Fruit and frugivores

Publishers often don't seem to clearly see their real role in the world of scientific knowledge exchange, but libraries don't seem to, either. Both roles have evolved considerably in the last decade and a half.

For publishers it means that owning and selling content is now becoming a relic of the past, and only still exists because of the considerable inertia in the system. Their role is now clearly what it always was in disguise, namely a service to authors. The need for print and distribution made it perhaps inevitable to get a distorted view of the situation, and selling the carrier – paper – was easily confused with selling the content, but a publisher's real 'market' was, and is, authors. That's also – as appropriate for a 'market' – where the competition takes place. Only authors have a meaningful choice between publishers; libraries (readers) do not.

As for libraries, their role in the past has always included dealing with publishers. After all, they are in charge of the incoming collection of literature, and making sure that their constituency of readers has access to what it needs. Now that the role of publishers has become more clear, namely the role of service providers to authors (which is clearest with open access publishers), many librarians still feel the need to be involved, this time on behalf of their constituency of authors. But authors never were the library's true constituency, at least not when it comes to the authors' dealings with publishers.

So why should libraries take it upon themselves to play the intermediary between authors and publishers. Have authors asked for that? Have university administrators asked for that? Have funders asked them to take up that role? Or is it a consequence of the publishers asking libraries to support OA publishing? I suspect it is the latter. But libraries could decline. They are not in charge of research funding, so why should they be involved in paying for the necessary publication of research results, the cost of which is an integral part of doing research? It certainly isn't provided for in their collection budget.

There is of course nothing against libraries being in charge of the 'outgoing' collection – the papers written by researchers at the library's institution – as well as the incoming one. But it is my impression that a clarity of understanding of such a role is missing, particularly of the budgetary implications.

Take this blog entry in "The Scholarly Kitchen". It is fairly typical for such comments to take as read the idea that libraries pay for OA article processing charges. But logical it isn't. And any comparison between the cost of subscriptions and the cost of OA publishing is bound to be misleading, as it is, in the expression of Stevan Harnad, comparing apples with orangutans. (The analogy may be more appropriate than might first appear: fruit/frugivores – articles/researchers ['textivores'?].)

Library 'membership' of an OA publisher is a supporter-scheme for OA. A stimulus in OA's early stages. It can never be – and shouldn't be – a subscription substitute. Susan Klimley, the Serials and Electronic Resources Librarian in the Health Sciences Library at Columbia University, who is quoted in the blog post, got it right (I paraphrase): The library creating author funds to pay article processing fees helps to reinforce a fundamental disconnect between who creates, and who pays for, article publication. Setting up a pot of money is not going to solve that problem. Authors need to be more sensitized to the cost of producing information, and author publishing funds work against that aim.

Jan Velterop

Preparing for the previous war

Whilst ‘green’ OA and ‘gold’ OA may be equivalent when it comes to open access, to be frank, there is a difference in usefulness. The matter is one of practice rather than of principle. The issue is PDFs.

Gold OA almost always includes an HTML version as well as a PDF. And if anything is missing, it is the PDF. Green OA, on the other hand, more often than not offers just the PDF, and not a machine-readable HTML or XML version. Both are, of course, fine for the traditional form of knowledge intake, via the eye, by reading the articles. But they are not both suitable for computer-assisted intake, via machine-reading and text-mining. That is not easily possible, in practice, with PDFs, and not at all with bitmap PDFs (at least not without cumbersome procedures involving prints and optical character recognition, or OCR scanning).

Not having machine-readable access may not be a problem for everyone, but in disciplines where there is a growing over-abundance of new papers, traditional human reading is not an option if one wants to stay truly up-to-date. In areas such as the ‘-omics’ (genomics, proteomics, metabolomics), but not only in those, the ability to perform text-mining is of crucial importance.

There is no reason in principle that a machine-readable version of one’s paper is not deposited in one’s repository, and advocates of ‘only green OA’, ‘primarily green OA’, or ‘green OA first’, ought to encourage HTML deposits. They are readable by machine and human eye alike, and therefore vastly superior for the purpose of knowledge sharing.

OA to PDFs may be better than non-OA, and that of course remains the case. But relying on OA PDFs for knowledge sharing and dissemination is not dissimilar to ‘preparing for the previous war’.

Jan Velterop

On OA, language barriers, and the meaning of 'ambush'

I missed the original “Open and Shut?” blog post, but reading Walt Crawford’s “Cites & Insights” for November 2009, I saw that Richard Poynder “seems to suggest that [I] have been an effective agent for ‘ambushing the OA movement’”. Ambushing? Not being a native speaker of English, I thought I’d better look up if ‘to ambush’ could have another meaning than “staging a surprise attack”, and to read Poynder’s original article. Actually, Poynder, in his post “Open Access: Whom would you back” of 10 March 2009, doesn’t just ‘suggest’ that I have been an effective agent for ambushing the OA movement, but he asserts: “Velterop began to mastermind stage two of the publisher's strategy for ambushing the OA movement: accelerating take-up of Hybrid OA in order to marginalise Green OA.” Perilously close to libel, Mister Poynder!

Poynder is entitled to his views, of course, but it would be nice if he could expound them without misrepresenting and insulting people (yes, I am offended, and an apology on his blog is appreciated!). He doesn’t do OA any favours, either, with a blog post that is teeming with inaccuraces, conjectures, and mistaken inferences, and given that, it doesn’t surprise me that he even misses the fact that BioMed Central, now Springer, actively promotes repositories (green!) and offers services to universities to install them. Fortunately for OA, there are many more people like me, who truly work on advocating OA in its wider sense, and who are not drawn into what in my view is a narrow-minded pseudo-orthodoxy that only sees green.

The idea that whatever I did or advocated with regard to accelerating gold OA was in any way an ‘attack’ on green OA (“…in order to marginalise…” even) is preposterous, and that it could be a surprise is nothing less than absurd. The surprise is more likely that anybody could see advocating OA in general and working on gold OA as an attack on green OA.

How advocating gold OA as one of the routes to OA could be an attack on green OA is a complete mystery. The original Budapest Initiative recommended two, complementary, strategies, that later came to be called ‘green’ and ‘gold’ open access by Stevan Harnad. Both were hailed as welcome strategies to achieve Open Access, and Harnad, as well as I, and all the other participants of the meeting that effectively kick-started the ‘movement’, signed the Initiative. Poynder was not on the OA scene yet. Although the Budapest Initiative spoke of ‘OA journals’, a little while later the Bethesda Statement clarified that Open Access is a property of individual works, not necessarily journals or publishers. Poynder has a problem with so-called hybrid journals, but according to ‘Bethesda’, the OA articles in hybrid journals are true open access. No surprises there, no attack on the OA movement, no ambush. Just genuine, pure OA. Of articles in otherwise traditional journals.

