Thursday, August 6, 2009

Reinventing Academic Publishing | 1 > 2 > 3 / James Hendler

Letter from the Editor / Intelligent Readers


Although quoting yourself is generally considered tacky, I've been involved in several recent activities and discussions I'd like to share with you. These largely arose from "Publishing on the Semantic Web," a column that Tim Berners-Lee and I coauthored in Nature back in 2001 ( In that column, one of a series of opinion pieces about academic publishing's future, we discussed the Semantic Web's potential impact. We ended with this somewhat brash statement:

The semantic web will provide unifying underlying technologies to allow these concepts to be progressively linked into a universal web of knowledge, and will therefore help to break down the walls erected by lack of communication, and allow researchers to find and understand products from other scientific disciplines. The very notion of a journal of medicine separate from a journal of bioinformatics, separate from the writings of \ physicists, chemists, psychologists and even kindergarten teachers, will someday become as out of date as the print journal is becoming to our graduate students.
In the past year, I've found that this quote is resonating more and more and that some of the big players in academic publishing are starting to think along these lines [snip]. Not all of them are considering using Semantic Web technology; some are inspired instead by Web 2.0's community-oriented features. However, the notion of breaking down the lines between traditional disciplines and reaching out to audiences beyond the academic bench scientist is becoming an important "meme" in academic publishing.

More Than Just Technology

One leader in this area has been Nature itself, which launched the Nature Network [], a social-networking and blogging site aimed primarily at scientists. Users can create a social network, share forums and blogs, and use tags to create semantics. [snip]

Lately, I've been hearing from other publishers and magazines that they're also considering doing more to enhance their online sites with community-oriented features. They have been motivated by Nature's lead, by users' increasing reluctance to pay for hardcopy articles when so much is free online, and by the increasing facility that young scientists, [snip]

It's becoming clear that making a successful community-oriented Web site requires more than just the technology. [snip]While ... [some] sites have taken off, others have languished owing to misunderstanding the mismatch between the technology and the community they want to reach.

Overcoming Resistance

Which brings us back to academic publishing. As publishers try to promote new models of communication among scientists, with an eye toward finding some new role in the process, they need to respect the way science works. Although this, like many other things, might be changing owing to the Web's impact, some natural points of resistance must be overcome before new, more community-oriented, interdisciplinary scientific sites succeed. While scientists have gloried in the Web's disruptive effect on publishers and libraries, with many fields strongly pushing open publication models, we're much more resistant to letting it disrupt the practice of our disciplines.

At the Science Foo Camp (tagged on many blogging sites as "scifoo") held at Google in August 2007, several sessions dealt with academic publishing's future. The topics included open-source publishing; publishing "pre-review" (or with community reviewing of some sort); and the use of blogs, wikis, and other new technologies to enhance scientific communication.

However, motivated by comments arising the first day, the second morning featured the session "Culture of Fear: Scientific Communication and Young Scientists." This session, led by postdoctoral researchers Alex Palazzo (Harvard) and Andrew Walkingshaw (Cambridge), explored issues that those starting out in scientific fields face when using these new technologies. The job market for scientific positions, especially in academia, is tight. So how do a team of scientists, sharing partial results pre-publication, assign credit? Authorship blurs when small amounts of information, which might contain key insights into making processes successful, are publically shared. How does a blogger get credit for the information that leads to an eventual publication at a competing lab?

Another theme of the session was peer review's role in scientific fields. Although some pseudoscientists have claimed that we use peer review to keep their brilliant insights out of our precious literature, most scientists truly appreciate the filter that peer review provides. The high standards publications maintain are a useful way to ensure that ideas are well argued and strongly evaluated before being published. On the other hand, some feeling has always existed in the community that, especially with respect to funding, the peer review process might be overly constraining and considerably delay new ideas from coming to the fore. [snip] These factors have motivated many in the community to discuss new mechanisms, based on emerging Web technologies, that let us communicate more ideas more quickly.

For example, one model involves publishing after a minimal peer review and then creating some sort of postpublication metrics as to the paper's value. Some online journals are already exploring this model. However, as Alex put it in his [],
Until the scientific establishment reaches a consensus as to whether these post-publication metrics are indeed useful for determining the credentials of a scientist in the shorter term ... .
What Can We Do?

