The post-journal era

Most of the scholarly publication today goes more or less like this: a scientist writes a manuscript about research funded by her university and/or the grant fairy (usually a government agency) then submits it to a commercial peer-review journal. An editor (either working for free or for "honorarium") reads her manuscript and sends it to appropriate peer reviewers (payment? what payment?). Then, if her manuscript is accepted, her institute's library gets the privilege of buying access to the published manuscript. This state of things is very profitable for the commercial publishers' stock owners, but less so for scientists, libraries and the general public, who rarely get to read research they paid for. While many people agree this system is, shall we say, less than optimal, attempts to remedy the situation have been less than successful, and the commercial publishers might be targeting our research budgets next.

The latest attempt to renovate the system is by Priem & Hemminger (2012). At the beginning of their paper, they suggest that previous attempts in reinventing scholarly publishing have failed due to two reasons:

1.Change to peer review are just patches on a fundamentally broken scholarly journal system
2.Proposals offer no smooth transition from the present system.

Today, the journal fills four main functions: It archives scholarly material and time-stamp the researchers' contributions, if disseminates scholarly products and it certifies contributions (if it's published in a high-impact journal it must be of value). Priem and Hemminger want to make each of these functions independent from the others.

Their first suggestion is to "refactor" the system. This means locating "parts which are confusing, inefficient or redundant" and improving them without hurting the rest of the system. Their second suggestion is the "decoupled journal" (DcJ) (more about this later).

Overlay journals
These journals were suggested by Ginsparg (1997) and only provide the "stamp of approval" to an already published-archived-registered material. Despite the promise the overlay model represents, it hasn't been successful so far, and almost every journal which tried it went back to the traditional coupled model.

The PLoS One model

PLoS One is an open access journal which publishes work not according to what the editors and reviewers consider significant, but consider only the paper's methodological quality. They decoupled the significant approval from the methodological approval. PLoS One also decoupled copy-editing: they warn in advance that they don't copy-edit in details, and instead provide a list of services which do just that. This model has proven to be profitable: PLoS One published more than 5,000 papers in 2010 at 1350$ each (and the other PLoS journals charge even more). The flaws here, beyond the price, are the exclusivity: authors publish only in one journal, and the danger of a future with only a few mega-journals.

Post-publication review services
There are  a few existing post-publication peer review services, the best-known of them are Faculty of 1000 (F1000) and Mathematical Reviews. F1000 "...identifies and evaluates the most important articles in biology and medical research publication." F1000 is supposed to function as additional help for researchers in managing their reading. It has actually been shown to identify quality papers which were overlooked by leading journals (Allen et al., 2009).

Mathematical Reviews is and abstracting service, but as Priem & Hemminger say, it is "occasionally called into service as a post-publication peer review venue when the traditional journal fail in their role as certifiers. In this case, abstracters may abandon objectivity and attack papers and their reviewers directly."

These services have one major problem: they aren't brand names, and can't replace the certification of well-established journals, no matter how much their peer review is sound.

The Deconstructed Journal
Smith (1999) had three insights about the Deconstructed Journal (DJ):
1. The means (journal) and the functions are not the same.
2. Any system that will be implanted instead of the journal has to be at least as good.
3. Several cooperating agencies could successfully replace the central publisher.

Priem and Hemminger cite van de Sompei et al. (2004) and Smith (2003) as those who pointed out the advantages of a deconstructed system:

"...encourages innovation, adapts well to changing scholarly practices, and democratizes the largely monopolized scholarly communication market" 

However, van de Sompeis' and Smith' proposals are a bit outdated, because they hadn't taken into account the social media.

The functions of the decoupled journal
The Decoupled journal (DcJ, rather than DJ) is the updated version of the DJ. This is a universal, or meta, journal, where everything scholars produce and share is stored long-term, added to other projects, linked to, commented about...etc. etc.With the DcJ, publication is the first step in the process of revisions, reviewes, etc. Scholarly items will need persistent IDs, storage, and mirror backup in order to survive long-term. This can be done with persistent identifiers such as the DOI and institutional or subject-area repositories (ArXiv, Pubmed).