Hybrid journals were an attempt at transiting existing journals to OA. In some cases it worked (Nuclear Acid Research), and in other cases not (yet). I would be the last to deny that the hybrid model is problematic. Because it gives a choice to authors, it cannot impose either the traditional model or the OA publishing model. And because of the widespread, but naïve, perception that a journal’s subscription price is, or should be, proportional to the number of papers published, it is not understood and sometimes severely criticised. Publishers, therefore, have good reason to dislike the hybrid model as well. They will, I suspect, move in the direction of full OA (what might be called the “pay-or-go-away” or “POGA” model), or revert back to subscriptions/licences (the “licence-sphere”, or “L-sphere” model).

Poynder brings up the affordability issue. And he complains about the level of article charges. That’s to the point, and fair comment. But it seemingly hasn’t dawned upon him that gold OA is open to competition, and these charges are bound to converge on a level that reflects this competition. Green OA, on the other hand, relies on the L-sphere, with its monopoloid characteristics, remaining intact for the foreseeable future. Dismissing the role of gold OA publishers in moving OA forward, because they see it as a business opportunity, is deeply misguided. It is like dismissing companies for making equipment to generate clean energy and reduce CO2 emissions on the grounds that they may benefit from doing that. Or venting the opinion that what these companies do is bad, because there might be even better techniques. Quite absurd.

Poynder seems to have it in for publishers, any publishers, be they OA publishers or not, and sees any differences between OA publishers and traditional subscription publishers as “a figment of OA advocates' imagination.” As one of the early OA advocates, I couldn’t disagree more. Besides, if OA is about publisher bashing and money only, then it’s bound to fail. Sure, a more economical system may be a desirable side effect of OA, but can’t be the core aim of it all. The mistake Poynder (and, I’m afraid, his guru Harnad) make(s) is to see so-called ‘green OA’ – seemingly not even OA as such ­– as an end in itself. It isn’t, and it shouldn’t be. The ultimate goal is to universally share (scientific and scholarly) knowledge, in what I call the noösphere (a term taken from Pierre Teilhard de Chardin), a ‘knowledge-sphere’ around the world that everyone can ‘inhale’. And OA is just one of the methods to share knowledge. Any OA. Including gold OA, and even ‘delayed OA’ (after all, ignoring the value of opening up older knowledge is devaluing older knowledge). Is delayed OA ideal? No, of course not. But OA itself is not ideal and is no more – or less – than one of the first steps to be taken to come to true knowledge sharing, to a true noösphere. OA is mostly about sharing documents, often enough just in PDF format. Access to documents is great, but it still leaves formidable barriers to knowledge sharing intact. One of the examples I have in mind is the language barrier.

English may be the lingua franca of scholarly exchange; the notion that there is no unique scientific knowledge available in other languages is absurd. And even the notion that if it is available in English its true availability is universal is a wholly unrealistic one.

But it’s not just the barrier put up by different languages. Even between native speakers of English a lot of knowledge that is published and openly available in English is nonetheless lost. Lost in ambiguity. Researchers are famously (infamously?) sloppy with their language. And publishers, although they sometimes ameliorate the worst excesses, do not, on the whole, seem to set a lot of store by disambiguation of scientific literature. OA publishers are no better than traditional ones in that regard.

Open Access is a most significant element in getting to a global noösphere, and although it’s clearly not the only element, all efforts to promote OA, in any form, help. Unlike dismissing gold OA, which doesn’t.

Jan Velterop

Open wider

There seems to be a bit of a discussion between Joe Esposito and Stevan Harnad on Liblicense, loosely about the significance of OA and of peer-review.

Quoting Joe Esposito (reacting to an article by Richard Poynder on 'Open and Shut'):

"The real thrust of the world of open access is neither green nor gold, but what I have termed "unwashed," that is, the vast and growing – and growing and growing and growing – world of material that is not peer-reviewed. Take Poynder's own article, for example, or posts to this list. Look at the material that is accumulating in IRs, arXiv, and elsewhere; think about all the blogs and Twitter feeds.

The evidence is mounting that many advocates of open access have never actually used the Internet. The myth persists that OA publishing is just like traditional publishing except that it is free to the user. While there are some segments of OA that are just that, it is a shrinking part of the open access material that is being generated. And it is minuscule compared to what we will see in the years to come.

This doesn't mean peer review is going away. It simply means that peer review is evolving to conform to the characteristics of the online medium, just as the novel grew with the printed page and tennis is a game played around a net. Increasingly peer review will be post-publication, not pre-publication. I suspect all this talk about Gold and Green is a waste of everybody's time."

Quoting Stevan Harnad (reacting to Joe Esposito):

"Or could it be that some of the opponents of Open Access to the 2.5 million articles published annually in the planet's 25,000 peer-reviewed scholarly and scientific journals have never actually done any scholarly or scientific research, hence never published in a refereed journal, and never had any need to consult one for their scholarly and scientific research?"

Open Access to peer-reviewed material is important, but to reduce the scholarly knowledge exchange to just peer-reviewed articles is to ignore the massive amounts of data and knowledge that are shared in other ways. I see the importance of unrefereed scientific published material increase. Dramatically. As long as it is open.

But what does that do to the trustworthiness of that information? Isn't the whole point of peer-review to make sure that what is published conforms to accepted standards of scientific inquiry so that the reader can have a certain amount of trust in the results that are presented? Well, of course. But what is presented in journal articles are mostly results derived from data. Interpretations and annotations of data. Seldom the data themselves. Journal publishing evolved in the past, when the physical reality of sharing actual raw data was nigh impossible, so almost every scientist had to rely on the interpretations as published in journals. But now that we can share the raw data (view Tim Berners-Lee's call for sharing raw data), and tools to manipulate those raw data become widely available, relying on journal articles may well take second seat. And now that instant comment on data as well as on journal articles has become possible, with blogs, twitter, and what not, review after publication is a reality of today (albeit not used all that widely yet).

Furthermore, technology is emerging that is able to quickly identify if data and articles are in essence in line with the scientifically accepted knowledge of today, and is merely confirmatory in nature, which makes the outliers stand out. Those can either be scientific rubbish, or potential breakthroughs, and a peer-review process is well-spent on them, ante (the technology is a great tool for editors!) or post publication.

Peer-review may or may not survive in the way it is now. But it seems clear to me that openness of published articles as well as raw data is, after initial hesitant steps, bound to show explosive growth.

Jan Velterop

Harold Varmus...

...on the Daily Show with Jon Stewart: video

Getting the right arguments right

Congressman John Conyers has publicly responded, on the Huffington Post, to the call from Larry Lessig (initiator of Creative Commons) and Mike Eisen (initiator of PLoS) to speak up.

Peter Suber, in turn, responded in detail to John Conyers. Admirable detail, and a discussion with well-articulated arguments, like this, is the way forward, in my view. In an earlier post, 'Aiming at the right target', Peter is saying "Let's not make it easy for the bill's supporters to say that the critics simply don't understand". He is right, and in that vein I feel that I should humbly offer some advice.