So, we arrive at the crux of the issue facing many of us, whether we're the editor in chief of a magazine such as IEEE Intelligent Systems or the head of a major press or publishing house. How do we embrace the new technology and encourage more of the sharing that Tim and I were calling for, without causing career risk to the very people to whom the technology is most familiar—the younger scientists? If we don't think through the social issues of usage, the technologies alone won't have any significant impact and will go largely unused.

One option—and I'd like to see more effort in this area—is for innovation to come "from the top." Eventually, as these young scientists become the leaders of our fields, they will bring these new technologies with them. But with the world in its current shape, needing the help of scientists for our very existence, we can't afford to wait that long. Rather, we need to find ways to bring more senior scientists into contact with the positive side of these technologies.

In computer science, where the barrier has been lower than in some fields for senior people to learn to use new computer technologies, we've seen some of this happen. For example, Tim Finin has been instrumental in bringing bloggers to the AAAI conference, which has caused others to read, and in some cases create, blog content. [snip] When young scientists see their field's leaders embracing new technologies, it's that much easier for them to demonstrate to the rest of us, without fear of retribution, what these technologies can do.


It's time for us as computer scientists to take a leading role in creating innovation in this area. Some ideas are simple—for example, providing overlay journals that link existing Web publications, thus increasing the visibility (and therefore impact) of research that cuts across fields. [snip]

In my next column, I'll discuss current ideas regarding new technologies for academic communication that we as a field might be able to help bring into being, and some of the obstacles thereto. I look forward to hearing your thoughts on the subject.

Full Text Available At

IEEE Intelligent Systems, Vol. 22, No. 5. (2007), pp. 2-3.

Letter From The Editor / Interlligent Readers


Last issue, my letter focused on some trends in academic publishing that journals, magazines, and other scientific-publishing endeavors are facing. I argued that we computer scientists should take a leading role in helping create technologies that will break down the walls between different disciplines.

An obvious response is, "haven't we already?" That is, Tim Berners-Lee's invention of the World Wide Web, coupled with Sergey Brin and Lawrence Page's PageRank algorithm that powers Google, has led to a world where scientists publish preprints and papers on the Web and can find each others' results without having to subscribe to the same journals. Doesn't that solve the problem? Just pick your favorite chemical, check it out on Google (or even better, Google Scholar), and there's the paper you need. What more is there to say?

New Medium, Old Ways

Unfortunately, the reality of sharing papers on the Web doesn't live up to this ideal. With rare exceptions, Web-based journals and open source publications and preprint servers have been modeled on the same field and subfield considerations that print journals and scientific communication have been using for decades. [snip]

So while we've made journals electronic, with positive results on distribution, we still haven't really done much to revolutionize the scientific-communication aspects of scientific publication. If a computer scientist searches for some term in the field—say, "case-based reasoning"—in an online journal, he or she will likely find papers of interest. [snip] Despite the prevalence of online literature and the ability to search with great ease, jargons—the different ways different fields describe similar things—still get in the way.

This is true even of sites that have tried hard to provide organizational structures to help people find each other's work. Scientific publication sites such as PubMed
[] or arXiv [] , for example, organize papers on the basis of disciplinary terms familiar to the scientists who use them. [snip]

This is particularly troubling because many, if not most, of the key scientific discoveries of the next generations will require interdisciplinary approaches. [snip] Unfortunately, despite the growth of these larger science projects, the publishing still tends to be in traditional journals, arranged along disciplinary lines and reviewed by experts in the traditional fields. [snip]

Overlay Journals

This need for better support for interdisciplinary work is exactly what's motivating many of the new solutions being considered online. Rather than simply replacing print journals with online journals of the same ilk, people are considering new models that can more easily cross disciplines and find papers (or projects and so on) related to their interest areas. One model that's becoming more common is the overlay journal (sometimes called a deconstructed journal, after John Smith's 1997 paper "The Deconstructed Journal"). The idea is to create an online publication by taking some crosscutting theme and providing links to papers published elsewhere. By providing links rather than republishing, the overlay journal provides a service to both the reader, by linking to many publications, and the publishers, by bringing more eyeballs to their sites. [snip]

Models of Curating

A number of different models are being explored for how best to "curate" such overlay publications. One model is to have the overlay journal function as an independent publication. The IEEE Computer Society will be taking this approach with Computing Online, a site that will serve multiple purposes. One purpose is to provide an overlay functionality across the different Computer Society magazines ... . The new publication will thus provide a means for a wider audience to see our magazine's articles, and we'll be providing articles to that site, reducing its need to solicit and produce new material. [snip]

Another model has a more open Web feel to it. For example, the University of Southampton's Leslie Carr is creating a submitter-based Web science overlay journal. Submitters can fill in a simple form (or share metadata from other publishers) to have a paper listed on the site. The submitter
  • points to the original publication,
  • proposes where to link it into an evolving hierarchy of terms (basically a folksonomy seeded by a set of terms from a domain ontology, thus providing Semantic Web metadata), and
  • briefly comments on why to include this paper.

