Opinion: Transparency in Science Publishing

As a new age in scholarly publishing dawns, improved standards for openness in communicating scientific information promise to eliminate biases and publication delays.

By | August 28, 2012

image: Opinion: Transparency in Science Publishing Wikimedia Commons, Vmenkov

The world of scientific publishing has been buzzing in the past few months, with many leading publishers working on new initiatives. Some have been exploring alternatives to traditional publishing processes, others rethinking standard business models. This surge in inventiveness has been fuelled by widespread and growing discontent with the limitations of conventional journal publishing.

The Research Works Act, which made the rounds of the US Congress earlier this year, brought the question of access to the fore and motivated scientists to become activist in their support for open-access publishing. Many universities (for example Harvard University and the University of California, San Francisco) have strongly urged their researchers towards open access, and, in the first nationwide push in the same direction, the British Government announced a couple of weeks ago that all publicly funded research will be published open access by 2014.

There has been a rising tide of blog posts, seminars, and workshops discussing the problems of the peer review system, with numerous proposals being floated for how to fix it, and also much discussion about the need for more openness and transparency, particularly with respect to the data behind research findings. (See "Bring on the Transparency Index," The Scientist, August 2012). In many areas, we have seen a move towards self-publishing, for example on preprint servers like ArXiv and F1000 Posters.

Concerns about access and peer review have coincided with discussions about new initiatives for measuring researcher outputs, assessing their impact, and evaluating the "‘invisible"’ anonymous work that researchers perform for the scientific community (such as refereeing articles and sitting on grant committees) that takes up significant time but for which they are not formally recognized.

These discussions have pushed publishers to explore alternatives to traditional publishing (such as data journals like GigaScience and data repositories like figshare and Dryad), and to rethink standard business models (for example PeerJ and eLife). (See "Whither Science Publishing," The Scientist, August 2012.) We at F1000 are also pushing to change the way scientific research is published, by implementing a completely open peer review process at our new publishing program, F1000 Research.

At F1000, we believe that if everything is out in the open, then biases will lose their power and errors will quickly be addressed and discussed. Furthermore, the contributions of referees, whose role in improving published science is vital, can be publicly acknowledged and formally recognized as important and valuable outputs.

The F1000 Research publication model works as follows: New submissions go through a rapid internal pre-publication check and are then published immediately, labeled clearly as "Awaiting Peer Review." Expert referees are then invited to review the submissions and are asked to do two things: first, assign a quick "Approved" (i.e., seems OK), "Not Approved" (i.e., does not seem OK), or "Approved with Reservations” (i.e., is a sensible contribution but the referee has strong reservations about one or more key aspects of it, such as the methods used or the conclusions drawn) status within a matter of days. The paper's status will be prominently displayed along with the referee’s name. Second, referees are asked to write a more standard referee report that they sign and publish alongside the article (this is optional if the referee status provided in the first step was "Approved"). Authors are then encouraged to revise their articles in response to the referee’s comments and each article version will be separately accessible and citable.

Other journals have implemented variations on the open peer review system just described. (See “I Hate Your Paper,” The Scientist, August 2010.) Biology Direct, for example, often publishes reviewer comments of accepted articles, but these reports are different than the ones prepared for the authors, and initial referee recommendations regarding whether to review the article or not are kept private. BMC also uses open peer review in some of its medical journals, but referee reports are only made public for articles accepted and published by the journals. And the BMJ journals practice optional open peer review, in which referees may sign their reports if they wish.

All of these models are quite different from ours: they are selectively open and structured to avoid risk of hurt feelings or reputations, while we are publishing first and making referees’ decisions and reviews—positive, negative or undecided—entirely transparent.

