I’m Excited! A Post Pre-Print-Posting-Powwow Post

I just got back from attending a meeting organized by a new group called ASAPbio whose mission is to promote the use of pre-prints in biology.

I should start by saying that I am a big believer in this mission. I have been working for two decades to convince biomedical researchers that the Internet can be more than a place to download PDFs from paywalled journal websites, and universal posting of pre-prints – or “immediate publication” as I think it should be known – is a crucial step towards the more effective use of the Internet in science communication. We should have done this 20 years ago, when the modern Internet was born, but better late than never.

There were reasons to be skeptical about this meeting. Change needs to happen on the ground not in conference halls – I have been to too many publishing meetings that involved a lot of great talks about the problems with publishing and how to fix them, but which didn’t amount to much because these calls weren’t translated into action. Second, the elite scientists, funders and publishers who formed the bulk of the invite-only ASAPbio attendees have generally been the least responsive to calls to reform biomedical publishing (I understand why this was the target group – while young, Internet-savvy scientists tend to be much more supportive in principle, they are reluctant to act because of fears about how it will affect their careers, and are looking towards the establishment to take the first steps). Finally, my new partner-in-crime Leslie Vosshall and I spent a lot of time and energy trying to rally support for pre-prints online leading up to the meeting, and it wasn’t like people were knocking down the doors to sign on to the cause.

However, I wouldn’t have kept at this for almost half my life it I wasn’t an eternal optimist, and I went into the meeting hoping, if not believing, that this time might be different. And I have to say I was pleasantly surprised. By the end of the meeting’s 24 hours it seemed like nearly everyone in attendance was sold on the idea that biomedical researchers should all post pre-prints of their work, and had already turned their attention to questions about how to do it. And there was a surprisingly little resistance to the idea that post-publication review of papers initially posted as pre-prints could, at least in principle, fulfill the functions that pre-publication review currently carries out. That’s not to say there weren’t concerns and even some objections – there were, as I will discuss below. But these were all dealt with to varying degrees, and there seemed to be a general attitude these concerns can be addressed, and did not constitute reasons not to proceed.

Honestly, I don’t think any new ideas emerged from the meeting. Everything that was discussed has been discussed and written about extensively before. But the purpose of the meeting was not to break new ground. Rather I think the organizers were trying to do three things (I’m projecting a bit here since I wasn’t one of the organizers):

  • To transfer knowledge from the small group of us who have been in the trenches of this movement to prominent members of the research community who are open to these ideas, but who hadn’t really ever given them much thought or attention
  • To make sure potential pitfalls and challenges of pre-prints were discussed. Although the meeting was dominated by members of the establishment, there were several young-PIs and postdocs, representatives of different fields and a few international participants, who raised a number of important issue and generally kept the meeting from becoming a self-congratulatory elite-fest.
  • To inspire everyone to act in tangible ways to promote pre-print use.

And I think the meeting was highly effective all three regards. For those of you who weren’t there and didn’t follow online or on video, here’s a rough summary of what happened (there are archived videos here).

The opening night was dominated by a keynote talk from Paul Ginsparg, who in 1991 started an online pre-print server for physics that is now the locus for the initial publishing of essentially all new work in physics, mathematics and some areas of computer science. Paul is a personal hero of mine – for what he did with arXiv and for just being a no bullshit advocate for sanity in science publishing – so I was bummed that he couldn’t make it person because of weather-related travel issues. But his appearance as a giant head on a giant screen by video-conference was a fitting representation for his giant place in pre-print history. His talk was very effective in squashing any of the typical gloom-and-doom about the end of quality science that often happens when pre-prints are discussed. A little bit of biology exceptionalism came up in the Q&A (“Yeah, it works for physics, but biology is different…”) but I thought Paul put most of those ideas to rest, especially the idea that all physics is done by giant groups working underground surrounded by large metal tubes.

The second day had two sessions, each structured around a series of a dozen or so five minute talks, followed by breakout sessions and then discussion. The morning focused on why people don’t use pre-prints – concerns about establishing priority, being able to publish in journals, getting jobs and funding – and how to address these concerns, while the afternoon sessions were about how to use pre-prints in evaluating papers and scientists and in finding and organizing published scientific information.

