I wanted to make a presentation about Open Research and Open Science for our internal doctoral seminar at the Dresden University of Technology (my slides from the seminar in German language are available here). For this purpose, I tried to sum up for myself, what Open Science and Open Research mean. I confess, I found it quite difficult. Anyway, this is what I came up with:

I started by trying to define the terms ‘open science’ and ‘open research. They are very often used synonymously, although I cannot agree, that they should mean the same. I therefore reviewed the definition ’science’ and ‘research’.

Fig. 1 : Science and Research

There is a close connection between science and research. Science uses research, a process of systematic inquiry, as meant of gaining new knowledge (Bordens & Abbott, 2007, p. 2; Graziano & Raulin, 2009, p. 26). However, not all research takes place in science. In fact, scientific research has to fulfil very specific criteria (Heinrich, 1993, pp. 62-66; Shugan, 2004, pp. 174-175), e.g. be public, replicable, unprejudiced, independent and it must advance the state of the art (Heinrich, 1993, pp. 62-66; Shugan, 2004, pp. 174-175). Research outside these restriction is non-scientific. This does not mean it is worse than scientific research. It simply has different aims. (During my presentation, I had a little discussion with one of the participants, who basically differentiated between scientific research and bad research. I do not share this view. I agree with the authors cited here, that rigorous and valuable research exists outside of science. It just has different purpose and hence different restrictions).  But science is not just about research. According to Bordens & Abbott (2007) science is also a way of thinking and viewing the world. Going back to open science and open research, this would mean, that there is open research outside of open science and open science outside of open research.

Now, what does “open” mean? David (2004) offers a very nice historical overview of the development of science from secretive activities towards openness (see also Nielsen, 2008). According to them, openness developed from the need to judge scientific merit. David, den Besten & Schroeder (2009) describe two levels of openness: the openness of research process and the openness of the research results. These are similar to Merton’s (1979, pp. 223-280) communalism and universalism (four or nowadays five CUDOS by Merton – see also David et al., 2009). Communalism calls for the resignation of the intellectual property rights on scientists’ findings and for common access to resources. Universalism demands, that the ability alone should be used to judge the scientists and the quality of their results – not individual factors like race, nationality, religion etc. The European Charter for Researchers goes even further and asks researchers to carry out their research for the good of the mankind. I think this already poses many interesting questions. Why do researchers publish their results? Do they do it for career purposes or for the development of science and hence the society alone? I think, that different publishing practices result from these two aims (i.e. publish or parish).

Further questions arise, if we view the development of ICT and their influence on research. The possibilities created by the technology make us reflect, how open the science should be. Because now there are different levels of openness possible.

• Publication of results – fine, but is a journal or a book open enough?
• Availability of resources – then how about sharing data?
• Free access to research projects – shall I then open my whole research process so that anyone can join any time?

These questions also mirror the areas associated to open science:  open access,  open data and open process (also open notebook and open source). I have collected a few links on these. This is of course not a full list – just a few places to get further information and ideas.

Open Access

• Open Access Initiative – a lot of information about Open Access, its history and issues
• Direcory of Open Journals
• Public Library of Science – committed to making the world’s scientific and medical literature a freely available public resource
• arXiv.org -  the greatest archive of open access scientific work
• Sprouts – an archive for scientific work on information systems
• Academic Publishing Wiki

Open Data

• openPSI – making publicly collected data avalilable
• Swivel – platform for sharing data
• many eyes – platform for sharing data

Open Process

• OpenWetWare - the open notebook wikis
• myExperiment – exchanging workflows

The discussions around open science and open research gave me lot to think about. I think there are no easy answers here. Everyone has to make a choice and find his or her position. The technology may act as an enabler, but the question of open science is more about culture and ethics (e.g. one of the presentation participants pointed out to me, that when collecting data in social sciences, the researchers assure the participants not to use the data for purposes other than this research – passing such data to others would not be ethical). Just as that there is science beyond scientific research – a particular way of thinking and viewing the world, there appears to me to really be open science beyond open research. The open research can utilize the chances the technology offers for sharing whatever we want. Open science, however, further calls for a culture of openness within science.

My scientific workflow includes email between myself and lab members and collaborators, annotations on previously published papers, adding information and ideas to the lab wiki, Python programs to create visual displays and run experiments with them, and Python and R code to plot the results and do the statistical analysis.