After the publication of a draft, it's time for preparation. Preparation is defined by the authors as "Changing the format of a work to make it more suitable for a given (human or electronic) audience". Today, many companies sell authors services (like copy-editing), but preparation is still mostly left to the journal. The DcJ will allow authors the freedom to choose the preparation they prefer (say, PDF or HTML format). PLoS One, as mentioned before, already leaves copy-editing to authors, perhaps showing the beginning of a trend.

After the preparation comes the assessment. Defined as "Attaching an assessment of quality to a scholarly object". Today's method of assessment, peer review, is usually anonymous, unpublished to the general public, and done by invited reviewers. The reviewers give their opinion in free text first, then a final assessment whether the material should be published.

In the Priem & Hemminger model, reviewers don't decide whether the material is publishable or not  (it's already published!) but certificate it. In the future, Nature could become "Nature stamping agency" and give papers its "seal of approval". It will even be able to do so by giving grades, rather than just accept or reject the paper. There will be agencies that will only review the soundness of the work (like PLoS One does today), agencies who will certify only certain parts, open peer reviews and blind peer reviews. Other forms of assessments - blog posts, number of downloads, and even tweets - will be stored as well. The authors see the DcJ as a way to allow peer-review to evolve freely, without its tight coupling with the other functions of the journal.

With libraries' budgets tighter than ever (even Harvard decided that commercial journals are just too expensive ) I expect more and more authors will choose the DcJ route. However, it could be that a certification bottle-neck will be created, with the prestigious journals of today becoming the prestigious stamping agencies of tomorrow. The number of expert peer-reviewers in each field could become a limitation as well. Will our grandchildren complain about the amount of money they have to pay for a Science certification? Only time will tell.

Allen L, Jones C, Dolby K, Lynn D, & Walport M (2009). Looking for landmarks: the role of expert review and bibliometric analysis in evaluating scientific publication outputs. PloS one, 4 (6) PMID: 19536339

Ginsparg, P. (1997). Winners and Losers in the Global Research Village The Serials Librarian, 30 (3-4), 83-95 DOI: 10.1300/J123v30n03_13

Priem, J., & Hemminger, B. (2012). Decoupling the scholarly journal Frontiers in Computational Neuroscience, 6 DOI: 10.3389/fncom.2012.00019


Smith, J. (1999). The deconstructed journal – a new model for academic publishing Learned Publishing, 12 (2), 79-91 DOI: 10.1087/09531519950145896

Smith, J. W. T. (2003). The deconstructed journal revisited: a review of developments ICCC/IFIP Conference on Electronic Publishing-ElPub03: From information to knowledge. (Minho, Portugal).

Van de Sompel, H., Payette, S., Erickson, J., Lagoze, C., & Warner, S. (2004). Rethinking Scholarly Communication D-Lib Magazine, 10 (9) DOI: 10.1045/september2004-vandesompel

Reinventing Discovery, Part II

This is the second part of my review of Michael Nielsen's book "Reinventing Discovery - The New Era of Networked Science" (first part is here). Last time we talked about Galaxy Zoo, the Polymath Project, and why scientists don't (usually) do Wikis.  This time I'd like to focus on the book parts which talk about ArXiv

ArXiv

First of all, I have to say I've been using ArXiv extensively lately as part of the ACUMEN project, trying to figure out who and what can be found there. The place is a bit of a mess - it's not Pubmed - but it still left me in awe, because not only that most of the astronomers I've searched had papers there, most of them contributed at least one of the papers themselves (you can see who submitted the paper). 

ArXiv comes with a service called SPIRES (now inSPIRE) which can tell you how many times a paper was cited, who's citing who, and so forth. This way, it's possible to measure at least some of the impact of preprints (if you're a high-energy physicist). So, not only ArXiv makes the scientific communication faster, it also helps evaluate the impact of this kind of communication more accurately. 

