# What is wrong with Scientific Publishing and can we put it right before it is too late?

I sat down today to write code and and found that I couldn't – I had to write about science publishing, so here goes. I intend this will be the first of several posts. I often blog in forceful style (rant?) but here will try to be as objective as possible. I'd like to start a discussion and engage responsible STM publishers. I'd like to see if we can define what the basis of publishing is. Why? And how?

But I am going to start with a strong assertion. STM publishing is seriously broken and getting worse. It is being driven by forces largely outwith the directing influence of the scientific community (although not necessarily outwith their ultimate control). This is manifested by activities which have nothing (in my view) to do with science, and I will explain that.

A brief topical aside. Non-UK readers may not realize the enormity of what has happened in the UK and what the lesson is for scientific publishers. The News Of the World – a popular UK newspaper - broke the law repeatedly by phone-hacking of victims of crime. Public outrage exploded and with 24 hours a 150-year old newspaper had ceased to be. That is the power of the masses – it is too rarely exercised – but when it happens it can be unstoppable. The "public" had existed in a cosy, if unpleasant, symbiosis with the publisher, eagerly demanding new salacious material and paying for it. But when the newspaper overstepped … a bang, not a whimper! There were no discussions, no slow decline. A week ago there were the usual rumblings, but no one predicted this – at least in public. The power of the crowd in a media-literate society is frighteningly rapid. The same fate can await complacency in STM.

That is the potential power that the scientific and academic community has over scholarly publishers. (In this post I am going to restrict discussion to serials publishers in STM). I'll state the simple premise:

• Unless the process of scientific publication is rapidly and effectively revised there will be a catastrophic crash. It will be unpredictable in both its timing, speed and nature. It will destroy some of the current participants. It will change parts of the scientific process and will change academia.

I have no special knowledge so that's a Cassandra-like statement (although I have no wish to play that role). I am surprised how few of my general colleagues (e.g. not the OKF) share my concerns about the state of STM publishing. They do not realise the dystopia we are already in and its apparently inexorable progress.

Before you switch off from this analysis, I intend to offer constructive dialogue to all parties. I know publishers read this blog (I was rung up yesterday by the Marketing Director of the RSC in response to yesterday's blog.) I wish, honestly and constructively to analyse, the benefits that STM publishers can provide. Some of them do provide good services to science, but I find it difficult to see value from many others. They have the chance, if they wish to answer some (I hope) objective questions.

Similarly I have been critical of academic libraries, but do not see them as the cause. They should have altered us earlier to problems instead of acquiescing to so much of the dystopia. They are part, but only part, of the solution.

I have therefore come, perhaps belatedly, to the conclusion that the crisis is of our (academia's) making. I used to blame the publishers and I still can and will when appropriate. (The manufacture and sale of fake journals is inexcusable – as bad as Murdoch's phone hacking). But the publishers are a symptom of our disease, not the cause. Cassius says:

Men at some time are masters of their fates:
The fault, dear Brutus, is not in our stars,
But in ourselves, that we are underlings.

So I will start with some axioms, on which future posts may build. If we can all agree then this serves as a basis for future decision making

• Science and scientists have a need and a duty to publish their work.
• Funders rightly and increasingly require this in a formal manner.
• This work should be available to everyone on the planet. Ideally the costs incurred in doing so should be invisible to the reader.
• The purpose of publication in whatever degree of formality is:
1. To establish priority of the work
2. To communicate the work to any who wishes to consume it
3. To offer the work for formal and informal peer-review and to respond to discourse
4. To allow the work to be repeated, especially for falsifiability
5. To allow the work to be built on by others
6. To preserve the work

I'd like to formalize this list – it's a first draft and I want to make sure we haven't omitted anything. I'd also like to know from any party, especially a publisher, if they disagree. There are publishers, for example, who believe that part of the process of publication is to restrict access.

