More about the current state of scientific publishing and how to start change

Additional observations

Our lab has an ongoing fruitful collaboration with AK Hadjantonakis at the Developmental Biology division of MSKCC in New York ( and a recent visit coincided with the publication of an article from Leslie Vosshall on the current state of scientific publishing and the effect it has on careers and, overall, the field ( Leslie kindly made time to see me and we had a good exchange during which we shared our views of the problem and ways towards solutions. She proposes some in her article by making a rational appeal to the common sense of authors, reviewers and editors and while I agree with much of what she says, my feeling is that what we need is a global active engagement of the community to shape a peer review and publishing system that is more in tune with the times and stops the increasing deterioration of the essence of our profession. As Leslie puts it “scientific publishing is an enterprise handled by scientists for scientists, which can be fixed by scientists”. It is strange that for all that we complain about the system, we do very little to implement actual change. We need to act and do this by getting actively engaged in, first and foremost, giving our views on the system. A global engagement is important because only in this manner we can implement change.

Any discussion of the current state of scientific publishing revolves around four interrelated issues: Open Access, Impact Factor, the mechanics of Scientific Publishing itself and, of course, Peer Review. I am tempted to comment on all of them but, because of my conversation with Leslie will keep a focus on the last two.

It is clear that we have forgotten that scientific publishing is all about OUR work and that while it is fine that somebody profits from it, what cannot happen is that these people determine the rules of the game. I have written before about Nature setting up rules about authorship and contributions (What’s in an asterisk: the power of Nature ) but this is not restricted to Nature and it surprises me that we just go along with it even if Nature in its website is not very clear about this and works by stealth. But this is just one example of how far we are allowing the system to go, how far we are allowing the publishers to play us. There are other examples of this. For example, how come that in the age of e-publishing many journals have a less than 10% rate of manuscript acceptance? How can this be justified? Do they not agree that there is a further 10% -or even 20%- of manuscripts that could make it…if they had space? And they have space, e-space! What is the real reason for these quotas? The reason is not to help the science and certainly not the scientists, the reason that comes to mind is that such quota plays in the hands of the Impact Factor (IF), it ensures that publication in those journals is artificially (and I mean artificially) difficult so that the journal will receive higher and higher quality papers -though this does not necessarily mean that they are good science. This of course has a circular effect on the impact of the IF and the scientists. The arbitrariness of this situation and what could be done about it is made clear in a comparison of the research articles published in the March 2013 issues of PLoS Genetics (78) and PLoS Biology (14). They are both journals from the same publisher, both pride themselves in serving the community, have similar IF 11.45 (180 articles in 2011) for PLoS Biology vs 8.69 (548 articles in 2011) for PLoS Genetics, and look at themselves as flagships for a scientist based movement. What is the reason for this difference? It could be claimed that PLoS Biology was set up to compete with the higher end of the market but I would have thought that the ambition would be to change the way scientific publishing works and not to be changed by this. Is it that PLoS Genetics is not an ‘elite’ journal? What kind of elitistm does PLoS Biology aspire to? The reason for the difference is, of course the editors and their policies. One PLoS Genetics, understands what is the role of the journal, PLoS Biology on the other hand has become a victim of what it tried to avoid. And this is the point: many journals set up an arbitrary barrier to publication because publishers believe that a way to raise the IF is to reject more papers. It is clear that this is not the case (the difference in IF between the two PLoS journals is not commesurate with their different acceptance rate i.e. the impact factor of PLoS Biology is not 5.5 times higher than that of PLoS Genetics, in fact it is 1.3 times higher. Is this worth it?  What keeping acceptance levels below 10% really achieves is to make life difficult for us, the scientists. It does not improve the IF of a journal. A paper is not a grant: within a grant committee there is a fixed pot of money and therefore a limit to what you can fund, many good grants cannot be funded and the decision is agreed to be difficult and often arbitrary; this is not the case of an e-journal. There is room. There is no justfication not to publish good papers.

All these are facts to ponder and act upon by forcing journals to change their habits. How do we do this? By moving to journals that are willing to listen to us and are actually there to do their job: help us put out our findings in an efficient, transparent manner

The real problem right now, the one we need to address urgently is, as highlighted by Leslie Vosshall, what she calls the ‘glacial pace’ of the reviewing process. Here we are all in it together. This is a state of affairs (for another  succinct review of where we are on this and how we have come to it, read the second half of the recent posting of Mike Eisen ( ) which involves all of us as a community. We are all victims and perpetrators of the crime, because let us face it, the way we handle papers as reviewers is close to a ‘criminal’ activity masterminded by the editors whom we allow to use us to perpetrate the ‘crimes”. I shall state up front that I believe in peer review. I also believe in free commenting on papers after publication (and not just in journal clubs, but in blogs and journals), and that the point is not, as advocated in many sites and places these days, to remove all barriers to publication, but to adapt the system to the times and to get it to work for us, not against us. Remember: the peer review system is us and we need it, but not the way we are doing it now. The mystery of the situation is how is it that we have allowed journals to use us to make life so difficult for ourselves. While the practices that we all know too well are most prevalent in HIF journals, they increasingly operate in aspiring HIF journals and things are not getting better. But rather than ranting about this, it is good to state what we want: a fair, expedite, transparent reviewing process. Some journals, most notably EMBO J and eLife are taking steps in this direction and it is difficult to understand why other journals do not want to follow. As I have said before, many of the practices of EMBO J and eLife should be adopted by other journals.