As a novel approach to publishing in the life sciences, the first question you might ask is whether nor not it is working.  It’s too early to draw concrete conclusions at the moment, as we only soft-launched in mid-July, and we plan to spend the next few months fine-tuning our model and our processes before more formally launching on a full platform at the end of 2012. However, with the publication of our first articles a few weeks ago we have already been able to validate many of the core principles of what we’re trying to achieve, which is very encouraging. We are enjoying an unexpectedly high and positive response rate from referees agreeing to conduct F1000 Research-style open reviewing, and in a very timely manner: we have had several articles reviewed by a minimum of two referees within 48 hours of being published.

We are also seeing useful comments on the articles from interested scientists, and there are debates opening up between authors and referees about issues such as competing interests. We are watching this one closely as navigating and interpreting disclosures can be tricky—it seems reasonable to expect that in an increasingly siloed world of specialized science, a referee who is qualified to comment may, or perhaps should, have what many would judge to be relevant disclosures to make. Since all our referees are named, this question and concerns arising from it can be addressed openly.

Many had predicted that our “publish first, peer review later” model would attract substandard work and that we would be inundated with poor quality articles, but we are very pleased to see that this has not been the case thus far.  Furthermore, the fact that our referees are clearly quite happy to openly criticize where they have concerns further supports our hunch that scientists will think twice before submitting sloppy articles as this will lead to open criticism of their work, which will be eternally linked to their paper by way of the article citation.

It is exciting to watch F1000 Research develop, even at this very early stage, and it will be interesting to see how these first articles and exchanges influence the openness and transparency of future authors and referees. We also look forward to feedback from the scientific community on other new publishing ventures, such as eLife, which is scheduled for launch later this year and plans to use a unique model for the funding of open access, and PeerJ, which proposes lifetime author membership fees as an alternative to article processing charges.

The first substantially new business model to hit science publishing was open access, which we launched with Biomed Central over a decade ago.  After a long interregnum, publishers and scientists are clearly now primed for more radical change.  F1000 Research is very pleased to be among the innovators who are testing new models and who will, ultimately, help make real change a reality.

Rebecca Lawrence is the publisher of F1000 Research.


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Avatar of: corrigible


Posts: 42

August 28, 2012

Being a person who believes in science, believes in transparency, and desires more public access, what makes me happiest is to see so much dialog as is taking place. Just as has been said about Steve Jobs, whatever may have been a bit odd about his personality and personal history, he was able to see the same things everybody else saw and think beyond the envelope. If, and to the extent, one or more publishers can do that and come up with
ways of building business in such a way as to promote more interest in peer review without corrupting peer review, or watering down the scientific "product," both the highest and best services of science AND expansion of public interest may be facilitated.
Of course that is not the only issue. The scarriest issue for those who labor for little until and unless they come up with something that is valuable "intellectual property," have much to lose by having their work "mined" by others who would claim a right to it. Yet, if public funds, or organizational funds, are solicited and utilized, there arises a legitimate question as to whether the worker -- who could not proceed WITHOUT such patronage -- could afford to arrive at the "intellectual property" in question. Does not the public have some rights, some control, some expectations in the result?
This is NOT INTENDED TO ANSWER the issue. It is merely to encourage the DIALOG.
Possibly there could be one or more publisher who has a Steve Jobs way of looking at an approach and/or a methodology that no one else might ever think of. And it might revolutionize the industry.
Sometimes just doing the same thing the same way and working harder and longer than anybody else, or getting by on less income than anybody else (without going under) is not the "solution."
Wherever change occurs, there is some "creative destruction" and some new and different and newer and better way found by some one or some few, and many, unwilling to change or think outside the envelope, who end up crushed and gnashing their teeth.
Whatever evolves out of it, and whoever prevailes, our best hope must be that it will both advance science efficiently, and expand public appreciation of that advance.
Agreed? Or disagreed?

Avatar of: EllenHunt


Posts: 74

August 28, 2012

My problem is that I have never published a paper without going through at least one round of revisions with reviewers. Reviewers like the taste better afterward. Nor have I reviewed a paper without having something to say that authors needed to respond to.