I will say again; let us be careful because this rather enticing statement that everybody should be able to see everything could lead to chaos. Speak to people in the medical profession, and they will say the last thing they want are people who may have illnesses reading this information, marching into surgeries and asking things. We need to be careful with this very, very high-level information. (Dr John Jarvis, Senior Vice President, Europe, Managing Director, Wiley Europe Limited) examined by Ian Gibsons select Committee in the House of Commons, Westminster, UK, 2004-03-01) (http://www.publications.parliament.uk/pa/cm200304/cmselect/cmsctech/399/4030102.htm

I hope that 7 years have removed this attitude.

The historical purposes of publication did not include bibliometric evaluation of the publication as a means of assessing scientists or institutions. This is the monster we have allowed to be born and which we must now control. I do not believe it should be part of the formal reasons for publication. And if it retreats to informality we should take formal steps to control it.

So I'd be grateful for reactions, in the comments section. I will not edit and will attempt to keep comments objective.

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### 20 Responses to What is wrong with Scientific Publishing and can we put it right before it is too late?

1. Luis Ibanez says:

Peter,

I couldn't agree more with you.

The STM publishing system is seriously dysfunctional and needs to be replaced.

It inefficiency cost billions of dollars a year on lost effort and obstructions to the flow of knowledge.

In the path to change, sometimes is useful to focus on the bright spots were change is happening effectively, and to use those spots as illustration of how the STM Publishing System 2.0 will look like.

I have listed some of those bright spots in this blog:
http://www.kitware.com/blog/home/post/102

For six years we have been running the Insight Journal (http://insight-journal.org/), where papers are published online 24 hours after submission, they are open for public peer-review, reviewers themselves are rated by readers, the papers are required to include source code, data, and parameters, and an automated system extracts the source code, compiles it, runs it and verify the output of the code. With this process we have now 2185 registered users, 484 publications, 836 reviews. The process is so effective, that we can trace to it the addition of

This week, the "Reproducible Research: Tools and Strategies for Scientific Computing" workshop will take place on Vancouver. http://stanford.edu/~vcs/AMP2011/. Here you will find a very passionate community whose members are focused on making a reality of the ideas that you have described in your blog post.

PLoS ONE (http://www.plosone.org/) has embraced the concept of reproducibility in computational sciences, requiring source code to be included, along with data and execution scripts.
http://www.plosone.org/static/policies.action#sharing
It is ironic that Biologist understand this problem better than Engineers do...
http://www.kitware.com/blog/home/post/120

"Open Research Computation"
Is also another bright spot where reproducibility has been brought to reality.

---

Our experience with the Insight Journal has been, that the change will come from the younger new generation, as long as we (the older generation) avoid to corrupt them with the disturbed notion of "publish or perish".

As long as we educate the new generation of researches on the basic principles of how a real scientific publishing system should work (just as you outlined in your blog above), and we offer some concrete examples of how this can be implemented in practice, then "generational replacement" will naturally take care of the problem.

• pm286 says:

>>Thank you so much - this gives me encouragement to post the next analysis - I intend it first to the symptoms, and then causes and then remedies...

The STM publishing system is seriously dysfunctional and needs to be replaced.

>>>It inefficiency cost billions of dollars a year on lost effort and obstructions to the flow of knowledge.

This is the most obvious effect.

>>In the path to change, sometimes is useful to focus on the bright spots were change is happening effectively, and to use those spots as illustration of how the STM Publishing System 2.0 will look like.

>>I have listed some of those bright spots in this blog:
http://www.kitware.com/blog/home/post/102

Thanks,
It's also great to have found others at Kitware where you promote business models on top of Open Source.

>>For six years we have been running the Insight Journal (http://insight-journal.org/), where papers are published online 24 hours after submission, they are open for public peer-review, reviewers themselves are rated by readers, the papers are required to include source code, data, and parameters, and an automated system extracts the source code, compiles it, runs it and verify the output of the code. With this process we have now 2185 registered users, 484 publications, 836 reviews. The process is so effective, that we can trace to it the addition of

>>This week, the “Reproducible Research: Tools and Strategies for Scientific Computing” workshop will take place on Vancouver. http://stanford.edu/~vcs/AMP2011/. Here you will find a very passionate community whose members are focused on making a reality of the ideas that you have described in your blog post.