I can’t summarize everything that was discussed, but I have a lot of  thoughts on the meeting and where to go from here in no particular order:

I was surprised at how uncontroversial pre-prints were

Having watched the battles over Harold Varmus’ proposal to have biologists embrace pre-prints in 1999, and having taken infinite flak over the last 20 years for promoting a model of science communication based on immediate publication and post-publication peer review, I expected the idea that biologists should make their work initially available as pre-prints to be controversial. But it wasn’t. Essentially everyone at the meeting embraced the basic concept of pre-prints from the beginning, and we spent most of the meeting discussing details about how a pre-print system in biology can and should work, and how to build momentum for pre-print use.

I honestly don’t know how this happened. Pre-prints are close to invisible in biology (we didn’t really have a viable pre-print server until a year or so ago) and other recent efforts to promote pre-print usage in biology have been poorly received. There is lots of evidence from social media that most members of the community fall somewhere in the skeptical to hostile range when discussing pre-prints. Some of it is selection bias – people hostile to pre-prints weren’t likely to agree to come to a meeting on pre-prints that they (mostly) had to pay their own way to attend.

But I think it’s bigger than that. I think the publishing zeitgeist may have finally shifted. I’ve felt this way before, so I’m not sure I’m a good witness. But I think people are really ready for it this time. The signs were certainly there: after all Ron Vale, who organized ASAPbio, is no publishing radical – his publishing record is everything I’ve been trying to fight against for the last 20 years. But now he’s a convert, at least on pre-prints, and others are following suit. I don’t know whether it’s because all our work has finally paid off, or if it’s just time. The Internet has become so ingrained in our lives, maybe people finally realized how ridiculous it is that people all over the world could watch the ASAPbio meeting streaming live on their computers, but they have to wait months and months and months to be able to read about our latest science.

In the end I don’t really care why things seem to have changed. Even as I redouble my efforts to make sure this moment doesn’t elude us, I’m going to celebrate – this has been a long time coming.

Glamour journals remain a huge problem

One of the most shocking moments of this meeting came in a discussion right before the close about how to move forward to make pre-prints work. Marc Kirschner, a prominent cell biologist, made the suggestion that people at the meeting publish pre-prints of their papers at the time of submission so long as it is OK with the journal they plan to submit it to. I don’t think Kirschner was trying to set down some kind of abstract principle. Rather I think he was speaking to the reality that no matter how effectively we sell pre-prints, in the short run most scientists are still going to strive to put their work in the highest profile journals they can get them into; and we can make progress with pre-prints if we point out that a lot of journals people choose to publish in for other reasons allow them to post pre-prints and they should avail themselves of this opportunity.

This was the one time at the meeting where I lost my cool (a publishing meeting where I lose my cool only once is a first). It’s not that it surprises me that journals have this kind of hold on people. But I was still flabbergasted that after a meeting whose entire point was that it would be really good for science if people posted pre-prints, someone could suggest that we should give journals – not scientists – the power to decide whether pre-print posting is okay. And I couldn’t believe that people in the audience didn’t rise up in outrage at the most glaring and obvious example of how dysfunctional and toxic – one might even say dystopian – our relationship to journals is.

This is why I maintain my position – echoed by Vitek Tracz at the meeting, and endorsed by a handful of others – that science communication is never going to function optimally until we rid ourselves of the publish or reject paradigm employed by virtually all journals, and  until we and stop defining our success as scientists based on whether or not we could winkle our way into one of the uber-exclusive slots in glamorous journals. If anything is going to stop the move towards pre-prints, it’s going to be our proclivity for “glamor humping” (as blogger DrugMonkey has aptly dubbed this phenomenon). And if anything has the power to undermine the benefits of pre-prints, it’s if we allow this mentality to dominate in the post-journal world.

People have weird views of priority

One of the few new things I learned at this meeting is how obsessed a large number of people are with technical definitions of priority. We spent 30 minutes talking about whether pre-prints should count in establishing priority for discoveries. First of all, I can’t believe there’s any question about this – of course they should! But more importantly who thinks that questions of priority actually get decided by carefully scrutinizing who published what, when and on what date? It’s a lovely scholarly ideal to imagine that there’s some kind of court of science justice where hearings are held on every new idea or discovery, and a panel of judges looks at everything that’s been published or said about the idea is presented, and they then rule on who really was the first to publish, or present, the idea/discovery in a sufficiently complete form to get credit for it.