A long-term goal is to link these things together so that each project in the lab has an electronic paper trail of different python programs that were written, emails that were exchanged, experiment variants that were tried, data that was collected, statistical analyses conducted, and manuscripts that were written.

I want all this for two reasons.

1. Most importantly, to compensate for my failing ability to keep abreast of all the lab projects and remember everything we’ve done for each. I should be able to type ‘Frohlich’ into a searchbox somewhere and see all the materials related to our experiments on the Frohlich effect.
2. Second, to move closer to open research, where others can see what we’re doing, get in touch if they’re interested in collaborating or know something relevant, and see our unpublished negative results so that they needn’t repeat all the associated work.

There’s a lot of discussion recently about how to move towards open research and open notebook science (e.g. Cameron Neylon and Ian Davis). I don’t know how much others are already saying this, but to me the way forward is to create a system that would appeal to nearly every scientist’s desire for #1 above regardless of whether they support open research: a system to archive what the lab does in an organized fashion so that each lab member can access it. I find this easiest to do by using web archiving systems like Google Groups for lab email and files. I don’t have most steps working in easy and automated fashion and I don’t have the programming skills to get them working with necessary ingredients like version history, linking code and output files, etc. However once someone does, bona fide open research would be just a matter of changing the permissions so that anyone in the world can access it.

Matt Wilkens, post-doctoral fellow at Rice’s Humanities Research Center, recently launched Work Product, a blog that chronicles his research in digital humanities, contemporary fiction, and literary theory.  Matt details how he is working through the challenges he faces as he tries to analyze the relationship between allegory and revolution by using text mining, such as:
•    Where and how to get large literary corpora. Matt looks at how much content is available through Project Gutenberg, Open Content Alliance, Google Books, and  Hathi Trust and  how difficult it is to access
•    Evaluating Part of Speech taggers, with information about speed and accuracy

I think that other researchers working on text mining projects will benefit from Matt’s careful documentation of his process.

By the way, Matt’s blog can be thought of as part of the movement called “open notebook science,” which Jean Claude Bradley defines as “a laboratory notebook… that is freely available and indexed on common search engines.”  Other humanities and social sciences blogs that are likewise ongoing explorations of particular research projects include Wesley Raabe’s blog, Another Anthro Blog, and Erkan’s Field Diary.  (Please alert me to others!)

Peter Suber featured the link to Stian Håklev’s presentation on Open Research, Open Educational Resources and Open Learning- Experiments and Ideas. Stian made the presentation at the Indian Institute of Public Administration, on August 13, 2008. Here is also the link to the Stian’s blog post on the presentation.

Speaking about his impression of the event, he said:

I spoke to a group of perhaps 25 librarians and professors, trying to give a ‘whirlwind’ tour of the field of open research and open learning, both in general but also in terms of its usefulness for developing countries. It seemed to be well received, and I had several requests afterward for more information.

His closing remark on the presentation:

By making India’s research and teaching available, you benefit the world- and India itself!

A lot of hype has been wasted and applied to Open Science these days. What is it good for? Scoop someone’s work? In some cases maybe, in others not.

Let’s take for example stem cell research. Say you are working on a groundbreaking research that requires some kind of secrecy, because some guy in another lab is trying the same thing. If you decide to open your notebook the guy-next-door can check it and maybe have an insight and modify his approach and find the desired result before you do. If the guy-next-door is a “nice” guy you will share the discovery, if not you will end up with crumbs. In this case Open Science is only good if it is a two way street, as everyone is sharing data, results and publications freely.

On to the a bioinformatics example. Say you are working on a software the would allow analysis to be more elaborate and exact to some kind of biological problem. Your notebook is open, you software is on Github (or any other repository), so anyone can see it, especially the guys (non bioinformaticians) which analysis will be improved. You are the only one that knows the code and most of the algorithms in it, and you test, release and publish. Great … but wait: the analysis is wrong and there are some major errors on the results. You look, search, dissect your code and cannot find the bug or error. You, frustrated, mentions it in your notebook. Some guy from the internet notices it and decides to check the code and in 10 minutes finds the error/bug. Everything solved and marvelous results are expected.

As anything there are many sides, many different angles that Open Science can be viewed, and it might not serve everyone at first, but it is clearly a great start. The only question is where it is going to take us. What is it good for?

