Plausible Accuracy

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.

The plethora of job listings over at BioMedCentral is almost enough to make me want to cross the pond. They have positions available in production, web work, editorial roles, and sales.

If you are in the U.K. and interested in OA jobs, make sure to give them a look. They also seem to be one of the better companies at keeping their job offer pages up to date, so even if there is nothing that strikes your fancy now it might be worthwhile to check back later.

Full disclosure: I had some extremely preliminary contact with some people over at BMC in regards to jobs, but this was before they realized that I was a yankee. I had of course been looking at their website for some time before this in the hope of finding a telecommuting-type position. They didn’t seem to be against remote employment, but I’m not entirely sure how the logistics work out for such a long separation.

From the ChemSpider blog:

We are adding our finishing touches to some markup tools for Open Access articles at present and they will unveil shortly.

Don’t leave me hanging! Are these automated tools that put XML all over the manuscript, making it facile to slice and dice the articles as we please? Do the tools you’ve developed do the slicing and dicing largely?

Regardless, I’ll be keeping my eye on further developments.

In case you can’t read it, the title says “Who else is sick of sites hosting research papers that show all their content to Google so it gets indexed, but when people visit, they want you to pay exorbitant fees?

Link

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.

According to my Wordpress dashboard, this will be the 100th post here at PA.  I’m fairly pleased with the response that the blog has gotten so far, and I feel like my decision to keep the focus tightly on Open Access was a good one.

I have to admit feeling a bit like I’m both preaching to the choir and shouting into the wind at the same time.  Most of the comments come either from a dedicated core (awesome) or others in the OA movement who I presume are getting pings from Google hits (also great).  At some point though, I’d like to start hooking into that next layer; people who might be interested in doing more things with OA but don’t know how or are unfamiliar with all of the great options.  We can sit here all day and pat one another on the back for a point well made, but it’s the public-facing products and discussions that will really make a difference.  By this I mean the things that you’re already familiar with; sites like OpenWetWare, journals like PLoS, public talks by proponents of OA, etc.

You might say I’m interested in expanding PA’s deliverables.

At the moment I’m sort of investigating some of the projects that are already out there.  To be honest, I do feel like the OA movement is in some ways disjointed, in that there are many projects which are being maintained by small groups and have relatively narrow impact.  This isn’t necessarily bad - this is the sort of “grass roots” community-based enthusiasm that many causes would love to have.  I’m more interested, however, in applying whatever minimal force I can bring to bear in a way that has more widespread effects.  I’m not sure what this is yet, but I’m thinking hard about it.

Once again, thanks for reading.  It still amazes me that one person pecking away at a laptop keyboard can engage in these discussions in a (hopefully) productive way.  I look forward to continuing the conversation with all of you.

Here is a short introduction video:

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

The more time I spend delving into the Open Access community, the more I realize that it is deeper and more organized than I would have thought in the not-so-distant past.  Not only are there many people who spend a fair portion of their day thinking of ways to make the practice of science more open, the people I’ve encountered are frankly brilliant.  Where someone like myself might have a somewhat naive vision reminiscent of the peace love & happiness campaign, those who are truly driving the causes of Open Access are remarkably grounded and realistic.

Now, I’m not saying this merely to kiss some butt (although I did apply for a position at PLoS today, so there is definitely some gluteal smooching at work), but because I feel like the leaders of the movement have done a great job addressing potential “problems” of OA adoption.  Of course there are some concerns that need to be refined and worked out as thing go along, but it seems to me that most of the “deal breakers” have been resolved in a way that should satisfy those who matter - the people doing the science.

In light of this, why is the adoption of Open Access not proceeding even faster than its already heady pace?  Perhaps from my side of the fence, where all things Open Access appear logical and highly desirable, I simply can’t comprehend why others might not agree.  Part of me wonders, though, if apathy doesn’t play a part.

Let me draw an analogy here with cable T.V.  I’m sure most of us remember the days when over the air broadcast TV was about the only game in town.  It was cheap, but the selection was limited and quality could have been better.  Then cable came along, and you could get a much greater selection and a higher quality picture.  People signed up in droves.  Over time, though, the programming degenerated, content was diluted, and costs kept rising.  Since this happened over time, it wasn’t necessarily strongly noticed by those who had the service, and there was no one incident that led to people giving up on it.  The average family kept cable because they didn’t really think there was another choice; cable had become ubiquitous.  Now we are at a point where we see people abandoning cable for things like the internet or home DVD rentals.  Even those who keep cable want increasing control over it, in the form of DVRs.  The costs of cable are out of proportion with the benefits, especially when there are newer, cheaper, and in some ways better communication media available.