But I got news for all the people counting submission dates on the head of a pin – outside of patent cases, where such courts really do exist, at least in theory, that ain’t the way it works. True priority is constantly losing out in the real world, where who you are, where you work, where you publish and how you sell yourself are often far more important than submission or publication dates in determining who gets credit (and its trappings) for scientific advances.

Cell Press has a horrible, but kind of sane, policy on pre-prints

One of the things that I think a lot of people coming to the meeting didn’t realize is that many journals are perfectly fine with people posting pre-prints of articles that are being considered by the journal. Some, like eLife, PLOSPeerJ and Genetics actively encourage it. Others, like EMBOPNASScience and all Nature journals unambiguously allow pre-print posting. On the flip side, journals from the American Chemical Society and some other publishers will not accept papers if they were posted as pre-prints. And then there’s Cell.

Cell‘s policy is, on the surface, hard to parse:

If you have questions about whether posting a manuscript or data that you plan to submit to this journal on an openly available preprint server or poster repository would affect consideration, we encourage you to contact an editor so that we may provide more specific guidance. In many cases, posting will be possible.

Fortunately, Emilie Marcus, CEO of Cell Press and Editor-in-Chief of Cell, was at the meeting to explain it to us. Her response was, and I’m paraphrasing but I think I’m capturing it correctly, is that they are happy to publish papers initially posted as pre-prints so long as the information in the paper had not already been noticed by people in the field. In other words, it’s ok to post pre-prints so long as nobody noticed the pre-print. That is, they are rather unambiguously not endorsing the point of pre-prints, which is to get your work out to the community more quickly and effectively.

This is a pretty cynical policy. Cell clearly wants to get credit for being down with pre-prints without actually sanctioning them. But I actually found Marcus’s explanation of the policy to make sense, in a way. She views Cell as a publisher, and, as such, its role is to make information public. If that information has already been successfully conveyed by other means, then the role of publisher is no longer required.

This is obviously a quaint view – Cell is technically a publisher, but it’s more important role is as a selector of research that it deems to be interesting and important. So I think it’s more appropriate to look at this as a business decision. In refusing to help make pre-prints a reality, Elsevier and Cell Press are acting as if they believe pre-prints are a threat to their bottom line. And they’re right. Because if pre-prints become universal, who in their right mind is going to subscribe to Cell?

Maybe the other journals that endorse pre-prints are banking on the symbiosis between pre-prints and journals that exists in physics being extended to biomedicine. In questions after his talk Ginsparg said that ~80% of papers published in the arXiv are ultimately published in a peer-reviewed journal. And these journals are almost exclusively subscription based. So why don’t libraries cancel these subscriptions? The optimistic answer (for those who like journals) is that libraries want to support the services journals provide and are willing to pay for them even if they’re not providing access to the literature. This may be true. But the money in physics publishing is a drop in the bucket compared to biomedicine, and I just can’t see libraries continuing to spend millions of dollars per year on subscriptions to journals that provide paywalled access to content that is freely available elsewhere. I could be wrong, of course, but it seems like Elsevier, who for all their flaws clearly know how to make money, in this case agrees with me.

I don’t know what effect the Cell policy will have in the short run. I’d like to think people who are supportive of pre-prints will think twice before sending a paper to Cell in the future because of this policy (of course I’d like it if they never considered Cell in the first place, but who am I kidding). But I suspect this is going to be a drag on the growth of pre-prints — how big a drag, I don’t know, but it’s something we’re probably going to have to work around.

There are a lot of challenges in building a fair and effective pre-print system

The position of young scientists on pre-prints is interesting. On the one hand, they have never scienced without the Internet, and are accustomed to being able to get access to information easily and quickly. On the other hand, they are afraid that the kinds of changes we are pushing will make their lives more difficult, and will make many of the pathologies in the current system worse, especially those biased against them, worse. Even those who have no reservations about the pre-prints and/or post-publication review, don’t feel like they’re in a position to lead the charge.

This is one of the biggest challenges we have moving forward. I have no doubt that science communication systems build around immediate publication and post-publication review can be better for both science and scientists. But that doesn’t mean they automatically will be better. Indeed, I share many of other’s concerns about turning science into an even bigger popularity contest than it already is; about making it easier for powerful scientists to reinforce their positions and thwart their less powerful competitors; about increasing the potency of biases the myriad biases that poison training, hiring, promotion and funding; about making the process of receiving feedback on your work even less pleasant and uncollegial than it already is; and about increasing the incentives for scientists to prioritize glamour over doing rigorous, high-quality and durable work.