In one of his arguments he points out the problem with the old NIH policy, which, he says, "...had the effect of steering publicly-funded research into journals accessible only to subscribers, and whose subscription prices have been rising faster than inflation for three decades". It is the second half of this sentence that is misleading. Technically it is true, of course, especially if he refers to average prices. But it is misleading by omission.

There are at least two reasons why the comment about inflation has to be put in context in order to avoid being misleading:

1. The average journal prices have risen faster than inflation, but the average number of articles published in them as well, reflecting the above-inflation rise in scientific output. The correct measure should not be the average journal price, but the average price per article published. That may still have risen faster than inflation, and I haven't done the math, but having those data would turn the argument of inflated prices into a real one, or render it irrelevant.
2. Secondly, scientific journal publishing is a global pursuit. Inflated prices may just as easily be an effect of a precipitiously plunging currency (at the library's side), or a steeply rising one (in the publisher's country), as of publishers' pricing policies. Indeed, if much of the work hadn't been sweat-shop-ized, outsourced to low-wage countries, price rises might have been much bigger. As with so many of the goods we purchase these days.

I think the arguments for open access are strong enough without the inflation red herring.

Jan Velterop

Footing the Bill

Should you need any further evidence that the American democracy is in essence a lobbyocracy, the anti-open-access bill of congressman John Conyers provides it. Of course it isn’t called the ‘Anti Open Access Bill’, but the “Fair Copyright in Research Works Act”. But then, this is the way of the world these days: euphemania.

The Americans are not alone in living in a lobbyocracy, where powerful special interests rule the roost. In other countries the people do as well. Take Australia. But Australians don’t seem to do euphemisms. They call a spade a shovel, and they have a web site to address these matters, unambiguously called lobbyocracy.org, exposing money flows in politics. (By the way, lobbyocracy.info and lobbyocracy.us are still available today, March 3rd 2009, should anyone want to do the same in the US.)

It is amazing how misguided the reasoning is of Conyers' bill (Peter Suber does a sterling job exposing the fallacies in his Newsletter). "Fair copyright in research works", huh? For a scientist, fair copyright is a notion used to ensure attributed plagiarism, otherwise known as ‘citation’. It is one of the most important things about copyright. No, it is the most important thing about copyright. For a researcher.

For publishers it’s different. For them, copyright, or rather, the transfer of copyright, is a way of payment for the services they render. Though they call themselves publishers, these services are hardly to be called publishing any longer (in the sense of ‘making public’). They are procedural services resulting in the labelling of an article as ‘peer-reviewed and accepted by’ a given journal. The act of publishing is on the web these days, and anyone can do it. This is, of course, precisely the problem. The publishers’ business models are based on the idea that it is they who are publishing. They did, but that’s the past, when print was the only means of dissemination, of making public.

That said, the 'publishers' do fulfill a role that is needed in science. Researchers are required to publish in peer-reviewed journals. Essential for survival in the ego-system. ‘Publish or Perish’, remember? Of course, they also need to read, although the imperative isn’t quite there. No such thing as ‘Read or Rot’, after all. But to publish is the key to any career as a scientist at all. This fact should inform the business models: he who has the most interest pays.

Back to copyright. For publishers who think they publish, the transfer of copyright is just a way in which the author pays for the publishers’ services. If the value of that copyright is eroded – or in the view of some publishers even nullified – by funders’ mandates and embargoes, they have a problem. The most straightforward way out of that is of course substituting a monetary charge for the transfer of copyright. This is what the open access publishers have understood. The so-called ‘gold’ open access model.

So what should traditional publishers do? (I’m assuming that an egregious bill such as Conyers’ will fail.) Should they refuse articles that come with open access mandates attached? After all, they do not come with the required ‘payment’ of full copyright transfer. And embargoes are problematic (although the argument that articles have appreciable economic value after the typical embargo period of 12 months is rather weak, to say the least, seeing that almost all of the revenues of a publisher are realised in advance, as the subscription and licensing model demands). Refusing is hardly possible if they want to stay in business at all, since the authors are obliged by their funders to withhold transfer of copyright for anything other than temporary (a period of generally a year) and have no choice. Here, too, open access publishers have the advantage. After all, they simply do refuse articles that come without payment. With some discretionary exceptions, their policy could be expressed with the slogan “Pay, or just go away!”

But one thing I rarely see or hear. That is the notion that mandates with embargoes are a threat to ‘gold’ open access publishers as well. Especially the mandates with short embargoes, of, say, six months. What if researchers can wait that long to see most articles? And authors to publish their articles? Neither on the side of the reader or the writer would there be an incentive to pay for the necessary service that publishers do provide, be it in the form of transfer of copyright or plain money.

Which brings me to my final point. Payment for ‘gold’ open access publishing the way it is done now is also problematic. The reason is that payment for the services of a publisher is fully loaded on the published articles (and the same is true for ‘toll-access’ publishing as well, of course). And yet, much of the work is related to articles that do not come through the peer-review process and are rejected. A truly fair system would charge a submission fee, for which the publisher would organise the peer-review process. Like a driver’s test. You don’t just pay when you’ve passed and get your driver’s licence. You pay every time you take the test. It would probably also mean alleviation of the peer-review burden, since submissions would be carefully pitched to the journal of the appropriate level for the article, and not be allowed to cascade down the journal hierarchy.

Could that be a bill to put before Congress? Requiring that all scientific research is published with open access and that the only charges scientific journals can make are submission charges?

Jan Velterop

Industry-funded research IFfy?

In his column Bad Science, in The Guardian on Saturday 14 February, Ben Goldacre drew attention to an article in the British Medical Journal by Tom Jefferson et al in which the observation was reported that...

"Publication in prestigious journals is associated with partial or total industry funding, and this association is not explained by study quality or size."

The Impact Factor (IF) of the journals in which research funded by the public sector was published averaged 3.74 and the IF of the journals in which industry-funded research was published averaged 8.78. As Impact Factors go, that is a substantial difference. And, as Jefferson et al indicate, there was no discernable difference in terms of quality, methodological rigour, sample size, et cetera between the articles in question. Goldacre doesn't have an explanation. The suggestion is given in his column (he admits it is an "unkind suggestion") that it may have to do with journals' interest in advertisements and reprint orders – which can indeed be massive – from the very same industry that funds the research these journals publish. He doesn't say it, but this could mean, of course, that the journals accept articles based on research funded by industry, particularly the pharmaceutical industry, more readily than articles based on publicly-funded research.

I don't have an explanation for the phenomenon, either, but I doubt that journals accept industry-funded articles more easily than public sector articles. For a start, most publishers do not have in-house Editors-in-Chief who decide what's published and what not. That doesn't mean the publishers cannot have an influence on those Editors, but often it is already so difficult for them to get Editors to comply with everyday, sensible wishes, that I think this would be rather far-fetched. For publishers that do have in-house Editors-in-Chief, such influence may be more easily exerted.