I think there are some parallels to be drawn here with the state of STM publishing.  The machinery of a large publishing house was really necessary in order to produce a high-end product (by this I mean science journal) and to distribute it.  Over time, however, the journals kept raising prices, to a point where it has become painful for universities to keep up their subscriptions.  Unfortunately, there is little choice - your faculty and students need access to the literature to be effective researchers.  Now, Open Access has come along and shown a way to reduce costs, largely by relying more on web technology to deliver content and removing cost overhead associated with maintaining tight content locks.  The open distribution of the information is not only good for the library’s bottom line, it’s good for science and the world as a whole.  The groundswell of Open Access is growing, and the only ones who stand to lose are publishing companies who refuse to admit it.

So my question is why more scientists don’t get behind OA.  Some of it I think is an unwillingness to take what is viewed by many as a gamble; tenure might come easier if you just fit in with the mold and publish in “accepted” journals.  It’s the same motivation that drives people to Starbucks rather than the great corner coffee shop.  It’s just inertia - why make an effort to find and publish in an OA journal when the “standard” ones are out there?  Largely its an informational issue - we need to extoll the benefits that OA publishing has over locked-down journals.

I should close by saying that I’m not in any way deriding the progress of OA.  I think it’s clear that huge strides have been made, especially in the last year or so.  Much like a member of the audience watching a juggler, once I’ve seen him do 3 pins I immediately want to see 4.

Using web-based tools to manage labs is a key interest of mine.  I believe that these tools are more or less already available, and would greatly aid investigators who are already spread thin due to competing demands on their time.  This is why I’ve made calls for open source LIMS packages as well as taken some initial steps towards building one myself.

My efforts to create a system have not had a high sense of urgency about them.  There are several reasons for this; it will be some time before I have to worry about this myself (if ever), I have other work to do which is actually related to my Ph.D., and because I tend to get discouraged when I run into programming challenges that I can’t handle quickly.

The whole thing has become more important to me, however, since one of my good friends (who posts in the comments occasionally as The Argonaut) is preparing to begin his career as a tenure-track professor.  He needs a solution, and rather soonish.  I’m not sure if I’ll be able to create something functional in the time period he’s got before he starts his job, so I thought I would try to cobble together a list of already-available technologies that I think are really useful, and can be installed today.

First of all, set up a Google Calendar.  Use it.  Post everything there, and share it with your lab.  I’ll repeat this - use it.  It’s easy to think of taking the time to list what you are doing on a calendar as an inconvenience and waste of time, but it’s invaluable (both for your own scheduling as well as your students).

Install some sort of version management system.  Trac + Subversion is a good way to go.  This sort of system is used very often in software development, but I think it has applicability to any project, including research projects.  The system is designed to assign and monitor workflow of a project - just think of it as a file folder of your progress, in every project going on in the lab.  Trac has a built-in Wiki, which you can use to store protocols and other lab-wide documents that you’d like to share.  You can use Subversion to get version control of your grants and papers, rather than dealing with endless iterations of new word documents.  It’s becoming more trendy to use a distributed version control system, so you might look at using Git as opposed to Subversion.  Both should integrate with Trac, although Git requires a plugin (makes sure to check out the entire trac-hacks site, as there are many useful plugins there).

If Trac seems too daunting, you can try out MediaWiki, the software that runs Wikipedia as well as OpenWetWare and many other great sites.  The version control isn’t quite as rigorous (you’re left looking at page edit histories), but it’s a bit more user-friendly.

So at this point you have a calendar and project management running.  This is a pretty solid base, and you’re blowing most labs out of the water as far as organization.  I would leverage the wiki functionality of Trac to build in some other things like inventory management as well.

The last thing you probably want is a public-facing website.  You have several options here, although a content management system (CMS) of some type is going to make life a lot easier.  If you just want a simple website, you can use blogging software such as Wordpress, or MovableType.  These are relatively easy to install, theme, and update with new content.  If you’re looking for something more powerful, you may consider the free and open-source Drupal.  It’s more complicated to use, but also has a lot more functionality.

If you can manage to get all of these running and convince your lab to use them, congratulations!  It will probably take some time to become familiar with using each of these systems, but for the most part they are accessible to novices.  The effort it takes will be well worth it.  Of course, it would be best if all of these functions lived under one roof, rather than split across 3 or 4 different software packages.  This is the goal of a LIMS, and I should probably GB2W on my pet project…

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.