Unfortunately, not everybody gives ArXiv the honor it deserves. Nielsen tells how when he was writing the book, a physicist told him that Paul Ginsparg, ArXiv's creator, was wasting his talent on "collecting garbage", reflecting a disregard certain scientists have for "mere" tool builders. I don't know if this attitude is common in the scientific community, but it's discouraging nonetheless. 

Open Access can be problematic 

Citizen science isn't always all that - in the Polymath Project, there were people with good intentions but not much knowledge, their contributions didn't have much value to the project and had to essentially filtered out. 

Misinformation - premature publications , especially in fields the mainstream media takes interest in, can spread far and wide, confuse the general public and discredit research projects in the eyes of the public. 

How we can be more open (if you're reading this, you probably don't need these suggestions). 

In the last few pages of the book, Nielsen suggests practical steps toward open science. A scientist can upload old data, code, etc. online for reuse (be sure to tell people how to cite it!); He/she can open a blog, contribute to other people's open science projects, or try to create a new one. Nielsen advises to "be generous in giving other scientists credit when they share their scientific knowledge in new ways" which I think is an excellent advice, even though the formatting and style guides are a bit behind the times when it comes to social media. 

  

All in all, Reinventing discovery is a great book, however, I was a little disappointed to find only a small section dedicated to science blogs. The author explains that he had enough of the hype around blogging and that he doesn't want "to cover that well-trodden ground again", but I think the book could have benefited from a few more pages about the subject (yes, I know I'm not very objective here...). Also, though the book deals with - and recommends - open access, it isn't under Creative Commons licence (you can read why here). 

Nielsen, Michael (2011). Reinventing Discovery Princeton University Press Other: 9780691148908

Publishing Open Access is Good for Your Academic Reputation

In the academic world, reputation is the currency of choice. "Reputation," of course, is a very loose term and can include anything from publishing in high-impact journals to being a good advisor to your students.

How does OA contribute to your academic reputation?

The first significant scholarly repository, arXiv.org, was started by high-energy physicists, but quickly expanded to include other scientific disciplines. Today, archiving in arXiv.org is practically a necessity for physicists. Archiving provides the physics community with faster communication, better access, and the opportunity for an unofficial peer-review, even before the work has been submitted to a journal. Unfortunately, journal publishing is still important for official purposes (promotion, tenure, etc.) and so libraries are still forced to buy physics journals.

Another example is PLoS. PLoS peer-reviewed journals charge the authors a fee in return for publishing, and papers are published under Creative Commons licences. PLoS journals probably wouldn't have been as successful (PLoS Biology had the highest IF in its category in 2009) if libraries were asked to pay for them. It pays off for authors to pay PLoS for the prestige of publishing in such high-impact journals.

Eysenbach (2006) found that immediate-OA papers in PNAS, in comparison with those who weren't immediately available in OA, were more likely to be cited earlier and more often. However, Davis et al., who studied papers from 11 journals published by the American Physiological Society, haven't found an increase in citations for OA papers in the first years after publication. They did find that these papers had significantly more downloads and unique visitors, which means OA papers reach wider audience.

Open Access also allows scientists to build reputation in places and among people who otherwise wouldn't have been able to read their researches (the MIT OCW is very popular in developing countries). Given how important citation metrics are to a scientist, publishing Open Access seems to be a very logical step, career-wise.

Willinsky, John (2010). Open access and academic reputation Annals of Library and Information Studies, 57, 296-302

Davis PM, Lewenstein BV, Simon DH, Booth JG, & Connolly MJ (2008). Open access publishing, article downloads, and citations: randomised controlled trial. BMJ (Clinical research ed.), 337 PMID: 18669565

Eysenbach, G. (2006). Citation Advantage of Open Access Articles PLoS Biology, 4 (5) DOI: 10.1371/journal.pbio.0040157