I am jealous and wish I could be with you. I assume vcs is Victoria Stodden>

>>PLoS ONE (http://www.plosone.org/) has embraced the concept of reproducibility in computational sciences, requiring source code to be included, along with data and execution scripts.
http://www.plosone.org/static/policies.action#sharing
It is ironic that Biologist understand this problem better than Engineers do…
http://www.kitware.com/blog/home/post/120

>>“Open Research Computation”
Is also another bright spot where reproducibility has been brought to reality.

I am on the editorial board...

>>>As long as we educate the new generation of researches on the basic principles of how a real scientific publishing system should work (just as you outlined in your blog above), and we offer some concrete examples of how this can be implemented in practice, then “generational replacement” will naturally take care of the problem.

I shall try to separate out the basic costs, the added useful value and the vanity that comes from impact and must be eliminated.

More later...

2. Henry Rzepa says:

Item 5 in your list (to allow the work to be built on by others) sounds an ideal of science (Newton standing on the shoulders of giants etc), but it is often interpreted as \to allow the work to be built on by others, but not before I have milked it dry myself\. Part of the issue is mis-match in timescales. Thirty years ago, a major project chemistry might last 5-6 years (and several generations of PhD students), but the publication process often took two years or longer (I have direct experience of this in the 1980s). One could set a publication in train, and then spend a further two years exploiting it without too much fear of competition. Nowadays, the (grand challenge) chemistry takes just as long (if not longer), but the publication process takes months (or in some cases just weeks).

At any rate, this mismatch is often cited as why many scientists are reluctant to offer reproducibility as part of their primary publications (or even to enhance it as part of supporting information), and of sensible and open deposition of data in readily accessible and re-usable forms.

• pm286 says:

Yes,
The Internet changes many timescales including the collapse of unassailable organizations...

P

3. Barbara Fister says:

Thank you for this post. I agree with what you say except that I was a bit stunned by the idea that libraries were remiss about altering people to the situation. I've been an academic librarian for 24 years, and not only have been alerting as many people as I could to this unsustainable juggernaut for nearly a quarter of a century, it was hardly a new cause when I joined the Cassandras. The problem is hardly anybody among the faculty cares. It's just a library problem, so not really a problem at all.

I do agree that librarians have been much to quick to acquiesce to the demands for instant access to articles on behalf of our users who want them, regardless of library issues. I doubt very much that individuals would shell out the $35 -$50 (US) that we routinely spend to obtain an article for "personal use and study," (though perhaps people wouldn't blink at building those costs into a grant - whatever, so long as somebody else pays) but I'm troubled that we're investing so much in so ephemeral a need and are not putting those resources into anything that lasts or can be shared. That's wrong. But we're not the ones who decide whether a library is functioning, our users are - and most of them don't care so long as they get their hands on what they need right now. The future, I guess, will have to take care of itself.

The fact is our scientific heritage is now intellectual property belonging to non-scientists. If you want to stand on the shoulders of giants, you'd better be prepared to pay the company or society that rents out that shoulder space! (and only for personal use, mind! don't even think about anyone getting on your shoulders! That's not part of the terms of use.)

• pm286 says:

Thanks Barbara,
Very useful - I will hope to draw these threads together.

• Barbara Fister says:

I'm really pleased with your axioms and plan to share them with students when we discuss the purpose of publishing scholarly work. (I also have them read John Ziman's Nature article, "Is Science Losing its Objectivity?" which deals with the commodification of research.)

• pm286 says:

Thanks - I am hoping that others will refine them (see the contribution from Daniel Mietchen and friends)

4. Nuwan says:

Thank you for this post and creating awareness of the impending problem. I am not very good at articulating my own thoughts, but I will try my best.

I think scientific publications are a victim of our own "research success measurement yardstick". I did my EECS graduate work in a far east university. Situation here is something like, your productivity as a researcher equals to the number of publication you write a year. On the first day I showed up in the graduate school, head of research summoned me and said "I want you to publish a journal paper and a conference paper every year! I won't accept your thesis until you publish 2 journal papers". In another words, he is putting the status quo -- publish or perish -- in few sentences. This pressure is even worse for junior academics, who are trying to build an academic career. Unless they author/co-author 20+ journal papers a year, their advancements in an academic institutions is most often ill fated.

