all, it is the blogger’s subjective opinion on a topic. But most importantly for citation purposes, blog posts are not peer-reviewed material. As long as people bear this in mind, I see referring to a blog post as a legitimate practice equivalent to pers. comm. There is a significant difference, however. By providing an URL the author (the editor) allows anyone who so wishes to check the original source for further details. As such, a blog citation serves as an enhanced pers. comm.

A sign of the (slowly rising) acceptance of blogging in academic circles is the inclusion of standards on how to cite electronic media in style manuals. As with printed media, there are now many acceptable ways to cite a blog post, varying from journal to journal. Citing this post can be done as following:

Keller, R. A. (2009) Citing blogs in scientific papers. [Weblog.] Archetype. May 27. (http://roberto.kellerperez.com/2009/05/citing-blogs-on-scientific-papers/). Date accessed.

And my recent post on the clypeus would be,

Keller, R. A. (2009) Homology Weekly: Clypeus. [Weblog.] Archetype. May 22. (http://roberto.kellerperez.com/2009/05/homology-weekly-clypeus/). May 27 2009.

Now, all the journals I want to keep track off offer TOCs e-mail alerts or RSS feeds but one: Zootaxa. This journal not only moves fast as part of its editorial policy but also publishes a lot of papers on ants. I was growing so annoyed by not having a RSS feed for this journal that a couple of weeks ago I contacted chief editor Zhi-Qiang Zhang to demand beg suggest such service. His kind reply was that they know they need to do it, they don’t know how to do it, and their staff is currently so loaded with publishing work that they don’t have the time to do it. But he would welcome any suggestions.

I, unfortunately, don’t know how to implemented this either, but cybertaxonomist Rod Page from the University of Glasgow does. He just set up a page where you can subscribe to a RSS feed for Zootaxa for your taxon of interest.

The timing was coincidence– he just happens to be working on some projects that need such feeds. If you follow iPhylo or any of Page’s blogs you know it took him one coffee break to build.

Thank you Rod.

Every now and then I get asked to a lab or seminar to give a talk about what I do as an editor at Nature, apart from lie on my back being fed grapes by flying babies.

I see before me a wall of faces, agog and drooling amazed to discover that Nature editors are almost really human.

It is interesting to know that as an editor he has to go through more or less 700 papers a year, yes, that is roughly three papers a day, every weekday of the year, from which only 35 to 40 get accepted.

A good lesson is that, given the journal’s general coverage on all science topics, submitting authors need to keep in mind that the editors as well as the readers will most likely not be particularly so into your specialized area of research as much as you are. So, basically, remember to keep the geek level low, because you need to be able to convey to a general audience why your results are of interest to them, why should they be as excited about the topic as you are.

It is a good read for us mortals sub-mortals hoping to land papers in the highest impact factor journals. Now, I just need to find myself a fossil ant with feathers, hmm…

Hat tip to Evolving Thoughts.

I have to confess that by the journal’s name and cover design I initially thought, with excitement, that it was a new open access experiment by Cell Press, publisher of the high-end and successful family of “Trends” journals. I was particularly intrigued since Cell Press already publishes Trends in Ecology and Evolution or TREE as it is called inside the cool geek¹ circle of evolutionary biologists.

It turns out to be a journal published by PAGEPress, located in Pavian, Italy. PAGEPress seem to be starting a whole series of titles in medicine and biology.

The journal description is a little odd though:

Trends in Evolutionary Biology is a new Open Access journal concerned with the origin of species from a common descent and descent of species, as well as their modifcation[sic], multiplication and diversity over time.

I also feel that they tried too hard in their scope description to include the term molecular as a selling factor (no pun intended):

Trends in Evolutionary Biology is a new, Open Access, international peer-reviewed journal that considers articles about all aspects of molecular and non-molecular evolution of all organisms.

Odd wording aside, it is still too early to asses this publication since they are still on the initial editor building phase. But, as an open access project, it is worth keeping an eye on its development and give the journal the benefit of the doubt.

The authors highlight that the effects of open access are stronger for publications within the natural science. The explanation is that in our field, compared to physics or social sciences, it is rare that one can get preprints through freely accessible databases maintained for that specific purpose. From my own experience with the publishing dynamics in biology,  I was very surprised to see how many preprints in topics related to philosophy of biology one can get from PhilPapers, an online database for philosophy that just went public on January 28, 2009! Let me stress the word preprint here. In the narrow field of ant taxonomy it almost never happens that authors submit their papers to antbase.org for example, a database created for that purpose, even after they have been published.

But the main point of this paper is that the influence of open access was also stronger in the developing world, where individual scientists may struggle to get access to relevant publications through their funding strap host institutions. This result puts more sound into the argument that Donat Agosti, creator of antbase.org, has been putting forward- biodiversity is greatest in the developing Southern Hemisphere and we will all benefit the most from facilitating local conservation related science by making the necessary data available without restrictions. Keeping access to taxonomic descriptions restricted is akin to imposing a copyright on species².

Now, you won’t be able to read the full article unless you have a subscription to Science which is, I think, a delicious irony.

References

The reviewer writes:

Lessig argues that a strict divide between the world of sharing and the world of commerce is counterproductive. He wants to refocus attention away from the stalemated copyright wars and towards a more vibrant ‘read–write culture’ that remixes rather than replaces what came before.

