The Mission Bay Manifesto on Science Publishing

Earlier this week I gave a seminar at UCSF. In addition to my usual scientific spiel, I decided to end my talk with a proposal to UCSF faculty for action that could take make scholarly communication better. This is something I used to do a lot, but have mostly stopped doing since my entreaties rarely produce tangible actions. But I thought this time might be different. I was optimistic that recent attention given by prominent UCSF professor Ron Vale to the pervasive negative effects of our current publishing system might have made my UCSF faculty colleagues open to actually doing something to fix these problems.

So I decided to issue a kind of challenge to them to not just take steps on their own, but to agree collectively to take them together. My motivation for this particular tactic is that when I ask individual scientists to do things differently, they almost always respond that they would love to do things differently, but can’t because the current system requires that {they | their trainees | their collaborators} have to publish in {insert high profile journal here} in order to get {jobs | grants | tenure}. However, in theory at least, this reluctance to “unilaterally disarm” would go away if a large number of faculty, especially at a high-profile place like UCSF agreed to take a series of steps together. I focused on faculty – tenured faculty in particular – because I agree that all too often publishing reform efforts focus on young scientists, who, while they tend to be more open to new things, also are in the riskiest positions with respect to jobs, etc…

My goal was to address in one fell swoop three different, but related issues:

  1. Access. Too many people who need or want access to the scientific and medical literature don’t have it, and this is ridiculous. Scientists have the power to change this immediately by posting everything they write online for free, and by working to ensure that nothing they produce ever ends up behind paywalls.
  2. Impact Factors. The use of journal title and impact factors as surrogate for the quality of science and scientists. Virtually everyone admits that journal title is a poor indicator of scientific rigor, quality or importance, yet it is widely used to judge people in science.
  3. Peer-review. Our system of pre-publication peer-review is slow, intrusive, ineffective and extremely expensive.

And here is what I proposed (it’s named after the Mission Bay campus where I gave my talk):

The Mission Bay Manifesto

As a scientists privileged to work at UCSF we solemnly pledge to fix for future generations the current system of science communication and assessment which does not serve the interests of science or the public by committing to the following actions:

(1) We will make everything we write immediate freely available as soon as it is finished using “preprint” servers like,, or the equivalent. 

(2) No paper we write, or data or tools we produce, will ever, for even one second, be placed behind a paywall where they are inaccessible to even one scientists, teacher, student, health care provider, patient or interested member of the public. 

(3) We will never refer to journal titles when discussing my work in talks, on my CV, in job or grant application, or any other context. We will provide only a title, a list of authors and publicly available link for all of my papers on CVs, job and grant applications.

(4) We will evaluate the work of other scientists based exclusively on the quality of their work, not on where they have published it. We will never refer to journal titles or use journal titles as a proxy for quality when evaluating the work of other scientists in any context.

(5) We will abandon the slow, cumbersome and distorting practice of pre-publication peer review and exclusively engage in open post-publication peer review as an author and reviewer (e.g. as practiced by journals like F1000 Research, The Winnower and others, or review sites like PubPeer). 

(6) We will join with my colleagues and collectively make our stance on these issues public, and will follow this pledge without fail so that our students, postdocs and other trainees who are still building their careers do not suffer while we work to fix a broken system we have created and allowed to fester.

I am positive that IF the faculty at UCSF agreed to all these steps, science publishing would change overnight – for the better. But, alas, while I’d love to say the response was enthusiastic, it was anything but. Some polite nodding, but more the kind you give to a crazy person talking to you on the bus than one of genuine agreement. People raised specific objections (#5 was the one they are least in favor of), but seemed willing to take even a marginal risk, or to inconvenience themselves, to fix the system. And if we can’t get leadership from tenured faculty at UCSF, is it any wonder that other people in less secure positions are unwilling to do anything. I went back to Berkeley disappointed and disheartened. And then yesterday I heard a great seminar from a scientist from a major university on the East coast whose work I really love talk over and over about Nature papers in their seminar.

But my malaise was short lived. Maybe I’m crazy, but, even if we haven’t figure it out, I know there’s a way to break through the apathy. So, I’ll do the only thing I can do – commit myself to following my own manifesto. And ask as many of you who can see your way to joining me to do so publicly. If UCSF faculty don’t want to lead, we can instead.


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  1. Posted October 1, 2015 at 6:16 pm | Permalink

    Hello, if you were to stop publishing in “normal journals” then your work would no longer be archived in pubmed or web of science. Unfortunately it would be then come less visible to scientists who don’t already follow you.