A hypothesis I can imagine, however, is different and less sinister, although also to do with the massive numbers of reprints disseminated by the pharmaceutical industry. But this hypothesis would reverse cause and effect. Might it be that because of the wide dissemination, availability, and visibility of these reprints, the industry-funded articles are cited more often? After all, we know that articles are not only cited because they are the most appropriate ones, but also simply because they are the appropriate ones known to the author. (Sort of like when you ask a 'randomer' – a word I learnt from my 18-year old daughter and that I guess means random person – for the best restaurant in town, you are likely to get the best restaurant he or she knows, which is not necessarily the best restaurant in town). If articles based on industry-funded research are cited more often, the journals in which they appear get a higher Impact Factor.

If this hypothesis holds water, it would mean that wide availability is one of the important factors – with dissemination and visibility, and of course relevance – for being cited. In other words, could the results described in the BMJ article constitute evidence that open access could have a similar effect on Impact Factors as that – still hypothetically – caused by the massive numbers of reprints that the pharmaceutical industry purchases and disseminates?

Food for further study, I would think.

Jan Velterop

Deploring or exploring?

When Homo sapiens was still in the early stages of his evolutionary development, he hadn't yet figured out many other uses for water than to drink it. And perhaps to bath and swim in it. This is conjecture, of course, but the earliest evidence of the use of boats, or even just rafts, dates from much later than the emergence of Homo sapiens, so assuming that he was just using water to drink may be an acceptable point of departure for my story.

Water is one of the most abundant resources on earth, but if you're just using it to drink, you don't quite get much of its potential out of it. When people invented rafts, and developed boats – probably in the form of dug-out logs – a whole new world, literally, opened up to them. They all of a sudden didn’t have to see expanses of water as impediments to getting to the other side, and once navigation was thus discovered, waterways and seas became the most important transportation routes upon eventually empires were built. The rest is history, to use a cliché.

There is something similar going on with the way we use information. The image that I have in mind is that there are virtually oceans of information available to humans, but that the only use we make of that information is ‘by the drink’ – by reading articles or bits of articles. That way, the knowledge contained in the ever growing seas of information (just think of the amounts of information coming out of, say, microarray experiments), is unlikely to come out in full. There remains an enormous amount of “unknown knowns” (apologies for using a Rumsfeldism) if we do not find a way to do more with information than read articles and books, or consult databases. We have to develop ways of extracting knowledge out of large amounts of information. Thousands of papers, and thousands of database entries. Or hundreds of thousands. We can’t read those. We have to invent the equivalents of rafts and boats to navigate information. And still read, but manageable amounts (after all, we still drink, too).

In whatever information navigation we already do, we stay very close to the coast, and only to the coasts we know. We search. And we pretend that we are navigating the vast expanse of knowledge that search capabilities on the internet have opened up. But are we? Is searching not a retrograde step in terms of knowledge discovery? Aren’t we inclined to search for knowledge and relations between bits of information we already know to exist? And so foster more homophily in the process than before, when large-scale search wasn’t yet possible? And stay in our knowledge comfort-zone. Look for confirmation rather than for falsification. We should give chance more of a chance. Serendipitous discoveries are, after all, the 'stuff' of which breakthroughs are made.

Some people deplore the fact that more and more information becomes available. They talk of information overload or overabundance. And if the only thing you can imagine doing with it is read (‘drink’), then you may have reason to be negative about it. If you think like this you may seek solutions in selection, in limiting access, in having the choices made for you. But if you can imagine truly navigating the ever growing seas of information, you will not deplore the abundance, but instead, start exploring it.

Jan Velterop

The discovery of more knowledge (in repositories, research web sites, blogs, and the like)

In my previous post I was announcing the knowledge discovery 'button' that could be used to enhance any repository, science blog, or any researcher's, scientific society's, or publisher's site for that matter. Well, it is here now. Available to all. Incorporation of a small bit of code will equip any site who wants it with the knowledge discovery 'button' as you have it on this blog in the upper right hand side (the orange one that says "discover more..."). And with all the functionality that comes with it, of course. Even more functionality is being developed.

It really is a small bit of code that needs to be incorporated, and the fact that I managed to do it myself in this blog should give confidence to even the least HTML-savvy person that it really is easy. This is the code:

<script type="text/javascript" src="http://conceptweblinker.wikiprofessional.org/wikibutton.js"></script>

Just cut and paste it in the code of your repository, web site or blog and enhance its ability to serve up relevant additional knowledge to its readers.

As an example of what it might look like, click the "Discover more..." button and then look at this abstract of an article by Matsuda et al., entitled Silencing of caspase-8 and caspase-3 by RNA interference prevents vascular endothelial cell injury in mice with endotoxic shock. (Cardiovascular Research 2007 76(1):132-140;
doi:10.1016/j.cardiores.2007.05.024).

Abstract
OBJECTIVES: Septic shock and sequential multiple organ failure remain the cause of death in septic patients. Vascular endothelial cell apoptosis may play a role in the pathogenesis of the septic syndrome. Caspase-8 is presumed to be the apex of the death receptor-mediated apoptosis pathway, whereas caspase-3 belongs to the "effector" protease in the apoptosis cascade. Synthetic small interfering RNAs (siRNAs) specifically suppress gene expression by RNA interference. Therefore, we evaluated the therapeutic efficacy of caspase-8/caspase-3 siRNAs in a murine model of polymicrobial endotoxic shock. METHODS: Polymicrobial endotoxic shock was induced by cecal ligation and puncture (CLP) in BALB/c mice. In vivo delivery of siRNAs was performed by using a transfection reagent (Lipofectamine 2000) at 10 h after CLP. As a negative control, animals received non-sense (scrambled) siRNA. RESULTS: Marked increases in caspase-8 and caspase-3 protein expression in CLP aortic tissues were strongly suppressed by treatment with caspase-8/caspase-3 siRNAs. This siRNA treatment prevented DNA ladder formation and less phosphorylation of the pro-apoptotic protein Bad seen in CLP aortic tissues. Transferase-mediated dUTP nick end labeling (TUNEL) revealed that the appearance of apoptosis in aortic endothelium after CLP was eliminated by this siRNA treatment. Although all of the control animals subjected to CLP died within 2 days, administration of caspase-8/caspase-3 siRNAs indefinitely (>7 days) improved the survival of CLP mice. CONCLUSIONS: Gene silencing of caspase-8 and caspase-3 with siRNAs provided profound protection against polymicrobial endotoxic shock. The prevention of vascular endothelial cell apoptosis appears to be, at least in part, responsible for their beneficial effects in endotoxic shock.

