Yesterday, Nature published an article in which they take a look at the finances and business model of one of the major Open Access publishing houses, PLoS.  The article is generating a buzz; in the blogs, mainly because of a percieved negative slant that many are chalking up to conflict of interest.  Let’s use the time-honored tradition of pulling some quotes out of context to look for the bias.  First, the byline:

Science-publishing firm struggles to make ends meet with open-access model

Ok, sounds negative to me…

relying on bulk, cheap publishing of lower quality papers to subsidize its handful of high-quality flagship journals.

Insult (they publish crap) followed by an inherent compliment that they have high-quality journals.

But its financial future is looking brighter thanks to a cash cow in the form of PLoS One, an online database that PLoS launched in December 2006

Use of the term “cash cow” and calling PLoS One a “database”… ok now we’re firmly in the realm of hatchet work.  I’m not even going into the repeated F.U.D. stirring of the “open access means huge author fee” pot that the article does as well.

Ok, so I think I agree that the article is sort of unnecessarily rude and demeaning, but I wouldn’t really expect anything different from a for-profit publisher. The worst part is that everything Dr. Butler tries to imply is a failing of PLoS has been done many times over in the closed-access for-profit journal community.

Right, so let’s try to look past the blatant attack and take a look at the actual facts, shall we?  PLoS has received about $17 million in grants, and last year had spendings of $6.7 million on revenues of $2.86 million.  The high number of papers being published in PLoS One is bringing in a lot of revenue.

So, what this is saying is that PLoS has made a sound business decision to release and promote PLoS One, as it’s helping their financial situation.  The implication that the articles published in PLoS One are sub-standard is fallacious, and shows a complete misunderstanding of this new method of crowd-sourced peer review.  A paper is made available in PLoS One as long as the board of reviewers finds that it is methodologically sound.  After it is available, anyone in the community is free to comment, rate, and discuss the paper in a public forum which is permanently attached to that paper.  In other words, if I wonder what the community thinks of the paper, all I have to do is look to the sidebar.  This is a vast improvement over standard papers, which I have no real indication of the community acceptance for.  Perhaps this paper was published because it managed to “slip through” a sympathetic reviewer, but is widely considered flawed.  You have no clear way of knowing this, especially as a young grad student.  With commented, rated, and annotated PLoS One papers, however, this is clear from the moment you first read the manuscript.

I’m going on a bit of a tangent on journal quality here, so let’s get back to finances.  To my eyes, the facts of the article indicate that PLoS is actually not doing too poorly financially.  As PLoS One becomes even more popular and more people appreciate the freedom of publishing in the “top tier” journals as well, they should move quickly towards breaking even.  And although I’m sure Nature and other profit-hungry journals might look down on this business performance, I think it will be a great day for OA and the larger availability of scientific knowledge.

EDIT: Bora has a good roundup of all of the other commentary on this (apparently quite inflammatory) article.

Over at The Life Scientists room on FriendFeed (thanks to Bill for introducing me to the site), Pierre has posted a link to the Elsevier Article 2.0 Competition.  The details are scarce at the moment, but enough to pique my interest:

We will provide contestants with access to approximately 7,500 full-text XML scientific articles (including images) and challenge each contestant to be the publisher. In other words, each contestant will have complete freedom for how they would like to present the scientific research articles contained in the Article 2.0 dataset.

And there are prizes to be won as well:

First Prize:  	$2500
Second Prize: 	$1000
Third Prize: 	$500

I’m really hoping that I’ll be able to put together an entry. I’m not as familiar with Xquery as I should be, but I’ve got a couple of months to learn I suppose. I’ve already started brainstorming a pile of ideas of course. It’s what I do best.

I’m not sure if the rules will allow for teams, but I think it would be really great if some of the Open Access proponents could work together to generate a really fine product which relies on the many OA resources that are available on the internet. It’s a prime opportunity to demonstrate the value added by opening up the articles in this way.