    • Posted October 1, 2015 at 7:26 pm | Permalink

      not true – F1000 Research, which is all post-publication review – is in PubMed

  2. binay panda
    Posted October 1, 2015 at 7:12 pm | Permalink

    michael, even if my voice in this particular topic doesn’t count or matter, i fully endorse #1,2, #4, #6 in the manifesto. for #3 and #5, i dont think they are practical at this juncture (see below). i believe if everyone favors #1, there will be big shift and a lot of the problems will be taken care of. however critical, i don’t think #3 will gain any traction among the scientists, not because it does not make sense but it requires a big change in the mindset, a good wish but not happening anytime soon. my idea is to push for the rest of the points so that #3 becomes inconsequential. regarding #5, this is not an practical model as things stand currently. we have only 3 journals, f1000research, the winnower and scienceopen (unless i missed some) that practice open and non-anonymous post-publication peer review and unless many other journals change/shift their policies to adopt a similar system, endorsing #5 is going to make things impractical for many scientists. if i endorse #5, i have to stop sending our manuscripts to plos journals immediately, which i shall be reluctant to do. what I shall prefer is for the plos journals to shift towards a transparent, non-anonymous post-publication peer-review system. i am also curious if you pushed #5 internally within plos?

    i am going to push for #1-2 and #4, #6 in india, at least i can be vocal about it (which i am) and talk about it whenever i get a chance. we live in hope and can only hope that things get better.

  3. travc
    Posted October 1, 2015 at 10:51 pm | Permalink

    I don’t get the objection to #5.

    First off, a paper sent to a post-pub site (at least F1000reserach) does count as real publication if it receives sufficient positive reviews (at which point it gets indexed on PMC). I imagine all the other sites have or will soon have a similar arrangement.

    So what if there are only a few places which do post-pub review. Hell, that is a good thing IMO, we only need one of them. The ecosystem will probably (eventually) only support a few, and they will differ primarily on traits like allowing anonymous reviews (or not) and not on field. We have search engines, indices, blogs, ect…. In fact, I predict that traditional journals will become or be replaced by sites which provide short reviews and summaries of notable selected papers relevant to their readership (like is already happening in many blogs).

    I appreciate that impact factors and journal names are used to judge scientists for jobs and such, but…
    If you exclusively publishes someplace like F1000research because it is the right thing to do, you can make that a ‘selling point’. Do it on principle. There are quite successful researchers who only publish in open source journals as a point of principle… This is just the next logical step.
    Post-pub review leads to better science. Comments and revisions are a good enough reason alone to exclusively go that way. Plus it is a lot less annoying for you (the author), so double win.

    This may be a hard jump to make for some people, especially young researchers… but that means it is even more important that the people who can take the step do. Which is Michael Eisen’s point!

  4. Posted October 1, 2015 at 11:52 pm | Permalink

    I’d be happy to commit to the rules of the Manifesto for single-author papers. Being a theoreticien, I actuall do write some, so this is not a completely empty promise. But if I tried to force these rules on my collaborators, then I wouldn’t have collaborators for much longer. In particular early-career scientists cannot really afford to follow these rules before they a majority of senior researchers has fully accepted them.

  5. Posted October 2, 2015 at 9:11 am | Permalink

    I very much support your reform efforts in scientific publication, but realistically speaking, I have zero status in academic institutions.

    So, you absolutely have my endorsement, but it won’t mean much to your colleagues.

  6. Tom Wenseleers
    Posted October 2, 2015 at 10:51 am | Permalink

    The easy solution I think is that all publishers should formally allow publication of PDFs of articles on the authors’ own websites, and then it will all nicely get indexed by Google Scholar and everyone will have access to anything that gets published. I think that’s the least of compensation they could do for the fact that all those authors write those articles for free, never receive one penny for what they write, and on top of that do the refereeing for free as well. I don’t think that Open Access in its current form, e.g. as in the PloS system, is the solution as it’s hugely expensive – 2000 USD per paper is just too much just to produce a PDF, and really discriminatory towards all those labs in developing countries where they don’t have these kinds of budgets (hell, if I publish 15 papers a year, I also don’t want to cash out 30 000 USD a year just to get published in an open access journal, even if I had the money). And doesn’t everyone have access to all the world literature already through Libgen and SciHub and the like?

  7. Posted October 2, 2015 at 1:02 pm | Permalink

    At my current home of Stony Brook’s Physics & Astronomy Department we recently had a colloquium on modern publishing. As was your experience, there was a great deal of pushback against the notion of #5. In particular, it was noted that there’s no incentive for the senior people in your field to seek out and review your paper. I suppose this could be generalized to the claim that open review has no real vetting of referees and it’s unlikely the people you want to referee it will. With the current system, there’s at least an editor at a journal you’ve likely worked with and is esteemed in your field making a request of you and you have some sense of professional obligation (to varying extents). But will the same person seek out and review papers?

    I’m curious what your response to this critique would be.

  8. binay panda
    Posted October 2, 2015 at 8:31 pm | Permalink

    we must distinguish between open access publication and open/transparent/ethical science towards just and timely information dissemination. going by the swing, many of the clever commercial publishers started exclusive open access journals. now, that to me, is opportunism 101 and nothing to do with open science or open information dissemination. i agree, that paying $2000, or even $1000, for a single open access manuscript to get published is too much. i don’t understand why is it that in the era of open internet, publishing should cost that much? tim gowers recently showed that one can publish with $10 per article (‪, yes $10 per article by utilizing the existing system. this, to me, is the way forward, use the existing system/technology and make things better.

    why can’t biologists think about a bioRxiv overlay journal? michael mentioned in twitter feeds that this is exactly what they proposed nearly 15yrs back. can we reinvigorate that?