There are other actions that we should aim for. Something that we need to consider is to waive the anonymity of the reviewing process. I have heard many reasons for keeping this as it is, some of them are worth considering but it seems to me that in most cases, the driving force behind keeping the reviews anonymous is the one behind any such activities: being anonymous allows one to be unreasonable and to, sometimes, slander the author to the editor –and this can be done in a scientific manner. Why is it that we are not capable of standing up to what we say, that we are not capable to sign our statements……..I have mentioned before an important difference between PLoS Genetics and PLoS Biology; here is another one germane to the matter we are discussing. PLoS  has this important and interesting notion of the academic editor, someone who interfaces with the non academic editor in the reviewing process. In PLoS Biology the academic editor is made known to the authors (and the public) ONLY upon successful publication of the work. Interestingly, in PLoS Genetics the academic editor is made known to the authors whether the ms is successful or not. I have never heard people complain about this and for this reason it is another indictment against anonymity. Furthermore, there are many journals that are academically led and where the authors know the editors. I have never heard that this causes big problems with authors, I have never heard of arguments and discussions. People do not refuse to be editors in journals. Why then the anonymity with the reviewers? Anonymity will (and should) always raise suspicions. It is not going to be easy to remove this from the process, there is too much inertia, but a discussion of this issue should definitely be part of the transparent process. If we are not to waive anonymity we need to change, improve the way the reviewing process works and here, there is no substitute for good editorialship!

What else can we do? Actions

The call to responsibility that Leslie Vosshall has made is very good, but we also need to move into actions, some of them structural, some of them more personal. This is going to be one long slog but, like many other people, it seems to me that we need to start acting. Here I would like to expand on Leslie’s suggestions with some aspects of the process we need to recognize and below, some actions that we can begin to take individually:


We should avoid journals that have long decision times, multiple rounds of reviews and artificial low acceptance rates (there is no reason for any of this in today’s e-world) and submit our work, preferentially, to journals with a strong academic base or with a transparent review process a la EMBO J and eLife.

It would be good if people started posting reviews in their websites. EMBO J does it routinely with accepted papers, but only with papers that are accepted. One hears a lot about unfair reviews; OK  let us see them. One note though, check with the journal that you can do this so that you do not get into legal wrangles; journals control even what we can do with the feedback we receive from them.

Refuse to review papers more than once; let us make sure that editors do their job properly and make decisions without hiding behind the reviews.

The issue of prepublication is an interesting one that is being discussed much at the moment (more out of desperation I would think than anything else) but the notion of pre-publishing a paper for comments before or while it is being peer reviewed is a good one that works in other fields and might begin to place the impact in the right place.

At a broader level:

Remember that the decision to accept or reject a paper is not in the hands of the reviewer but in the hands of the editor. So, when you write reviews do not act as an editor. NB this has been said many times in different ways and we keep on forgetting it.

The role of the reviewer is not to improve the paper but to express how reasonable the conclusions in the paper follow from the data. Then the editor has to earn her/his salary. Most reviews these days are just long lists of experiments and reasons why the work is not complete rather than an actual look at the paper. The often conflicting reviews that we all receive on an interesting piece of work are a good indictment of this. Editors use the ‘third reviewer’ to reject the paper.

The decision for publication should lie with the editor and this is very important because there is no reason in a sensible world why there should be more than one round of review. See EMBO J and eLife.

It would be good to have a ranking of editorialship in which we rate editors and journals on the way they handle manuscripts.

Something for editors: scientists should be treated scientifically. Some editors don’t do this and, in some instances, fall back on the reviwers and are unable of an articulate defense of their decision. I have a series of interesting exchanges with a senior editor from an “aspirational HIF journal” in which to every discussion I tried to raise, all I was given in exchange was that the academic they were being advised by knew a lot more than I did about the field……ah, and that they (the editors) were confident of their decision making process…..this after allowing me a 25 page rebuttal of a review!

Remember, as Vosshall said:  this “is an enterprise handled by scientists for scientists, which can be fixed by scientists”

2 thoughts on “More about the current state of scientific publishing and how to start change

  1. PLoS ONE is doing now the experiments of (1) giving the reviewers a template for their feedback, which is constrained both in space and structure and (2) giving the reviewers the opportunity to waive their anonymity.
    It will be interesting to see how the reviewer pool answers to this and how this evolves with time. Someone (I forgot who) said in Twitter that if you cannot stand by what you say in a review, then it should not be said. In my own experience (PLoS ONE implemented this change while I was reviewing a paper for it, so I could only disclose my identity for the second round – yes there were two rounds), this is something one does not appreciate until it happens: I wrote my whole review, trying to be constructive (I swear), I reached the bottom of the template, saw that I could disclose my identity, thought for a second whether I wanted, I found I wasn’t very enthusiastic about it, then I thought it was a duty to do so, so I ticked accordingly, and then I re-read my review and found that I did want to edit a bit here and there. And I think the review was better after that.

  2. Pingback: How to evaluate our output | Martinez-Arias Lab

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