I will write more elsewhere about these issues and how I think we should try to address them. But it is of paramount importance that everybody who is trying to promote the move to pre-prints and beyond, and who is building systems to do this, be mindful of all these risks and do everything in their power to make sure the new systems work for everyone in science. We have to remember that for every bigshot who opposes pre-prints because they want to preserve their ability to publish in Cell, there are hundreds of scientists who just want to preserve their ability to do science. If this latter group doesn’t believe that pre-print posting is good for them, we will not only fail to convince them to join us on this path, but we run the serious risk of making science worse than it already is. And that would be a disaster.

Will attendees of the meeting practice what they preached

Much of the focus of the meeting organizers was on getting people who attended the meeting to sign on to a series of documents expressing various types of commitment to promoting pre-prints in biomedicine (you can see these on the ASAPbio site). These documents are fairly strong, and I will sign them. But I’m sick of pledges. I’ve been down this path too many times before. People come to meetings, they sign a document saying they do all sorts of great stuff, and then they forget about it.

The only thing that matters to me is making sure that the people who attended the meeting and who seemed really energized about making pre-prints work start to put this enthusiasm into practice immediately. I look forward to quick, concrete action from funders. But the immediate goal of the scientists at the meeting or who support its goals must be to start posting pre-prints. This is especially true of prominent, senior scientists. There were four Nobelists at the meeting, many members of national academies, and other A-list scientists. It’s a small number of people in the grand scheme of things, but if these scientists demonstrate that they are really committed to making pre-prints by starting to post pre-prints in the next week (I suspect that most people at this level have a paper under review at all time). I am confident that their commitment is genuine – indeed some have already posted pre-prints from their labs since the meeting ended yesterday.

Obviously we don’t want pre-prints to be the domain of the scientific 1%. But we have to start somewhere, and if people who have nothing to lose won’t lead the way, then it will never happen. But it seems like they actually are leading the way. There’s tons more hard work to do, but let’s not miss this opportunity. The rainbow unicorn is watching.

ArcLive Rainbow Unicorn

 

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20 Comments

  1. Posted February 18, 2016 at 10:30 pm | Permalink

    Mike – I was really excited about the ASAPbio meeting, but I was quite disappointed to hear several calling for the establishment of just one “preprint server.” Many reasons why that is a bad idea:


    Innovation tends to die off with monopolies and oligarchies.

    I fear discrimination could arise if one organization is responsible for what is/isn't worthy of a preprint.

    No one wants to be forced to choose a particular venue for scholarly communication, Academic Freedom.

    Already, the different preprint servers are fulfilling the specific needs of differing subject areas.

    It’s the dinosaur 800-pound gorilla publishers who got us into this mess to begin with. Why create another via regulation?

    Maybe I’m paranoid and there isn’t a conspiracy going on, but it seems those same “elites” you rail against are only in it if they are also in control. Or, the elites who are impartial are being lobbied to support just one central place by others with vested interests. Of course, I have my own COI, but at least I’m not calling for everyone to use just my venue, rather the opposite.

    • Posted February 20, 2016 at 10:01 am | Permalink

      I think this is one of those cases where centralization makes sense. Let’s use an analogy. Back in the 1980s when DNA sequencing began to take off, journals were finding themselves unable to publish the growing volume of sequence data. So they pushed for the creation of GenBank, which has become an indispensable resource for biology. But they didn’t have to go this way – each journal could have set up their own sequence server. Maybe the diversity of sites would have led to some creative development of sequence analysis tools by journals. But that almost certainly would have come at a steep price by having lost the convenience of having a single, open repository of sequence data. Indeed GenBank is a perfect model for what I think should happen with pre-prints – government managed pre-print repositories that are stable, that share data amongst them daily (as sequence databases do), and which have a sensible set of rules that keep them open and accessible, but filter out various sorts of problematic submissions.

      • Posted February 21, 2016 at 7:53 am | Permalink

        I completely agree with the view that a central repository or limiting to a few repositories for pre-prints in biology is more appropriate. I fully endorse the analogy with sequence databases put forward by Michael Eisen.