There has been a lot of heat on the net over the past few days as the Associated Press went after a blog for posting “blockquotes” and has declared that they will levy fees against anyone who quotes more than 5 words of one of their articles.  The predominant opinion seems to be that quoting an AP article falls under the terms of Fair Use, and that it’s ludicrous for them to charge for the privilege.  The AP disagrees:

AP considers taking the headline and lede of a story without a proper license to be an infringement of its copyrights

As I’m sure you can guess, I fall in with the crowd that believes the AP is just being ridiculous. First of all, I’m not sure that the headline of an article is a “Creative Work” (can I call this the Wilbanks Postulate?) Take this headline, for instance (for which I’m likely to be fined I suppose, as it’s over 5 words):

Obama opts out of public campaign finance system

Copyright 2008 Associated Press

This is a statement of fact, not a truly creative work.  I fail to see how one can copyright this and have a legal leg to stand on.

Secondly, a short excerpt clearly falls within the realm of Fair Use, especially given the link back to the article itself.

The problem is that the AP spends a lot of money writing their articles in the first place, and deserves to get some return on them of course.  If a blog comes along and copies the content wholesale, then this is a problem that needs to be addressed.  From my point of view, this looks like an “old media” company backlash against “new media”; an attempt to subvert and stretch copyright law past the breaking point.  They’ve worsened the situation by propping up a shill who claims to negotiate for all bloggers.  I hope that the AP comes to their senses and realizes that cracking down on spam blogs who are scraping their content is a completely different matter from squashing Fair Use and open discussion of world events.

Here is a short introduction video:

And a link to the original post over on the SC blog.

Donna Wentorth has published an interview with Lorrie Lejeune (of OpenWetWare) over at the Science Commons blog.  It is interesting, and highlights the “non-standard” thought processes going on at OWW:

To paraphrase what we state on the OWW wiki, some users of OpenWetWare think that the best thing to happen would be if somebody “stole” your idea and finished the work before you. Then you could go work on another idea. Good researchers usually have more ideas than they have time to explore, and having more people exploring those ideas will in the end benefit your research.

I am really happy that OWW is around and attracting users (the interview cites approximately 4000). I think it’s a good project with laudable goals. As of now, I do think it’s a bit limited by being so wiki-centric. Wikis are great for certain content, and not so great for others. I’d like to see them implement some other technologies in order to improve site navigation/usability, as well as to add new and interesting features to the toolkit. This would probably require a major reorganization of the current site, however, and I’m not sure if it’s feasible at this time. My gut feeling is that when the site was started as a collaboration between two labs, it just wasn’t designed to be as scalable as it could be. This isn’t anyone’s fault, but it means that they might have to go through some growing pains in order to make the service more attractive to an even broader community.

I also found something of specific interest to me (and perhaps you) in the interview; a link to an open guide/beginning of a book on using Python to do science. If you need me, I’ll be reading it.

Several recent links from Open Access News have reminded me once again of how strong the resistance to OA can be from publishers.

I’m a (5 yr +) member of the American Chemical Society, an organization which publishes several of the prominent journals in the field.  I have to admit that I hold the membership with a certain distaste.

Rudy Baum, the editor-in-chief of the weekly Chemical and Engineering News has long held anti-OA positions supported by arguments rife with Fear, Uncertainty and Doubt (FUD), as well as a fair does of self-delusion.  An example of just how confused Baum is about OA come from a 2004 editorial:

access to the STM literature is more open today than it ever has been: Anyone can do a search of the literature and obtain papers that interest them, so long as they are willing to pay a reasonable fee for access to the material.

Leaving aside the debate of what a “reasonable fee” might be, this quote shows that Baum has a fundamental misunderstanding of the difference between “accessible” and “open”. A front-row seat at the Metropolitan Opera is accessible for a “reasonable fee”, but I doubt people would consider it open to the general public.