That suggests strongly to me that certain scientists do pre-publication rounds with people they know on this system prior to open pre-submission. That would also be the sensible thing for those who started the site to do in order to prevent the problem that nay-sayers had been sure of.
I doubt very much that this system is actually single-tier and hence truly fair to all.

Avatar of: corrigible


Posts: 42

August 28, 2012

That's good information, Ellen, and food for further thought. In thinking about it, I try to put myself in the publisher's shoes. Is the object to muddy-up your contribution to science, or re-spin so as to favor a bias on part of the editor or editors? Maybe in some cases it could be. I would tend to think the primary motive is to preserve the science value and make the paper more likely to be read all the way through, the headline more likely to capture interest or even to tweak a little controversy.
As a science literate non-scientist (more into the history and philosophy of science, and more curiosity about what is occurring at the cutting edge over a wide band of the spectrum of research) I often discern poor writing style and, quite often, a seeming obsession of the author of a peer review paper with planting and maintaining the impression the author is so smart that no one could follow his/her thinking unless they, too, are extraordinarily brilliant and extraordinarily versed in what the author has to say.
From where I read, it appears to me the gist of Dr. Einstein's assertion -- that if one truly understands his subject he/she should be able to explain it clearly to a bar maid. Stilted composition, and esoteric language unfamiliar outside one's immediate laboratory or academic in-group not only is obtuse; it's also likely to turn off any reader who otherwise might have an interest in the subject matter. Using a two-dollar word to impart a ten-cent fact or point of argumentation may impress; but, as Ann Landers commented in her column, some fifty years or so ago, "When you try to make an impression on others, that very well may be exactly the impression you make."
There are various levels and kinds of transparency. One kind is the transparency of style which most efficiently communicates the message of importance. Whether disclosed overtly, or implied between the lines, some authors give the impression their primary message is not about science but, rather, "Look at ME. Look how smart I am. Look what fancy words I can use. Pity yourself if you are unable to follow my sentences and get my superior meaning."
What reader does not admire the most brilliant thinker and writer of all: the one who can take that reader's mind to new and wider understanding of things others merely excel at making dull and lifeless and vain and difficult to grasp.

Avatar of: Shi V. Liu

Shi V. Liu

Posts: 1457

August 28, 2012

I am very happy to see the launch of F1000Research because
it reinforces an approach that I have taken for over two decades in my attempt
to revolutionize scientific publishing (

In late 1999 I launched the world-first double-open (open
access and open review) scientific journal called Logical Biology (
). This happened years before the launch
of a similar journal called Biology
Direct (
). Later more such journals such as Scientific Ethics, Pioneer, Top Watch, International Medicine were published
under such a model by TruthFinding CyberPress (TFCP;
). Appeals were made to embrace this
revolution in scientific publishing ( Unfortunately, mainstream has seemed
neglected this development and many researchers and editors have expressed a
clear opinion of not citing publications contained in these journals even
though these publications have disclosed ground-breaking discoveries and novel
inventions that were re-discovered and re-invented. In addition, (corresponding) authors of
publications in other journals almost universally ignored the invitations from
these double-open journals to submit rebuttals against criticisms over their
publications. Thus, while I am happy to
see F1000Research join this “open scienceâ€쳌 effort in publishing science, I am
afraid that most “successfulâ€쳌 or to become “successfulâ€쳌 scientists may not jump
onto this double open platform of scientific communication, unless it can bring
tangible “benefitsâ€쳌 such as some impact factor to them AND do not led to any
“harmâ€쳌 to them such as exposing the flaw in their “scienceâ€쳌 or even fraud in
their research.

Avatar of: Shi V. Liu

Shi V. Liu

Posts: 1457

August 28, 2012

I saw my comment being shown after its posting but I do not see it now. Why?

Avatar of: Shi V. Liu

Shi V. Liu

Posts: 1457

August 28, 2012

Logical Biology and other double-open (open access and open review) journals published by TruthFinding CyberPress (TFCP) have done this for years. But more is better for changing the tradition.

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