If you click on any of the highlighted concepts (the colours disappear after a few seconds, so that you can read the text more easily, but they can be brought back by mousing over the button), you will get a number of options to explore further. First of all, 'add to search', which automatically extends the search argument with synonyms of the concept in question. For instance, if I search further in this way with RNA interference the search is automatically reformulated as "RNA Interference" OR "Post-Transcriptional Gene Silencing" OR "Posttranscriptional Gene Silencings" OR "RNA Silencing" OR "RNA Silencings" OR "Quelling" OR "RNAi" OR "cosuppression" OR "Sequence-Specific Posttranscriptional Gene Silencing".

The options of 'related authors' and 'related publications' are self-explanatory, I guess, and the option 'connected concepts' leads you to a page on which you find concepts that are connected to the concept you clicked on in one of three ways:

1. there is a factual connection – established in a process of curation, e.g. via the peer-reviewed literature or a curated database such as SwissProt;
2. there is a co-occurrence in the same sentence in the peer-reviewed literature; and
3. even though 1. or 2. don't apply, there is such an overlap in the connections that each of two concepts have, that there is a strong 'predictive' association between them, strong enough to 'invite' research to establish if the concepts are indeed factually connected.

Each factual and co-occurrence connection has an 'explain' option with links to the literature from which the connections were 'mined', and so to further discovery possibilities.

There are also links to relevant books, and even more is in the pipeline.

Go forth and multiply (the use of this button)!

Jan Velterop

Repositioning repositories

There are more and more repositories and their significance for open access as well as for the universities and institutions that operate them grows, too. Yet many repositories have fairly basic functionality. Some don't mind, and see repositories as a way merely to provide open access or to archive the institution's output. This is a pity. Repositioning them, making repositories attractive places to come to for researchers – and to come back to – would greatly help in their potential success. Many are already on that track. And various developers of repository software, such as MIT's DSpace, are already in the process of starting to experiment with embedding technology that helps the discovery of more knowledge by making it possible for repositories to become 'portals' of sorts.

It's easy enough. Have a look at the functionality that can soon be added to any repository (or blog, or personal site, for that matter) and click the 'button' on the upper right hand side of this page that gives you the opportunity to discover more knowledge. Within weeks we hope to make the code for that button publicly and freely available, for anybody to use on any site (watch this space!). And even more functionality is being worked on and in the pipeline. For now, this technology allows you especially to discover knowledge in the main 'domain of its experience', the biomedical areas.

Below, I am listing a few of the more than a million terms that are recognised as concepts and when you click on them, they open up a 'balloon' with links to more knowledge. I'm just doing that because in this blog you may otherwise not really find too many scientific concepts.

But look at these: hepatic stellate cell – immunoreactivity – squamous cell carcinoma – nonhomologous DNA end joining – monoamine oxidase type B (MAOB) – nuclear envelope – rough endoplasmic reticulum – Kupffer cells – plasma membrane – Ku70.

The first thing you can do is search further. The search will automatically include synonyms. Even something simple as skin is, when used to search further, automatically expanded into the search argument: "Skin" OR "Integument" OR "cutaneous tissue" OR "skin system" OR "Integumental system".

But you can also see authors and publications that are specifically related to the concept you're looking at. And you can see what all the other concepts are that are connected to this concept, and how they are connected. All connections are explained, and these explanations have links to the original source from which the connections were 'mined'.

Of course, this is just the beginning. More knowledge and information that is permanent and relevant can – and will – be added in these balloons. If there is anything you would like us to consider to add, please feel free to give feedback. We do like to hear from you! (Use the 'comments' link below or the email address in the top of this blog.)

Jan Velterop

Giving chance a chance, or the usefulness of serendipity

A post on the scholarly kitchen, entitled ‘Citation Controversy’, particularly a reference to the principle of least effort, sparked the train of thought leading to this post.

Scientific articles have references, which represent the connection of the article to other articles, and thus other knowledge. Articles in Wikipedia often have references, too. Although it is not rare that one sees the message “This article or section is missing citations”. The ‘Principle of least effort’ article in Wikipedia carries this message (on the date of posting this). Ironically demonstrating the principle, I think. Authors are often quite parsimonious when it comes to adding references to articles. And when references have been added to an article, there isn’t often a thorough check on whether they include all or enough of the appropriate ones. The omission of obvious references may be picked up by reviewers, but the omission of less obvious ones is easily missed. One of the sad things about omitting references is that it may reduce serendipity.

I have a suggestion for ‘Wikipedians’ who wish to add appropriate references and links to Wikipedia articles. In particular to Wikipedia articles in the areas of health and life science, and so encourage serendipitous discovery. I advise them to go to what I informally call 'wikimore', an enhancement layer where they will find that the text of Wikipedia articles is enriched with highlighted concepts. By clicking on a number of those highlighted concepts and adding them to a search query, you can search the appropriate articles to refer to in, say in Google Scholar, or in Wikipedia itself, and when found, add those references to the Wikipedia article, as a good Wikipedian would.

For instance, by clicking on the concepts ‘information seeking behavior’, ‘design’ and ‘library’, and subsequently searching in Google Scholar, I find this article:

Comparing faculty information seeking in teaching and research: Implications for the design of digital libraries, by Christine L. Borgman et al., in the Journal of the American Society for Information Science and Technology, Vol. 56, No. 6. (2005), pp. 636-657. DOI: 10.1002/asi.20154.

An interesting sentence from that article: “…faculty are more likely to encounter useful teaching resources while seeking research resources than vice versa.” In my view this demonstrates the drawback of a least effort approach (I like to call it the ‘laziness principle’), which by its very nature militates against serendipity. And yet serendipity is one of the most important routes to real breakthroughs in knowledge and understanding. A quote from an article by M.K. Stoskopf: "it should be recognized that serendipitous discoveries are of significant value in the advancement of science and often present the foundation for important intellectual leaps of understanding".

I’m not sure if the article I found (one among many others) would be a good reference to add to the Wikipedia article on the ‘principle of least effort’, but I do hope you can see that with wikimore you can, starting from a Wikipedia article, embark even better on a journey of serendipitous discovery than you already can without the enhancement layer that wikimore provides, since with wikimore, i.e. the concept web enhancement as applied to Wikipedia, every concept that is recognized in the text is a link to further information in itself, a ‘reference’, if you wish.

And while you’re at it, you might want to take a look at the ‘knowlet’ of ‘information seeking behavior’, and explore the concepts with which information seeking behavior is connected in the life and medical science area.

Happy exploring!

Jan Velterop

Open Access Day

Though I haven’t posted for a while on The Parachute, today, on Open Access Day, I feel I should.

Unfettered access to scientific research results is in my view one of the ‘infrastructural’ provisions that enables science to function optimally. So why isn’t open access universal and what can be done to make it so?