OAN linked to a piece in Issues in Science and Technology Librarianship which delves further into ACS’s “war on OA”.  The icing on the ACS cake, however, is this bullshit-ridden interview with the president of ACS publications.  I wanted to excerpt the parts of the OA discussion that were crap and pick them apart one-by-one, but I realized I was going to be talking about almost every sentence.  So here you go (my comments in bold):

What are your views on open access?

We are in favour of various access models [as long as we get paid] and think authors should have the right to choose. We don’t think that governments or others should mandate what authors do and require them to pay [Except us, of course - we can mandate what authors do and require them to pay]  Note that this is a textbook FUD argument of “OA means you, the hardworking scientist, will have to pay more” which has been refuted time and time again.

Immediately on publication each of our authors is given a link that they can put on their websites or funding body’s site free of charge. How nice, I can link to my own work for free! There is a limit of 50 downloads of their paper in the first year.  50 downloads might last a few weeks tops, even for a moderately popular article.

If the author wants to place the whole article on their website or funding body’s site then we have our ‘AuthorChoice’ model where authors pay [terribly exorbinant fees] to make their articles open access [and ACS still keeps the copyright, it's win-win, really]. Most of our revenue comes from subscriptions, with a bit [ok, a lot] from advertising. We don’t see many authors choosing the AuthorChoice option [because we don't explain it whatsoever in our publication guides]. We’ve had this model out for about a year and less than one per cent of papers are published this way (ibid). Not all authors have access to funds that they could use to pay to publish (Then how do they afford your page charges?  Note: another attempt at the OA = author payment crap) and most of our authors are pleased with the access that others have to their papers anyway [because many of them aren't aware of other options and don't have contact with people at non-R1 research institutions].

We enable authors to submit their raw data too [The more of their intellectual work we can own the better of course]. We put this outside our firewall [but not outside of our copyright] so it is open to non-subscribers too but we do not tag this information.

We left the matter of putting preprints in repositories to editorial discretion on the individual journals and the editors have chosen not to allow this [on pain of death/firing]. After publication there is the option to have the free author directed link or to pay for open access. The society feels it is better to have the published version available.  I don’t know what these last two sentences mean, but I get the feeling it’s another rehash of the OA = $$$ deal.

So, that was enlightening I hope.  All in all, this paints a picture of the ACS as a top-to-bottom nemesis of OA and all that it stands for.  I would argue that perhaps its members are not as happy with the organization’s efforts to retain an iron-clad grip on the fruits of research as the ACS might think.  Every time the membership renewal notice comes around, I pause a minute before sending in my check.  Perhaps next time that pause will be more permanent.

Over the end of last week, I noticed several items coming down the RSS tubes that seemed to be involved with the permission barriers we place on scientific data.  These posts also seemed to be interrelated as well.  At the time I couldn’t give them the attention they deservered, so I filed them away for later digestion.  I’d like to discuss them here now, at risks of kicking an anthill that seems to have settled down a bit over the weekend.

As far as I can tell, things seemed to start when Chemspider chose to license their data under a Creative Commons license.  This is obviously (from my point of view) an attempt on their part to do the right thing - ensure that their data is freely available, and to give them some controls to “enforce the freedom”.  Then the wonderfully muddy communication medium of the internet kicked in, and people started getting angry at one another.  It seems that Peter Murray Rust published (somewhat erroneously) a conversation between himself and John Wilbanks.  This conversation was taken somewhat out of context by the folks over at Chemspider, and the ball was rolling.

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I came across a blog post entitled “15 seconds of fame” on the blog “Spoonful of Medicine” by Juan Carlos Lopez, the editor of Nature Medicine.  Here are his thoughts on Open Access publishing:

In any case, I must confess that the talk got a little boring when people started asking me questions about open-access publishing. It was fascinating to see how difficult it was for some people to understand that scientfic [sic] publishing costs money, and that there are different models to recover your costs — the author-pays model, the subscription model, and everything in between.