Open Science and open research have been topics of interest in the past few years. I got introduced to this important topic in late 2006 through a video lecture by Prof. Hal Abelson, the originator of Creative Commons. Ever since I have been thinking of ways to practice open science in my academic surrounding. In this talk I present my opinions on open access journals, their necessity and possibilities and how they can be nourished in an Indian context. Some of the material is known to most of us but I talk on it for the benefit of those who are new to research publishing. There are others who have asked me questions on specific open access topics in my lectures. Some of their doubts are answered here. References to some relevant sites and recent discussions are given at the end in the text version of this podcast.

I am a faculty in an academic institute that requires as part of my duty to do original research. I must publish my original research in reputed journals pertaining to my scientific niche to improve my scientific standing and academic position and recognition among peers. More the quantity with accompanied quality more such recognition. I must publish research as a way of academic life.

I do research mostly in heat transfer, a relatively small (remote) corner within thermal science, within physical science, which itself is but a relatively small portion of the authentic scientific knowledge being generated. I need to publish my research in journals related to heat transfer. A quick web count looking for journal titles with the words heat or thermal gives a number between 15 and 20 depending on whether you include some physics journals that also publish such heat transfer stuff.

A journal that carries peer reviewed original research articles usually has an editorial board comprising of accomplished professors and researchers in the pertinent field of that journal. These editors receive the submitted copy of my research paper, categorize it within heat transfer, choose reviewers who are professors and researchers working in the relevant sub category of heat transfer and send my paper to them and ask for their opinion on its scientific merit, originality and usefulness. These professors review my paper as a voluntary service for the science community they belong to and send in their reviews about my work back to me through the editors of the journal. Assuming the work is reasonably error free and useful, upon revising the article by attending to the reviewers questions on a variety of things from the appropriateness of a model or equation to cited or not cited references to English, I need to send back a revised version of the paper for the approval of the editor. Some times this process of peer review goes through two or three iterations with apparently useful discussions on the content of the article. If the editor accepts the paper at this stage, it will be published in the journal in a future edition.

The peer review process and the associated personnel including the journal editorial board, the reviewers and the authors all belong to academia and associated research organizations. Until this stage, there is no copyright involved or transferred. everything works on mutual trust and single or double blind peer review. Here ends the role of all of the academics involved including me the author of the paper. As a sidelight I could add that most of the journal research literature is read by other such researchers and academics. If made available, the interested public are willing to take a look.

But the actual publishing of the entire body of research knowledge is done by publishers, the middlemen, are those who control entirely the key aspects like who could have access to such knowledge, how much profit the publishers could make, what sort of copyright the researcher who generates original knowledge could have and so on.

The journals escalate in reputation over the years, only because of the quality and sincere effort of the peer review and editorial board, all researchers and academics. Ironically, the accompanied escalating publishing cost and profit are determined by the journal publishers. The involved academics neither get nor expect a cut in the profits that is made out of their sweat. They are happy to see their work published in journals read by their peers.

The eventual actual publishing of the paper depends on me signing a transfer of copyright form to the publisher of that journal. Until I actually sign this, I hold all the copyright of what I wrote. Once I sign it, I transfer some of my rights to the journal publisher. And if I don’t sign it, I cannot publish my, otherwise technically correct, article in that journal.
In short, the publishing activity is controlled by middleman and remains closed.

There is another way. The open access way. The journals listed at http://www.doaj.org/, the directory of open access journals, follow this way. And the list is growing every year.

As a researcher, I do all the hard work, think of an idea, find the research methods and tools, find the funding if necessary to accomplish certain tasks to realize the idea and see its merit, write the results using the idea and analyze the pros and cons of the idea and send that research article usually to a research journal office comprising of other researchers. The subsequent peer review process that qualifies my idea for its worthiness as original useful scientific knowledge is done by these academics and researchers mostly for no fee. It is a service they all must perform because it will be reciprocated in kind and quality by other researchers in the community to uplift their research work. Strict but free of money.

In this reasonably democratic process of scientific knowledge generation, where is money and cost and profit involved? Only in the actual publishing of the journal? Then why can’t that be supported by one of the many democratic ways possible?

For instance, shift the entire journal online. It costs pittance to maintain a server space and host web domains and could be incurred life long in one philanthropic nod. Open source software can take care of the entire peer reviewing and publishing process with the editors needing to know how to operate one or two such software. Monetizing with appropriate Google ads on such web journal portals are a way to become self reliant.

Another way to do this is to have local consortium of research schools to maintain web spaces for journals in which their employees are participating as editors or reviewers or even authors. There could be an agreement between the journal editorial board and their respective academic institutions on the extent of financial support in magnitude and time. Guidelines could be charted for suitable cap for preventing any monopoly of institutes and representatives while maintaining the democracy of the publishing activity.