[...]

In Remix, he outlines the case for licences that make one’s work free for non-commercial use but reserve any right to commercial exploitation to the author — something that is traditionally anathema to the free-software movement.

In general, Lessig centers his arguments around debates that are of interests to a wide audience, like the ones surrounding the music industry and web-portals like YouTube. The issue of copyright is, however, of importance for science as well since it impacts the way scientific knowledge is disseminated and shared. An example in the realm of myrmecology concerns the taxonomic literature dealing with species descriptions that is stored in antbase.org: as of today, you can freely access all the taxonomic works produced on this group of insects since 1758 with the exception of the most recent ones, as they are protected by copyright laws.

In my view, you have to look no further for a prime example of the benefits of a read-write cultural than the practice of science itself, hence my interest in how the Science Commons projects develops.

The book is now in my (already long) reading list. You can (freely) access the review in full at Nature’s’ website:

How to end the copyright wars. Jonathan Zittrain reviews Remix: Making Art and Commerce Thrive in the Hybrid Economy by Lawrence Lessig. Nature 457, 264-265 (15 January 2009) | doi:10.1038/457264a.

Back then, getting papers in the subject of one’s interest consisted in meticulously thumbing  through the heavy telephone books for animals called Zoological Records*, writing down some potentially useful references, and filling a petition for copies at a special place in campus that dealt with international inter-library loans. After that, you only had to wait a couple of weeks to get photocopies of some papers that were not quite what you were looking for. It felt like I was doing some serious research nevertheless.

All this changed when I arrived to Cornell University in the U.S. to pursue a Ph.D. in Entomology. Cornell has the best library for entomology in the Americas, and with its rare book collection it rivals some of the bests in Europe. I went from having a modest access to scientific literature to having anything I could think off. Occasional Papers of the Southwester Entomological Station? Sure, we have it, no problem. It was like a never ending cocktail party with open bar.

And that was when my thirst for scientific papers began. It started as an innocent activity.  Social reading at first, a couple of papers a week in discussion groups and lab meetings. It quickly changed to reading articles by myself, anytime, anywhere. Soon I had already went through a chapter in a edited book and some meetings proceedings before lunchtime.

I inevitably became a regular of the entomology library, spending countless hours chugging away one monographic revision after another:

- I think you have had enough for today Mr. Keller.

- Huh? What time is it? I lost track of time…

- It’s closing time. You can leave those books on the desk, I’ll take care of them. Do you want me to call you a taxi?

- No. It’s O.K. Marty, I’ll take the campus shuttle. See you in the morning I guess.

I photocopy everything at first, not knowing where will I end up after graduation. But soon journals went electronic, JSTOR digitized back issues and, for ants, Donat Agosti compiled all taxonomic publications since Linnaeus and uploaded the pdfs to antbase.org. No need to carry all that paper around. And the best of it, all these papers accessible online at a mouse click. 24 hour long happy hour.

My reckless, addictive behavior continued as I moved to the American Museum of Natural History to continue my dissertation research. The library of the AMNH also has a substantial and comprehensive collection and they have been pioneers in all manners digital. I graduated last summer and haven’t been at the AMNH for some time now, but I kept accessing the library and its online journal subscriptions remotely.

All this changed a little more than two weeks ago. I received and automatically generated message telling me that my AMNH account was about to expire in two days unless renew! Panic. This is the account I use to access the digital library. Worst still, the message came during Thanksgiving weekend, so there was no one I could contact to prevent this catastrophic event from happening.

And so it did. It all suddenly came to an abrupt stop. Involuntary cold turkey. One day I was carelessly reading about the thoracic morphology of Archostematal beetles, the next day I needed to “log in or make a payment in order to read this story in full.” For the first time after all my years as a graduate student and postgraduate time I woke up feeling sick and withdrawn. My head felt like it was about to explode. I reached for the Internet in vain, as even antbase.org couldn’t help me since most of the recent articles about ant taxonomy are still published in copyrighted journals.

During the first week without access I tried to ease the anxiety by going through the free online abstracts. Some journals even let you read the first page without a subscription! But I soon realized that it was like trying to get drunk by sipping wine samples from the promotional stand in the liquor store. The employee has just so much patience.

I received Nature‘s table of content in my e-mail. I was afraid to open the message. What if there is a paper, letter or editorial comment that interests me? I knew I wouldn’t be able to read the full article. I decided it was better not to know for now. If there was something truly important, I thought, I’ll surely read about it for free in the Science section of the New York Times online.

By the end of the second week, in desperation, I reached a new low. I searched for some old papers on molecular systematics I had stored in my computer’s hard drive and read through the PCR protocols, trying to squeeze the last drops of information out of them. It made me feel disgusted. I was afraid someone was going to enter through the door and find me doing that, how embarrassing.

Everything is alright now. I contacted the secretary of my department at the AMNH and she kindly agreed to fill out the appropriate form and send it to IT department to have my account reactivated. The headaches and dizziness are gone. After what seems to me like the worst hangover I ever had, I still wonder, however, how does an individual outside of the institution can keep up-to-date on primary scientific literature, let alone do even the most basic research? Lets hope the open access moment keeps its momentum and we find ways of making the results from scientific research widely available while keeping publishers afloat.