After all, open access is easy. Just as I am posting this entry on a blog – open and freely available to any reader, anywhere, any time – I can post a scientific article. It is increasingly unlikely that there are many scientific researchers in the world who don’t have the possibility to publish their articles on a blog or in an open repository. And I use the word ‘publishing’ advisedly. The notion that publishing is something that happens in journals is rather outdated since the emergence of the Web. (Isn’t it interesting, by the way, that our word ‘text’ is derived from the Latin ‘textus’ which means ‘web’?)

Actually, I have to correct myself here. Journals do publish, but they are not needed for the act of publishing by itself. Publishing can easily be done by the authors. The significance of journals lies not so much the scientific content of their articles, but in the metadata of those articles. And by metadata I mean not so much the information about volume, issue, page number, et cetera – though that is useful for unambiguous citation – but in particular the information indicating that, and when, the article has been peer-reviewed (and often enough improved) in the course of a given journal’s editorial process. The role of a journal is to formalize an article, to affix the ‘label’ of the journal to it, indicating not only that it has been peer-reviewed, but also slotting it into what might be called a ‘pecking order’ of scientific publications. One only has to consider the weight attributed to a journal’s Impact Factor to get a sense of how important that pecking order is, or is at least perceived to be.

One of the reasons we do not have universal open access yet is that we keep on confusing the two: publishing (i.e. making public) on the one hand, and formalizing (i.e. affixing a scientific ‘credibility’ label) on the other.

Journal publishers, although still called ‘publishers’, are, in the Web era, mainly in the business of organizing the latter: affixing the label. That is no sinecure, as anyone who has done it will confirm. And as long as it is deemed necessary in the scientific ego-system – in order to get recognition, tenure, funding – it needs to be done. But it should not be confused with making research results openly and freely available.

Journal publishers have been in this business for decades, maybe even centuries. In the print world, publishing and formalizing were completely interwoven, possibly without anyone realizing it. The publishers were paid for their efforts by both readers and authors, though in different ways. Readers paid for access to the information via subscriptions, and authors for affixing the journal label to their articles by transferring their copyright exclusively to the publisher. That exclusively transferred copyright was worth a lot, because it enabled publishers to sell access to their journals, since anyone who didn't hold the copyright (which after copyright transfer included the authors) was prevented from disseminating articles, at least on any significant scale.

But we live in the Web world now, no longer in the exclusively print world. The value to publishers of copyright has decreased significantly since authors either started to ignore it – no-doubt encouraged by the opportunities the Web offers for wide dissemination – or were forced to limit the exclusivity of their copyright transfer, for instance because of mandates to make their articles openly available within a given period of time (within a year, for instance, in the case of the NIH mandate).

Given that open access is a great good to science and society as a whole (I treat this as an axioma), what to do?

Two options for researchers, not mutually exclusive:

1. Publish research articles freely and openly on the Web, on blogs, in repositories, et cetera, especially in those that allow public comments, and let laying the articles open to such public comments take the place of peer-review. This option may realistically be available only to tenured, established scientists and the very young ones with an independent and iconoclastic frame of mind.
   
2. Publish in the ‘traditional’ journal system, but choose journals that accept payment for organizing the peer-review and formalization process, and then make the article in question freely available with full open access immediately upon acceptance, and back this up by depositing a copy of the article in an open repository. This option may realistically be available only to funded scientists, but those who are not able to source funding for it can always resort to option 1.

A few remarks to conclude: There are indications – so far anecdotal – that ‘informal’ publications are gradually being taken more seriously by the science community and that helps the popularity of the first option. There are also indications that even the new and relevant scientific literature is becoming so overwhelming in size in some disciplines that proper manageable ways to get an overview of the state of knowledge, which progresses daily, need to be found. The analogy, if you wish, of a dependable weather report as opposed to just knowing the general climate supplemented by looking out of the window.

And lastly, isn't it fitting that this week, at the Frankfurt Book Fair, the worldwide publishers' jamboree, the inclusion of open access publishing into the mainstream of science publishing is being presented? I'm referring of course to the take-over of BioMed Central by decidedly mainstream publisher Springer.

Jan Velterop

Open Access and WikiProfessional

One of the first WikiProfessional instances is WikiProteins. An article in Genome Biology describes it in great detail. The lead author of that article, Barend Mons, reacts to the post by Euan Adie on Nature’s Nascent blog (“WikiProteins is a croc”, later changed to “WikiProteins – a more critical look”). Because it is important to understand the open access nature of the WikiProfessional project, I am reproducing Barend's reaction to the blog entry in its entirety here.

Jan Velterop

Although the rather sour blog by Euan is quite an exception in the overall positive reactions we receive on the beta site of WikiProteins, I feel that a matter-of-fact reaction from the lead author of the article in Genome Biology that announced it is warranted. It goes hereby.

First of all on Authorship: Jimmy [Wales] was instrumental in making the initial contacts between me and Gerard Meijssen who was then working on WiktionaryZ, now Omegawiki. He also gave invaluable advice on several aspects of the system and he therefore deserves as much of an authorship acknowledgement as the average senior author/professor who ‘conceived of the study’. See also Gerard Meijssens’ Blog about that.

On the interface etc., we all know this is beta and we struggled for a long time to make it as ‘good’ as it is. Obviously a flat file is easier than managing a relational database and therefore the interface can never be ‘really easy’. I agree with Peter Jan [one of the commentators on the Nascent blog entry] that constructive criticism would have been more useful.

Criticism on the commercial nature (as it were) of a company on a blog made available by another commercial company – one that makes money on others’ scientific contributions for as long as we have been studying nature – is a bit peculiar as well. With the involvement of Amos Bairoch, Michael Ashburner , Mark Musen, Abel Packer, Roberto Pacheco, Matt Cockerill and many others in this process, not to mention Jan Velterop’s reputation, it seems to me that the OA nature of the projects is sufficiently safeguarded. With my personal background in malaria, working for 15 years with colleagues in developing countries, I also built a public track record in pushing free access to information for developing countries.

The content in WikiProfessional applications is completely freely available under the Creative Commons Attribution license (we are working on making author credits more clearly visible). The Knowlets are indeed proprietary as we create added value and apply algorithms that by themselves now have taken several million dollars to develop. It has proven exceedingly difficult to get sufficient public funding for this project, which has been carefully internationally discussed and prepared for several years. Bill Melton and Al Berkeley are to be highly commended for taking the risk to fund the vision.

Also the Knowlet space is in Open Access for non-commercial use. I sincerely hope that seasoned investors like Bill and Al would be more imaginative than trying to monetize this site – and the others still to come – by ads only.

On potential fear of competition: let me tell everyone up-front that the authors on the paper have every intention to connect all information on important concepts via WikiProfessional, not trying to put it behind any barrier or to compete with anyone. Some may see us as a competitor to IHOP or Wikipedia pages on biomedical concepts for instance, which is not true, as you will soon see.