I think this is deleterious for the whole of sciences. Such quantitative success measures lead to enormous pressures on researchers, which eventually leads to:

1. Publishing poor quality papers with half baked ideas or less rigorous experimental evidence
2. Helping unheard/unrecognized journals to proliferate
3. Researchers losing their integrity and proliferations of research malpractices
e.g. - fabrication of data, dishonesty, plagiarism, fragmenting single publication into multiple publications (just to get the brownie points), intellectual piracy (trying to get your name into colleague's publications), publishing same results in multiple journals under different titles.

I was quite frustrated in academia and it eventually lead to my untimely departure, as I couldn't stand what was happening around. After doing a long and thorough investigation, when I publish a paper, I see others have published half a dozen by the means of malpractices listed above. In university administrators perspective, I am nothing but an unproductive "dead-wood". Finally I decided to do a 9-5 job in industry to earn the bread, and do research in spare time. This way, I won't have any of the drawbacks being attached to an academic institution, and allow me to be more independent and honest researcher.

I wish the science community (as well as universities) reward more for "quality" research and publications rather than pure volume. It is my hypothesis, this is the key reason why science is not progressing at present. As most researchers have to "survive" in their respective institutions, hence they work on research that leads to predictable results, which translate into papers; rather engage in high quality/productive research, which always comes with high risk, long term rigorous investigations and most often not, big price tags.

• pm286 says:

I think you have articulated this extremely well - and you give a very clear picture of the malaise.
P.

http://opensource.com/education/10/10/uncovering-open-access

• pm286 says:

Many Thanks Michael

6. anotherlibrarian says:

"Similarly I have been critical of academic libraries, but do not see them as the cause. They should have altered us earlier to problems instead of acquiescing to so much of the dystopia."
This is shockingly frustrating to me as an academic librarian. I'm relatively new to this field, as I started in librarianship about eight years ago. But from the first day, I was aware of what librarians were already then calling "The Crisis in Scholarly Publishing." And I was aware of librarians working incredibly hard to talk to faculty about these issues.

Could the problem perhaps be that at least some of you were listening? Because short of throwing tomatoes in your faces, I'm not sure what else we could have done.

I might re-phrase the above comment as follows:
"Similarly I have been critical of faculty's complicity in this, but do not see them as the cause. They should have listed to us earlier instead of acquiescing to so many publisher demands."

• pm286 says:

Thank you for this,
I appreciate that many libraries have tried to alert academics. In my recent posts I believe that most of the blame lies with academia. But there are many issues which come through the library and should be banner headlines. Here are two which I have blogged about:
* The introduction of Digital Rights Management on interlibrray loans. IMO this is a fundamental violation of human rights. AFAIK there has been no public outcry. I have sent FOI requests to the BL on why this happened - how many others have done the same
* The restrictions on the use of electronic content over an above copyright imposed by contracts between academia and the publisher. I am legally prevented from even indexing the electronic content from most publishers.

These restrictions continue to be added, year by year, and no one highlights or objects. How many libraries have refused to sign contracts on their content (not their price). If a sufficient number of institutions did this then contracts would be rewritten.

• Dan says:

"These restrictions continue to be added, year by year, and no one highlights or objects. How many libraries have refused to sign contracts on their content (not their price). If a sufficient number of institutions did this then contracts would be rewritten."

Oh, sure, we librarians can do that. If researchers are willing to accept fewer journal subscriptions in your area, longer ILL turn-around time, missed opportunities for networking, and the resultant inability to meet publication and grant deadlines on occasion.

As a researcher, this is unacceptable. I know that I find it to be so for my own research. The trouble is, as long as it's unacceptable, librarians have no way they can refuse to sign contracts. At this point, most negotiations between libraries and publishers are conducted with both parties knowing the libraries can't walk away from the table.