  2. Arjun Raj
    Posted February 19, 2016 at 3:31 am | Permalink

    The Cell Press policy is a serious drag for me. The Cell ecosystem contains a large number of journals that publish high quality work and have good visibility, and jeopardizing the possibility of publishing in any of those journals is a serious factor. Sigh. Then again, I think when they talk about “noticed people in the field”, they’re mostly talking about papers that, you know, people really care about, so maybe we’re fine… :)

  3. Josh
    Posted February 19, 2016 at 6:00 am | Permalink

    Back in December of 2013, I inquired about whether Biophysical Journal, which is part of the Cell Press family, would accept manuscripts previously posted on BioRxiv. At the time their response was that they would not. They did however say papers posted on the ArXiv were ok but that sites that assigned DOIs and used CC licenses were not, thus excluding BioRxiv. Not sure if the policy has changed since then though.

    • Posted February 20, 2016 at 3:31 am | Permalink

      Hi Josh

      The policy has changed. Biophysical Journal allows deposition in bioRxiv and you can in fact now directly transfer papers from bioRxiv to Biophys J, just like eLife, PNAS, and various other journals.

      • Josh
        Posted February 20, 2016 at 8:35 pm | Permalink

        That’s great to hear. Too bad it wasn’t the case when I first inquired, but I’m glad they sorted through their internal policy and game to a sensible decision.

  4. Drew Endy
    Posted February 19, 2016 at 7:09 am | Permalink

    Mike, why no mention of bioRxiv directly? It exists and works well. Hopefully their experiences via AsapBio don’t lead them to screw it up. From afar the entire meeting smells a bit of various establishment factions positioning to coopt various aspects of preprints in biology. Something along these lines seems inevitable and is some type of symptom of success. From another perspective, so much focus only on publishing in the open, as opposed to conducting the entire scientific process in the open (eg, see OpenWetWare as it existed 10 years ago) seems to miss a much bigger opportunity. The fact that the biology establishment seems to be largely unaware that the Internet exists when it comes to practicing biology as a human activity is a tragedy that won’t be fixed, it will be replaced. With respect and best wishes, Drew

  5. J.J. Emerson
    Posted February 19, 2016 at 9:12 am | Permalink

    I think the zeitgeist has shifted really quickly in my little corner of biology (evolutionary genetics and genomics). Posting preprints is considered by most of my peers to be uncontroversial, and many of my peers are ardent supporters of it (duh, you’re part of that group). We posted our most recent manuscript to bioRxiv and have nothing but good things to say about it. The biggest side effect has been interactions with colleagues:

    Colleague: Hey, I heard you did this thing. Can you tell me how you did it?
    Me: I’d be happy to. You might want to read our preprint first and see if you have any questions remaining.

    They often only ask for clarifications after reading the preprint. They’re happier because they get more and we’re happier because we have to work less.

    Under the old system, we’d be saying something like “Here’s the draft of our manuscript. ” to one person and “Here’s the draft of our manuscript. ” to another, etc. Now, we would post revisions to bioRxiv or simply correct some details in the bioRxiv comments section. Also, people are interacting with us who we’d’ve never have reached without bioRxiv.

    Anyway, preprints I think are here to stay (though this won’t happen if we don’t continue to push). It is the layering of PPPR onto the pre-print system that I think lags behind in community support.

    I say all of this with the caveat that my field lines up well with the highest rates of adoption of subfields in bioRxiv (evolutionary biology, genomics, genetics, bioinformatics). Thus, I’m almost certainly atypical.

  6. Posted February 19, 2016 at 4:43 pm | Permalink

    The most reasonable concern I’m hearing about post-publication review is that at least some people (reviewers) read every paper. The popularity effect will likely cause some preprints to get well covered and many, many others to get no attention at all.

  7. Nathan Pearson
    Posted February 19, 2016 at 7:00 pm | Permalink

    Actually, sounds like ‘We sanction* preprints.’ might neatly convey Cell press’s janus policy after all, no?

    *in both autoantonym senses…

  8. A. Martinez Arias
    Posted February 20, 2016 at 9:11 am | Permalink

    I agree that the meeting (followed most of it on line) was positive and that much was said in the open (and recorded) to believe that the attitude towards ‘preprints’ in Biology will change. The surprise was that much of worry about this form of communication comes from either ignorance (I was surprised how some of the people gathered did not know much about the topic-with some admissions to it) or interest (Cell Press) and that there is a need by us, the community, to inform and spread the culture because if we start it right (and many of us believe that it has) it will develop in a manner that will benefit everybody.