While the above methods open ways of starting a fresh open access journal downsides exist. The major downside is the so called reputation or the lack of such reputation of a fresh open access journal. Established scientists think twice to publish in journals which are not reputed, for, more such publications only detriment their scientific standing. Their merit will be questioned. Their ability, or its lacking, to publish in established, reputed journals, peer reviewed usually by authorities of the field, will be discussed in every appraisal. Whether the reputed journal is closed access or open access is an unimportant side issue in such appraisals. In such an academic scenario, as a fledgling researcher, I know that publishing exclusively as a matter of principle, in start-up journals because they are open access, is a sure fire quick fire way to commit academic suicide.

There need to be a way out to break this self imposed cycle of no win situation.

One way I could think of is, to start every open access journal with an editorial board and peer review group that already participated actively in the existing editorial boards of other reputed but closed access journals controlled by middleman publishers. This ensures the fledgling open access journal to quickly gain reputation amongst scientists of that field, once they are informed of the illustrious stars that deck the editorial board of that journal. If this process could thaw a few top scientists in that field to send their work to the open access journal, its future and reputation is ensured in the ensuing avalanche.

Another way I could think of is, instead of setting up a new open access journal, an existing closed access journal could be made into an open access one. This could happen with or without the agreement of the publisher. If the publisher agrees to work with one of the models of open access, then that is a start. We should immediately try that angle. For instance, the publisher could be negotiated to release into open access or the internet, the content of an issue, after two or three ensuing issues have appeared. This model could work for academic research publications with reasonable success.

Else, the journal subscriptions could be bought by academic consortium annually and made available open access.

For instance, in India, the institute of technologies can form a consortium and support open access journals. Annual subscriptions can be paid to maintain the open access status of journals served and participated by their employees.

If the publisher doesn’t agree for any sort of open access, the entire editorial board of a reputed journal could decide to boycott and resign their positions and perhaps start a new journal under a suitable name. The editorial board will provide the required credibility for such a venture to be supported by the scientists in that field to contribute to the journal and its reputation.

On the other hand, the publishers could simply appoint a new board team and continue. This risk has to be faced, for, every such mass resignation cannot be dealt with with such a publisher position. I think the academic community is sufficiently reactionary to maintain the required democracy.

There are other angles in which open access can be seen as the only correct way to do report research at least in the future.

I am a faculty selected and appointed by a selection committee that includes experts nominated in principle by the President of India. I work in an educational institute of India funded by the Indian government. In short, I am a government employee earning my salary from tax payers money.

My work includes doing original research of international repute in my chosen areas of interest and publishing it. Leave out the fact that I do this to generate and sustain my academic recognition among peers in the Indian and International scientific community. What about my indirect responsibility to those tax payers? If one such informed tax payer wants access to my research, want to know how his money is spent by the government on me, should I not oblige? Why should I do my research using tax payers money given to me through an academic or government sponsored research grant but publish it in journals controlled by middleman who control the access of such information for their own ends? I think the public of a country has a right to have access to the research content that their tax money funded.

Academia is a free place to foster new ideas and exchange it freely with anyone so that eventually such ideas help the society. For teaching existing knowledge in the form of courses, this free exchange is already proving to be successful. The MIT Free Online courses and locally the IIT Madras Free Online courses are examples of such a model of free exchange of knowledge with the interested public. In the same vein, true to its character academia allows me to generate new ideas as a researcher and shape it eventually into new and useful knowledge. It germinates and generates new knowledge. Why then it allows middleman in the form of third party publishers to control where such knowledge resides?

The rightful place for such knowledge to reside is where it is germinated and generated. Academia itself.

And open access journals are a right choice.

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[Note: This essay is the full text transcript of my earlier podcast on the same topic.]

Here is a fifteen minute podcast of my thoughts on open access publishing. Feed readers of the blog may not get to see the audio plugin in the feed. Come over to the blog site to hear the mp3 audio file. Let me know of your thoughts. Thanks.

[Download Podcast:OpenAccessPublishingByArunn.mp3 | hosted at www.divshare.com | size ~ 16 MB | run time ~ 15 minutes]

The transcript of this talk is available if you prefer reading.

Some recent discussion on open access publishing is going on at Danah Boyd’s post and an overview of open access is provided by Peter Suber in his Six things that researchers need to know about open access

The directory of open access journals carries a list.