We are planning to add locally maintained databases on genes such as www.dmd.nl to the appropriate concept page in WikiProteins much more prominently placed than today (now an indirect link via SwissProt data), but also locally-maintained databases on single gene mutations such as the growing number of Leiden Open Variation Databases (LOVD’s). We have a project starting to map all concepts in WikiProfessional, including all biomedical concept pages, to the corresponding pages in Wikipedia and other emerging wiki’s. People who find the WikiProfessional interface too difficult will be soon able to contribute to their own wiki of choice and their contributions will be seen in WikiProfessional anyway.

We collectively ‘own’ the basic data and anyone is free to ‘add value’ to these and make that ‘added value’ freely available to all or just for public not-for-profit use. Knewco is just one of the companies that derives value from the data and has decided to make the added value available to the scientific community for free.
I cannot wait until Nature will be Open Access as well, at least as far as the scientific articles are concerned. Then it will be easier to make full use of Nature content for the benefit of the scientific community.

One more point on equity and access: the collaboration with our Brazilian colleagues, with whom I co-developed and signed the Salvador Declaration on Open Access, referred to in the supplementary data of the Genome Biology paper, will soon result in crossing the language barrier to Spanish and Portuguese. The record for my beloved ‘malaria’ in Omegawiki will show you our ambition on in how many languages we would like to support the indexing on-the-fly. For Free.

I hope these further explanations take away at least the worst of Euans fears. I see in today’s version of the blog that he did not only change the original title of the contribution, but I also saw a more balanced reaction to Peter-Jan Roes.

However, Euan, if you still feel that some of your comments were justified and not yet properly addressed, please substantiate your claims and in the process it is highly appreciated if you give some constructive criticism. You would really help the community – and us – by doing that. Let’s keep discussing this project to make it better.

The meanings of 'free'

I've received questions about Knewco's WikiProfessional. How free it is; and if it is free as in 'free beer' or free as in 'free speech'.

Life's never simple: it's a combination of both.

WikiProfessional's million minds approach does rely on user input. That's nothing new in science – in fact, the whole scientific knowledge edifice relies on user input. The user-generated content in WikiProfessonal is indeed free as in 'free speech'. The relationship-concept matrix (the knowlet-database, dynamic, relational, and constantly recalculated, reacting to any infusion of new knowledge) is also free to users, but free as in 'free beer'. It took considerable effort to develop and build it – and to maintain it – so it actually is (will be) paid for, by advertising and sponsorships we hope. The users 'pay' as in 'paying' a visit, and 'paying' attention, which we can then use to attract appropriate advertisers. (For some reason we haven't quite figured out yet how to survive on plain air, and we need to generate income to sustain our activities.)

It is important to distinguish the knowlet part and the wiki part in the WikiProfessional database. Knewco (the Knowledge Navigation and Expert Wiki Company) owns the first one and the knowlet is patented. In due time, there will be feeds available from the knowlet database to whoever wants to (or pays for, this might typically be a premium service).

The wiki part of the database on the other hand contains publicly as well as privately available authority and community contributions. We don't 'have' those; we just use those, as anyone else can do, at least with regard to the public ones (one has to approach the 'owners', authorities – NLM, Swissprot/Uniprot, etc. – for these authoritative databases). With respect to the community annotations and contributions, those are freely available under a CC-BY licence (Creative Commons Attribution Licence), and eventually we may have this available in a suitable form for downloading. There may be a potentially fruitful collaboration with Open Progress with regard to standardizing the download/exchange format.

Meanwhile, go to WikiProfessional, use the system, give us feedback, register and contribute, and work with us on spreading scientific knowledge via collaborative intelligence.

Jan Velterop

A rose by any other name

"Doctors often exude an air of omniscience, but in truth they are surprisingly ignorant."

Thus began an article in this week’s Economist. Harsh language, but many a doctor, or other professional, including scientists, will recognize himself or herself in these words. The article in The Economist isn’t specifically about that, but the sense of information overload is surely a major contributory factor to this 'surprising ignorance'. After all, a lot of the information one gets to digest is ambiguous, redundant, fragmented, inconsistent, to name a few problems. As Herbert Simon, an American political scientist once observed: “What information consumes is rather obvious: it consumes attention. Hence a wealth of information creates a poverty of attention.” The problem of the information glut in a nutshell.

Today saw the launch of an attempt to combat this abundance, redundancy, fragmentation and inconsistency: WikiProfessional.

The idea is that the combined efforts of a ‘million minds’ would be able, in a collaborative intelligence exercise, to refine a system that 'distills' the essence of established knowledge as well as points to new knowledge that has a high likelihood of being established soon. What it all entails is explained in an open access article in Genome Biology.

The concept (so to speak) is so far optimized for the life sciences and medicine, but there is no reason why it shouldn’t work in other areas as well. And in languages other than English. It is based on concepts, and those are of course valid in any language. It’s just the words or descriptions used for them are different. As Shakespeare already noted in Romeo and Juliet: "What's in a name? That which we call a rose by any other name would smell as sweet."

Just imagine what that means. One of the beauties of the concept approach (as opposed to the keyword approach) is that search terms in one language could, for instance, yield search results in another. Think of Chinese researchers searching with Chinese terms for English literature (they can read English, but may find it more difficult to come up with search terms in English, in the same way that I find it sometimes easier to search with Dutch terms), yet getting served up with English search results. Things like that. Wonderful.

(I have to declare an interest: I’m running Knewco, the company behind WikiProfessional).

Jan Velterop

Wiki temperatures

In the Chronicle of Higher Education Jeffrey Young reports about a 'frozen' Wikipedia being more academically useful for students than the current version, which can be – and is – edited all the time, sometimes resulting in a lot of heat. There is something tremendously attractive in having unfettered editing possibilities, but also in having stable, authoritative articles in such an extremely useful web resource as the Wikipedia. In an academic environment, one would ideally have both. WikiProfessional, which is specifically conceived for the academic and professional environment, actually gives both. On the one hand it presents stable, vetted and authoritative knowledge, yet on the other hand it gives the utterly useful and necessary option for knowledge to be supplemented and annotated in real time by anyone wishing to do so. Both the authoritative version, and community annotations and additions, are presented side-by-side. Only when annotations and additions are deemed acceptable by the professional or academic community in question – peer-reviewed in one way or another – are they elevated to the level of 'received knowledge'.

For open access WikiProfessional presents a nice additional opportunity: 'annotations' can be links to particularly appropriate and relevant articles. And if such links were made to freely available versions of the articles in question, this would give WikiProfessional some of the functionality of a federated repository, not just enhancing an article's exposure and findability, but at the same time putting it in the right context in the Concept Web. This, in turn, may well further increase the chances of such an article to be cited.

Jan Velterop

Dealing with abundance – getting more out of the science literature than you thought possible

Open access is adding to the abundance of scientific information available to us. It is to be expected that this abundance will be growing fast, with the growth of open access. This is good, because only comprehensive and unfettered access to the science literature will make it possible for us to be truly abreast of the scientific progress that's being made.