    On the attitude of Cell Press, there is an interesting slant to a comment that you refer to, concerning the attitude of Cell: “they are happy to publish papers initially posted as pre-prints so long as the information in the paper had not already been noticed by people in the field” so….what happens at meetings? don’t people notice talks and posters?

    Just to repeat what you and many people reading this know: the main beneficiaries of a culture of preprints (or e-prints as arXiv calls them) in the biosciences, are the younger generation who are losing much by letting themselves be drowned by glamour seeking malaise that now takes too long.

  9. Posted February 21, 2016 at 3:55 am | Permalink

    In ASAPbio, the question of a better name for pre-prints has been rightfully raised many times. It is an important semantic question if we want to achieve the cultural shift that they allow. I came up with “post-research articles”. We should call them from the scientist’s perspective and not the journals’. Making “post-research articles” public is simply the next step after research, which might involve journals or not in the path to wide acceptance by the scientific community.

  10. Posted February 21, 2016 at 7:29 am | Permalink

    I’m glad that you’re going to be thinking and writing more about the potential unintended consequences here, Mike. I mostly want to talk about the ways a system that included only preprints and post-publication review could be a jump from the frying pan into the fire for elitism in science.

    First, though, I didn’t see a mention in the tweets of a risk associated with including self-published work in grant review. And that’s people rushing their work online to meet grant deadlines, when it’s nowhere near as good and as ready as they think it is. Was this discussed?

    Years ago when I was one of the editors of an internet-based research publication system that was only releasing quarterly at the time (Cochrane reviews and meta-analyses), I dreaded the lead-up to deadline: it wasn’t just that there was so much material and so little time – it was that those ones would need far more work. That’s not a coincidence: deadlines have pernicious effects.

    My bigger issue though is with making the playing field even less level than it already is. While obviously I think what this means for young scientists is a very big deal, I think there’s a big danger in approaching the issue of elitism from an age perspective. There are many highly privileged young scientists who themselves are an elite, especially if they’re white and male.

    Journals are, in many ways, a confounder here. Prestige of institutional base (both in studying and academic position) is arguably the most critical issue. That happens in multiple ways – from journals with very obvious close relationships to specific institutions, through to editors favoring people from their alma mater, and the heuristic that so many others apply to those names. In addition, there’s the English-speaking advantage. And the intersection of country, language, and institutional prestige advantage of the U.S. (I’ve linked to some studies about these issues in this post.)

    When you’ve got one or more strikes against you, you’re pushing it uphill at a journal for all sorts of reasons. But at least you have a chance, with the chance of attention that comes with it. I wrote more about this in a comment at Lenny Teytelman’s blog. After you’re in, good editing can make a massive difference to the chances of your work being easily read, especially if your first language is not the language of the journal you’re submitting to. The quality of expression matters more in some things than others, but it affects accessibility, popularity, and reputation.

    I think the social and psychological importance of journals is underestimated in these discussions, and that hampers the realism of discussions about how scientists’ behavior could be changed . I wrote a post at PLOS Blogs about that this week.

    There are scientists with an inordinate desire for money, power, and acclaim – and those whose extremely high opinion of their own work requires no confirmation from others. But that’s not most. Wanting your peers’ attention and esteem is integral to science: we need our work to be validated in several ways.

    With a massive increase in content, and without journals to provide an alternate route to attention, then prestige of institution and English-language privilege could be almost completely determinative. And with the odds stacked on gender, race, and more within those institutions, it would be dire to replace the hegemony of prestige publishing with the hegemony of institutional prestige.

  11. Posted February 21, 2016 at 7:44 am | Permalink

    The success of preprints is ultimately linked, in my opinion, with the need to change how “success” in Biology is quantified. The arXiv in Physics was successful because it implied a way to communicate fast new results, which were then debated by the community. I am sure that many decisions about faculty jobs, grants, etc, are also based on some of these reports (without the need of a more “formal” publication). This could be also linked to the fact that in many topics in Physics one typically asks about your last ideas, and not about where you are going to publish them (I used to be a Quantum Physicist). In any case, many things would change fast when institutions start telling people that (bio)arXiv manuscripts will be considered in their decision-making.