First of all, and I really wish someone would explain this to me; once again no mention is made of advertising revenue. To me, this is the prime elephant in the room that no one mentions when discussing recouping costs of publication.

Secondly, he’s right about the extremes of charges - the author pays everything or the journal makes money by selling subscriptions.  But as we all know, it’s disingenuous to implicate that Open Access means author pays through the nose and close access means the author doesn’t pay in anything but sunshine and rainbows.

While Dr. Lopez’s magazine does not levy page charges, they do charge quite a bit for color figures:

There is a charge of $1000 for the first color figure and $250 for each additional color figure. Otherwise, there are no submission fees or page charges.

These limited charges are actually low for “typical” journals, and Nature is to be commended, however I would argue that this still falls into the middle ground between “author pays” and subscription charges only. Consider that the full charge for publishing in PLoS One is the same as a Nature Medicine article with two color figures.  Oh, but you don’t have to pay to then read the PLoS One article, since it’s OA.  I’m not even mentioning other OA journals with lower or nonexistent page charges.

As Dr. Lopez says:

The talk got boring (at least to me) because I have very little patience with this discussion when people stop putting forward compelling arguments in support of their ideas

Indeed.

In my commentary on the Scientific American article on Open Notebook Science, I said that I wished that the author would have talked to some people who were against the idea.  This being the internet, I should have expected that the blogs would take care of that.

PhysioProf thinks that Open Notebooks are just a bad idea:

Reading other people’s lab notebooks will decidely not provide a “leap forward in clarity”. You can barely understand your own lab notebook entries weeks or months after they occur. Lab notebooks contain a huge amount of totally irrelevant obscure information, the vast majority of which relate to failed experiments.

PhysioProf is right on that notebooks do contain reams of stuff that is completely irrelevant.  In my case, these tend to be “Purified protein as before” entries - they don’t provide any new information, but comprise a large percentage of the content.

The thing that the Prof is missing is the opportunities that come from computer indexing of these documents.  As with the scientific literature itself, moving the content of laboratory notebooks into an electronic form means that we can start applying the tools of computer science to extract valuable information from a resource that is currently underutilized.

Don’t get me wrong; I think there are major problems with Open Notebooks.  The first is that, given the recalicitrance of researchers to write coherent entries now, when it’s pen and paper in the lab right next to the experiment, I can’t imagine trying to get them to do so electronically on a machine that may be in another room.  There are the usual issues of people stealing data pre-publication and things like this as well.  I don’t think they are as prevalent as many think, but I don’t think they are nonexistent either.  Although a time stamp on an electronic notebook post might provide some evidence that you came up with the idea first, it doesn’t make a lot of difference once the competitor’s paper is out or their grant is funded based on your work.

My personal goal is the advancement of Open Access to science in all forms.  I think that in the case of published papers, the path is more clear, less controversial, and requires less of a fundamental shift in thinking than for Open Notebooks.  I applaud the work that people are doing in this realm, but I think that it’s premature to push for widespread acceptance of the practice at this time, until some of the more fundamental problems are resolved.  I do support those who are very interested in the idea giving it a shot; only through larger trials can some of the issues be worked out.

But this week’s show (Mistakes Were Made, episode #354) did include an attribution of their use of NIN’s music from Ghosts, an issue I wrote about some time back.

In reading my old post, I realize I probably came off as sort of a jerk.  It’s always weird to go back later, and see how you can write something while of one frame of mind and it ends up sounding like something quite different.  At the time I wasn’t really trying to call out the show for being music thieves, but truly didn’t know the answer to the question I was asking - the proper way to use the CC license that the work was released under.

Regardless of whether they were influenced by PlausibleAccuracy (yeah right), I’m glad that they added the attribution at the end of the show this week.  Also, it was a pretty interesting show this time… go listen to it.  And then (if you like) donate a dime or something to cover your bandwidth (freeloader).