But we can find other publishers to work with? In some cases, no - I give you Elsevier as an example. In other cases, we can - but it involves looking at quotes from other vendors, matching up periodical lists of thousands of titles (that rapidly change without notice) with usage statistics from your library, figuring out where individual subscriptions need to be purchased to make up the differences, figure out which ones can't be transferred due to exclusivity agreements, setting up the proxy servers, reconfiguring your instruction program, and bringing hundreds of faculty on campus into the loop, at the end of which students wander in looking for journals X and Y that didn't make it through the process and which the professor didn't check on because they haven't changed their assignment in ten years and didn't bother to read their email. In the end, you've gone to an incredible amount of work for a solution about which you'll receive very little feedback aside from complaints.

Did I also mention the general lack of financial support for pursuing alternative solutions, or even for just about anything at all, from universities as a whole.

And there's a general lack of knowledge of even the basics among faculty. Some are very savvy and knowledgeable about their sources, but it's a hard time selling faculty on issues such as the ones you've raised when people are saying "I don't use the library databases; I just get all my articles from JSTOR" (a library database accessible through the Web at many campuses) or "Can't you work with other libraries to get databases cheaper?" (most libraries do buy in consortia).

Oh yes - I'd forgotten consortia. Now, consortia are one means of buying databases cheaper and giving researchers more access to the journals they need. They also mean that, even if your campus is passionately devoted to the furthering of scholarly communication, you're likely buying databases with a group of other people who have different communities of both faculty and students, different sizes, different departments, and different philosophies and priorities. This can mean that you might have to accept a less than ideal situation when you sit down at the table. Every time someone decides the deal costs too much and bows out, you have to go back and start over again with new numbers and new conditions, with which other people aren't going to be happy, possibly leading them to bow out, and starting the cycle all over again.

In conclusion, I would not ask librarians why they just don't sign contracts to preserve standards of scholarly communication without a large object behind which to stand within arm's length. Trust me, we're on board, especially if we can come up with simpler and less frustrating solutions for delivering this information. We're just waiting for everyone else.

• pm286 says:

Thanks Dan,
So there isn't really anything to be done.
It is up to me to discover these problems and to alert the world to them. But it won't do any good, so I will shut up.
The logical end of this is that a University will transfer these licensing issues to its purchasing office (it's cheaper than going through libraries) and that Apple/Amazon and others will sell "rented books" directly to students or to the publishers of their text books. I think this will hasten the decline of libraries even faster.

7. Susan Shock says:

This is an interesting thread--thanks to all for your thoughts. As a managing editor and copyeditor, I have to remind everyone that one part of what the publishing industry adds to the equation is copyediting. This can be very helpful in keeping communication clear--for example, should librarians have been altering us or alerting us? In this case we can guess what is meant, but in some scientific sentences an error like that could be obfuscating and work against the end goal of sharing scientific knowledge. When we talk about changing the publishing environment, I just hope we don't forget the role of copyediting.

• pm286 says:

Susan,
This is very important. Yes, the publisher DOES add value. This complicates the equation - a paper is part created by the author and part by the publisher. The question is who has the right to do what. Adding value per se does not mean the adder owns everything unless the original author has contracted (as many do). I am happy with the BMC OA model where the author/funder pays for the service of copyediting and publication/dissemination. I am happy to pay for this service and (while I have funds) do.

8. Musa Akbari says:

Thank you for your great insights. This is a covert yet fundamentally important issue to address. The only people aware of the peer-review process are researchers themselves, but papers that pass through and get reinterpreted by the media have profound effects on society, most of which the masses are unaware of.

In an effort to progress science towards open peer-review, I've launched a campaign for Meritocracy. It is a proposal for a cloud review system that serves as a platform for open peer-review, creates a free marketplace for research and development, and involves students through apprenticeships. Using today's technologies, I believe we can enable an elaborate system of checks and balances among peers of mutual expertise, while cutting time and cost barriers and promoting transparency to engage the public.

I'm currently running a campaign to gather supporters and collaborators for this mission
http://igg.me/p/67101?a=416044

A brief intro about the initiative