  12. Kevin Davies
    Posted February 21, 2016 at 5:58 pm | Permalink

    Thanks for the excellent summary of ASAPbio Mike. You state: “On the flip side, journals from the American Chemical Society and some other publishers will not accept papers if they were posted as pre-prints…”

    Allow me to clarify the ACS stance with regard to preprints. Policies regarding preprints are set by the individual chief editors of each journal, not by ACS. Of the roughly 50 journals published by ACS, a dozen explicitly consider manuscripts deposited as preprints. These include our open access journal ACS Central Science (edited by Carolyn Bertozzi), ACS Nano, ACS Chemical Biology, ACS Synthetic Biology, Inorganic Chemistry and Journal of Physical Chemistry. Several other journals may also consider papers submitted as preprints on a case-by-case basis. The remainder (about 20 journals) do not currently consider manuscripts that have been posted as preprints.

    • Posted February 21, 2016 at 8:31 pm | Permalink

      Thanks – I’m going to put together a users guide to pre-prints and will include that.

    • Posted February 22, 2016 at 12:47 pm | Permalink

      Those numbers are strange:

      “roughly 50” != “a dozen” + “several other” + “about 20”

  13. Posted February 24, 2016 at 12:05 am | Permalink

    My personal take is that the present system is broken in very significant ways. If a different system of any sort had ever been really tried, I think the system being broken would be obvious to almost everyone, but since many traditionalists have only ever known the one thing they defend it without much critical thought. I suppose the existing system works more effectively than nothing at all…

    However, I don’t see a huge urgency to implement the next system because I think it’s so very important, that it be a clear improvement for almost all, and fair. The reason that it must be a clear improvement is because the audience of research scientists is critical by nature, it could easily fail to reach a modicum of acceptance. The reason for the importance in general, and maybe this has been said elsewhere and I’ve not seen it, is that the published record of research is one of humanity’s most precious resources that establishes what we understand and when we understood it, in the large context of human history. That’s no small point and where the current system is a huge failure. To talk of this move to preprints in terms of promotion and grants seems so short sighted and petty to me. It’s like a failure to acknowledge the major shortcomings of the current system. Don’t get me wrong, those things aren’t insignificant on an individual scale, and I get that part of ASAPbio was getting granting agencies on board with this. It just seems like us not having our eye on the ball. We should be talking about what we really need, and getting some relevant creative types (design and user experience) involved. We should think as big as we can, and as long term as we can, refine the ideas, be realistic with how we roll it out and have a plan to evolve in a manner that will last. From there we can determine relevant metrics for funding, promotion, etc.

    There should easily be room to improve the value of review (to funders etc), and they could be more efficiently performed too. For one thing, the contemporary format of review could change, and should change. The value of overarching commentary, the likes of which typically starts a review and serves to prove to the editor that the reviewer read the paper, would be diminished and could be culled. Obviously some journals are implementing these into publications already, but I would say that they are requisite in the long term. It’s an important part of the record.

    Reviews themselves should be subject to some sort of scoring and feedback mechanism.

    And the role of editor must go. It represents a bottleneck in the distribution of understanding, and runs counter to independent critical thinking which is so valuable to the pursuit of research. I think the solution we come to should be inclusive of submissions overall, although I have little picture of the details in my mind at this point. I just can’t imagine there being too many entries/publications on my specific area of interest for me to not be able to wade through them and determine merit for myself. If you’re reading this and thinking there will be too many, I mean extremely specific to your area of of interest. Sure, there could be some bullshit in there, but there is now. I just do not trust a significant proportion of editors to make a decision on acceptability for my interests. And that’s not even factoring how little time they have to do it.

    I could go on…

  14. Dylan Rahe
    Posted March 5, 2016 at 8:26 am | Permalink

    Did anything come of yours and Lerslie’s call for an “International Peer Review Standards Organization”?

    Making a solid peer-review system for pre-prints that accurately and clearly assesses quality of papers is definitely needed if we’re going to replace the journals. Right now, when you say “she just got a Cell paper!”, or “he just got published in G&D!”, your colleague has an immediate (though potentially inaccurate) understanding of the quality and impact of the paper they just published.

    That’s the bar we should be reaching for, and we need to get somewhere close before it’s going to adopted widely.

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