  9. Posted October 3, 2015 at 12:59 am | Permalink

    A purely practical comment about point 5 in general and F1000Research price in particular. My main point is that PeerJ offers better service at lower cost (and I am not affiliated with PeerJ in any way).

    Let’s take my latest paper which just got accepted in PeerJ and contrast it to how it would have worked at F1000Research

    1. I submitted my draft to PeerJ PrePrints who made it available online within a day for free. It showed up on Google Scholar about a week later.

    F1000Research would take about a week and cost $1000 as it was >2500 words. On the other hand at this point it is typeset.

    2. I solicit reviews on social media and by emailing select experts. There is a commenting section on PeerJ PrePrints where these reviews can be added. I got some suggestions by email but no one added comments for this particular paper.

    From what I can tell the idea is much the same on F1000Research

    3. I revise my manuscript and put a new version on PeerJ PrePrints with another plea for comments/reviews. Then I submit to PeerJ. PeerJ finds 2 reviewers for me, typesets the manuscript (after minor corrections in this case), publishes the reviews, provides a comment section for further review, and gets it indexes, for $298 (in this case). Again, there is a comment sections where people can continue to review the manuscript and also the reviewers comments, which I choose to make public.

    So, from where I stand I pay F1000Research $1000 extra for guaranteed and immediate typesetting of a manuscript which may not get reviewed, while I pay PeerJ $300 for guaranteed reviews of a manuscript which may not get typeset (if it is rejected).

    I couldn’t care less about the typesetting. When I deposit my preprint I consider my work published – and I can do that for free. The remaining steps are taken mainly to be able to add it on my CV under “Peer Reviewed Publication” with additional indexing as a nice bonus.

    As Gowers has shown, if you remove the typesetting this can done for $10/paper.

  10. Souheil Houissa
    Posted October 3, 2015 at 3:30 am | Permalink

    Hello, I appreciate the way you proceed for having the maximum of consent about such an important decision. Although this is special to the faculty at UCSF, the methodology and the eventual output of your action may become very much useful for other similar circumstances in other institutions elsewhere in the world.
    May I suggest, if you don’t mind, that you give more than ONE option for the points that may be controversial so that your colleagues could opt for a more/less open/restrictive alternative. For example, #5 seems to be a “hard” position as you have expected. Therefore, it would be better if you suggest #5,option A, and #5,option B, so that you can see the feedback. It is essential that a policy should be balanced and realistic enough to be accepted by the majority of staff.
    I think peer review is possible for both pre and post publications, but it is more important to ensure access especially to pre publications by making articles freely available to the public by depositing a pre-publication copy in an open access repository. In other words, you should urge faculty to deposit in OA repositories and then negotiate, better be collectively with publishers to accept that. Thanks.

  11. Mark C. Wilson
    Posted October 3, 2015 at 10:40 am | Permalink

    Hi – a good initiative, keep trying.

    I think you mean “unwilling”, not “willing”.

  12. Vladimir Morozov
    Posted October 3, 2015 at 12:48 pm | Permalink

    Michael, I take my hat off to your endless and brave efforts toward open publishing. Few thoughts. I don’t think that appealing to academic peers is the way to go. It is difficult to convince a social group to destroy/replace its norms. I would make a case that the current publishing system badly serves the translation of academic research into goods for society. It slows down transfer of scientific knowledge; the existing peer review system can’t sort out true results from false/unreliable, and so on. Such argumentations would attract more attention from general public and industry

  13. Posted October 4, 2015 at 5:06 am | Permalink

    Your experience parallels mine. I recently learned that it only gets worse the higher up you move in the decision-making chain:

  14. Posted October 5, 2015 at 9:23 am | Permalink

    Update: I turned my comment into a blogpost and Eva Amsen, who works for F1000Research points out that their editors do ensure (as much a possible) that two reviewers respond in a timely manner. So, from my perspective, the main difference between F1000Research and PeerJ is now the price.

  15. Nick Matzke
    Posted October 8, 2015 at 8:33 pm | Permalink

    For this to be convincing, you need a point #7, something like:

    7. We will acknowledge that a great many authors with quality work — such as students, those without grants, those working on “side projects” and collaborative ideas not funded by specific grants, those at institutions who for whatever reason think it should be a personal expense covered by the individual to publish (I heard this — yesterday — from a distinguished researcher at a museum), those whose granting agencies refuse to allow grants to be used for publication costs, and those in developing countries — do not have access to the necessary funds to publish in many open-access forums. We do not think these funds should come out of their already-limited paychecks. We will refuse to publish in journals that do not have a well-advertised, easily accessed option for free publication for those with financial need, one that is monitored with regularly-released statistics.

    I make this point because open reading access for the public is great, but open submission access for those producing the research appears to be disappearing.

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