On the other hand, however, it will present us with even more challenges than we already face in terms of being able to deal with all that information. In certain disciplines reading all the relevant papers to our research topic means digesting thousands of papers per year – enough to fill our entire working time. Without assistance from the processing capabilities and speed of computers, we cannot hope to keep up with emerging trends in our chosen fields.

Few scientists can properly cope with mushrooming information and were they to read all the articles relevant to them, they would find that they almost always contain a very large amount of information already known to them. That redundant information is usually provided for the sole purpose of context and readability. The amount of actual new information is often surprisingly small and could have been conveyed in one or two sentences if the context were clear. Yet the essence of the scientific discourse is captured in those few sentences. The surrounding text of articles is, if you wish, the packaging in which the essence is transported, and analogous to the mass of fluffy stuff that's surrounding breakable item that's being shipped: emballage.

At Knewco, the company that I now work for, we aim to provide an environment for concentrating this scientific discourse – 'distilling' it from the abundance of sources, if you wish – and make it more productive by making it computer-processable. Very few scientists can read and digest all the articles and database entries that they would need to read and digest in order to synthesize the essence of the knowledge they need. So what we do is to enable and foster collaborative intelligence between machine processing power and human brainpower. Knewco 'distills' information to the essence of knowledge content from millions of documents, enriching it in the process with linked concepts and context.

This is not the same as making it possible to locate the one right document out of the abundance available. It is identifying 'atoms' of knowledge about a given concept from the literature and combining these atoms into 'molecules' of knowledge (we call those "knowlets" – a knowlet connects facts). Just as a graph can give you in one glance the essence of an enormous array of numbers in one glance, the knowlet gives you the essence of an enormous amount of scientific literature. It's like reading out of a picture instead of text. And as "a picture is worth more than a thousand words", a knowlet could be said to be worth more than the text of a thousand articles. Knowledge redesigned, as it were.

Perhaps more importantly, since a knowlet is a computer artifact, it can be used to identify related information, predict trends and intersections in data (see it as a kind of topology of knowledge), be used in combination with other knowlets of more complex concepts, and be updated in real time to keep information current up to the minute.

For technology of this kind to be optimally effective for scientific knowledge discovery, access to the literature is not sufficient by itself. It goes without saying that the source documents must be computer-readable to be optimally usable. Publishers as well as repositories may wish to take this to heart if they are serious about helping to speed up the pace of scientific progress.

Jan Velterop

Onwards from open access

As many of my readers will already know, I have recently decided to leave my position of Director of Open Access at Springer for that of CEO of Knewco Inc. Several reactions that I have since received indicate to me that my move is not necessarily understood by everyone, and I’ve even seen speculations that my leaving open access might mean that it is not going anywhere at Springer.

Let me say the following to that. First of all, OA has developed some very solid roots within Springer and I am most confident that OA is being further developed with alacrity by my successors at Springer.

Secondly, I don’t feel that I am leaving open access. Open access is not some club that one is a member of or not; it is a 'thought form' that one adheres to. And open access is only one of the ways in which the speed, efficiency and quality of scientific discovery can be enhanced.

Looking back on my career, I feel that my motives haven’t changed much. When I was working on IDEAL/APPEAL* (at Academic Press) in 1994-95 and later, I did this on the premise that there must be better ways to disseminate the research papers published in journals than just via relatively small numbers of subscriptions. The IDEAL concept (derided at first, but then imitated by just about all publishers, and often nicknamed BigDeal) was brought about by the realisation that if access to electronic journal articles could be pooled by larger numbers of institutions, then for the same publisher’s income – the same cost therefore to the academic community – the articles would be accessible to vastly more researchers. If ever the cliché
win-win was appropriate, it was here.

Open access logically follows on from that. The challenge was – still is – to find appropriate economic models to sustain professional scientific publishing with open access. The recently agreed arrangements between Springer and the Max Planck Gesellschaft, the UKB (all the Dutch universities plus the Royal Library), and Göttingen University, may point to a way forward. All articles from these institutions in Springer journals are published with open access under these arrangements.

If the underlying motive is, however, to get the most out of the scientific knowledge that has been gathered, which it is in my case, then moving on from open access to the semantic web – the concept web, if you wish – feels, at least to me, an entirely logical step. Not all knowledge after all is captured in journal articles. There is much more besides those, in databases, for instance, and in less formal web conversations. (A case can even be made that journal publishing ‘destroys’ data, for instance by reducing them to simple pixels in graphs, taking away the underlying richness of the data). Also, the connections between knowledge fragments are not always easily made purely by reading journal articles, in may areas a problem exacerbated by the sheer numbers of articles published. And all relevant. We are in a situation of overwhelming – and growing – abundance of scientific information, and methods that deal with that abundance are clearly needed. This is what Knewco people are working on, and I am very excited to join them.

Jan Velterop

*IDEAL: International Desktop Electronic Access Library – APPEAL: Academic Press Print and Electronic Access Licence

Charity and recycled paper

I don't think that assertions such as "...not all OA journals charge anything from either authors or readers..." or even "...the majority of OA journals do not charge anybody..." are very helpful for achieving widespread open access. One does come across them regularly, though. It seems more to do with the desire not to spend anything, or rather, to see that if any money is to be spent, it's done by 'someone else'. They may be mathematically correct, though.

The trouble is, 'journal' is in many respects the wrong entity in this regard. It may be a convenient one, but that doesn't make it right. Journals come in all different sizes. They range from publishing a few articles a year to publishing thousands. The variability is such, and the tail of minuscule journals so long, that I wouldn't even be surprised if it turns out that the smallest 50% of journals altogether represent less than 10% of articles published (I didn't do the calculation, but that's my sense).

I wonder, therefore, if the assertions above hold up if one looks at modal journals (i.e. journals with a modal number of peer-reviewed articles published per year; or perhaps journals with a modal impact factor).

Even if that should be the case, there is another issue. A while ago, I publicly pondered the question whether any of the non-charging OA journals (the ones that charge neither author nor reader) would be acceptable venues for articles that are the subject of funder mandates, such as the NIH or the Wellcome Trust. Not too many, I suspect. So far, I've heard or seen no answers to that question.

The non-charging OA journals are likely to operate on the fringe of scientific and scholarly publishing, and although they no-doubt have their function in the landscape, drawing this kind of attention to them at best takes away the focus from the mainstay of the academic peer-reviewed literature, and at worst, destroys these small journals, as there would be no way of coping with a flood of submissions without charging anyone.

It is relatively easy to sustain small fringe journals (some of them may be of very high quality, of course, though those are likely to cater to very small communities) on what the Dutch would call "charity and recycled paper" (liefdewerk oud papier). That's not scalable to the peer-review literature as a whole. Open access deserves to be taken more seriously.

Jan Velterop