The submitter can be the paper's author or someone else who feels the paper will be of value to the community. Mechanisms for determining how to moderate the site ... are still being discussed. This mix of submission with overlay seems to combine the best of several worlds.


[snip]. Beyond the overlay journal, we start to look at more novel ideas that depart further from traditional publishing. Such ideas include blog-based scientific publication, Web 2.0-based community sites, and sites enhanced by the Semantic "Web of data." More on this in part 3.

Full Text Available At

IEEE Intelligent Systems, vol. 22, no. 6, pp. 2-3, Nov./Dec. 2007


Letter From The Editor / Intelligent Readers


In this last part of my editorial trilogy, I discuss something that's becoming more and more important to academic communication—online scientific interaction outside the traditional journal space.

The importance of contextWe must change our focus from scientific disciplines to scientific "contexts." When looking at the most successful Web technologies, especially in what's known as Web 2.0, we see that many of the most exciting sites exploit a community or context focus. [snip]


The Power of Social Networking

Social websites for particular communities of scientists offer a way to, essentially, embedding the context into the site. A good example of this is, a social-networking site for experimental scientists. The site lets users share experimental workflows and develop communities around specific activities. A network of scientists can form, for example, around certain proteins' role in causing disease. These scientists can share methodologies and specialized techniques and discuss how to get better results in a relatively informal and blog-like way, while still being able to share the important work products that help them be more effective. While these scientists might still compete with respect to the data they're using and their published results, they can cooperate in developing and refining experimental methodologies. This crucial sharing of knowledge typically isn't publishable in traditional journals.

A more generalized version of this idea, and one I'm coming to rely on in my own work, is the Twine system, developed by [snip]

Twine is a social-networking site that focuses not on its members' activities per se but on sharing information products in user-created contexts. [snip]

In part 2 of this editorial trilogy I talked about overlay journals and how they could be used for sharing information across an emerging discipline. A problem is that if the group wanting to communicate is relatively small, setting up such a site involves a prohibitive amount of time and resources. Using something like Twine, we can create sort of an ad hoc overlay journal on our specific topic of interest. Twine wasn't created with scientific communication in mind, but something like this is obviously applicable to scientific discourse. The twine forms the context, and the members choose what to share as they create their own shared vocabulary. Unlike email, newsgroups, and even wikis, the open and dynamic nature of building the discourse in the social-networking context could greatly improve such information sharing.

The Source of Change

I'm excited by the emerging technologies for scientific interaction; these new technologies that expand on blog- and wiki-like ideas to create context mechanisms will become increasingly important to scientific discourse. However, whether change in online scientific communication comes specifically through technologies such as these or through new Web technologies just starting to be explored, I'm certain of one thing: this change is inevitable.

The other day, I was reading a blog entry by my friend and coauthor Dean Allemang [[. He says that when he suggests to people in management that their enterprise could use something such as a blog, wiki, or other self-organizing information space, they reply, "You just don't understand. Our engineers / researchers/analysts will never do that. It just won't happen!" I know this phenomenon well; I've heard it myself when I make similar suggestions to my academic colleagues about the use of technologies such as myExperiment or Twine.

Dean goes on to say, however, that there's a "new generation of people entering the workforce who have a different relationship with Wikipedia than their elders. [snip]. They share information as a natural part of their lives; why in the world wouldn't they do the same in their work contexts?

He makes a good point, one that's also true in academia. These same Wikipedia college students are becoming our graduate students and tomorrow's scientists. Just as a previous generation of students created the scientific websites that have become crucial to our daily work, this new generation is using emerging technologies to create mechanisms for sharing their interests. I hope those of us who hold more senior positions will find ways to encourage and endorse this work and reward their efforts. But even if we don't, the change will come. Frankly, I think that's a great thing.

Full Text Available At

IEEE Intelligent Systems, vol. 23, no. 1, pp. 2-3, Jan./Feb. 2008,

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