Closed Autism

We've all heard about it: the supposed link between autism and the MMR vaccine. Celebrity crusaders, admittedly of noble intent, campaign against vaccines, and entreat parents to protect their children from the perceived dangers of vaccination. Such a link, if existent, would be quite newsworthy. But all too often the media can be swept up in the sensationalist opportunity, and fail to consider evidence to the contrary.

And while the news media may facilitate the spread of celebrity influence, some websites blatantly distort the truth entirely, catering to those whose minds teeter on the brink of decisiveness. Yet one thing is clear, that all of these disparate players in the autism debate (celebrities, news reporters, web publishers, and even parents) are at minimum two degrees of separation from the evidence.

The first degree, and most direct source of interpretation, is the scientist performing the study. Though bias and conlfict-of-interest may play some role, the general concensus of the scientific community, at least on the autism-MMR issue, is coherent. But just as white light passing through a prism separates into its constituent colors, the scientific data, once presented to the heterogenous populous, may be interpreted a myriad of ways.

And these different perspectives, some patently ridiculous, are all given due consideration. Because the color of the initial light source (the science) is obscured from view by a veil of closed access. Walled-off from the buzzing discussions, science exercises little influence over public opinion.

Just a few days ago, I read a fascinating little piece on a link between autism and vinyl flooring online in Scientific American. Eager to examine the full results, I sought after the journal NeuroToxicology, a decidedly closed access publisher.

It is exactly this sort of thing that allows unfounded scandals to initiate, and perpetuate. In other words, insularity in academia can yield insanity in public.

Nathan

Why Open Acces? Why not?

It seems that the natural order of things tends toward openness. Nature was open; it was man that built walls and roofs. Water flowed freely; it was man that built dams and bottled it. Knowledge was open; it was man that closed it.

But entropy can be a good thing. Because it means that barriers, organization, and other impediments to free interaction do not impose their will. And two atoms must first make contact before they can react, and in so doing, create something new.

So too goes for science and ideas. Hypotheses from disparate fields may have great potential if brought together, but when not given free reign and open access, lie idly to waste. And right now, we have the hydrogen and oxygen separated into two different compartments. Break down that wall, though, and we get the knowledge that is water.

Nathan

Catch 44

In Joseph Heller's novel, the military introduces a requirement entitled Catch 22: the insane will be removed from flight duties if requested, but asking to be relieved from flight service proves the serviceman is, in fact, sane.

The Catch 22 is essentially whenever fundamentally flawed logic is applied in a surprisingly rational way. And unfortunately, one has been applied, with a modern twist, to scientific publishing -- Catch 22, Version 2.0, with multiplication, 44.

One argument against Open Access goes something like this: the scientists don't actually want OA, because if they did, they would make sure all of their research is published OA. And clearly, not all researchers ensure free access to their research, though the number that do is growing.

But here's the rub: this situation exists because of the Catch 44. New discoveries need past research to build upon (Newton's shoulders of giants), and scientists relying on OA are more likely to return the favor (publish their own research OA).

So in our current predicament, there often isn't enough OA research available in a targeted field of discovery for OA-dependent investigators to use. We end up with fewer OA-inclined authors and thus fewer OA-papers. Or at the very least, these authors, due to their lack of resources, publish less freqency.

This gives us a low signal-to-noise ratio (I call closed access research noise because its important message is hidden from the rest of us), so the noise prevails. And this ingenious trap de facto seems more likely to be enforced by law if the likes of John Conyers (D-MI) get their way.

Nathan

The grass is not Green on the other side

When the skies turn gray with impending storms and the hilltop fence looms gloomily over the expanse, many turn their thoughts inward and ponder the glory of what lies across the way. While this escapism may work for a little while, its empty promise soon reveals its hollow core when the true nature of the other side of the hill is revealed to be not as verdant as what was hoped. And the same holds true for Open Access, because although the antipodal decline may flaunt a grand diversity of flora, its face is pockmarked with the glaring signs of impracticality.

Green OA, in which papers are archived in freely accessible repositories, may seem a perfect compromise between Gold OA (OA publishing in which authors usually pay) and traditional closed access publishing. However, as the annals of American History have taught us (read Missouri and 3/5ths Compromises), when facing a profound question, a middle ground only manages to avoid decisiveness for so long. At some point, a decision must be made, and procrastinating only leads to increased strife (Bleeding Kansas, anyone?).

Compounding this issue, Green OA is markedly unsustainable. As papers are archived and freely accessible, traffic will be diverted from closed access journals to free repositories. In the basic functional definition of supply-demand economics, demand for closed access publishers will decline, as will their revenues. While as a proponent of OA, I wont shed a single tear at the downfall of a system I find exclusionary, however, such a collapse will cause problems. If Green OA is overemphasized, and Gold OA is not established, the peer review and editorial oversight required for the reliable communication of science would experience a vacuum of infrastructure. Free repositories such as PubMed or arXiv don't complete the critical functions; this burden is heaped upon publishers. Coordinating these things and publishing papers costs money, and these funds must either come from the author or reader end.

As of now, the middle ground is the most enticing option, though I personally find it myopic. If history has taught us anything, let it be not to repeat the mistakes of the past. And although the OA debate cannot hope to compare in magnitude with the profound questions of yesteryear, I feel the fundamental lessons remain highly relevant. With this healthy dose of retrospect, perhaps we can reach the pastures of promise not by trudging across dense foliage, but rather perambulate upon a golden path.

Nathan

There's more to Open Access than money

Open Access is much more than free access to scientific literature. It's progress, in the most fundamental meaning of the term: the next, infinitesimal yet integral, step towards scientific nirvana. It's stripping away the ancient vestiges of a bygone scientific paradigm. It's a scientific revolution as defined by Kuhn, though it doesn't change how we do science; it changes how we view science. And it's the goal towards which we strive.

Martin Luther King, Jr. noted that "the arc of history is long, but it bends toward justice." But history, just like a rolling ball, has inertia and will obey the Newtonian laws, follows its path until an outside force acts upon it. Now, the question arises as to the nature of this clearly potent mechanism. But the force that alters this trajectory is not of mystical or ephemeral construction. It is the power of action and conscience, words and deeds. Without these, history continues straight along on its merry way, unconcerned about the desires and hopes of its passengers.

Nathan

Open them up: Reinforced doors have long hidden intellectual incest

There's a reason why incest is illegal in every single US state and the District of Columbia. It drives its evolutionary course straight towards disaster. Genetic diseases caused by incest are plentiful and deleterious. But most of all, incest represents the bygone age during which royalties attempted to keep the "pure blood" within a closed group. But this blood soon spoiled with the ravage of disease.

Though scientific research may not immediately call to mind sexual relations between family members, the fundamental principles do not differ. Bedchamber doors have been replaced with payment pages and royal secrecy with registration requirements. And similarly to the royalty of antiquity, assumptions of superiority are a powerful driving force behind the institution.

Public outrage or participant opposition alone are not able to bring about an end to the practice. Instead, a combination of these forces is required. Through cooperation and careful application of strength, we can fling wide these stubborn doors hiding the abominable practice of intellectual incest.

Nathan

Intellectual Property or Intellectual Propaganda?

Everywhere you look, everyone wants to stand up for something. People are Pro- life, choice, and pretty much any noun with a positive connotation. No one wants to be anti-anything, because those are the naysayers who are destroying our country, right?

But this entire concept of antithetical positives creates a false dichotomy that inaccurately describes the options. Who's going to say "Oh, I just despise life" or "There's nothing I hate more than choice"? Pretty much no one, in my opinion. And honestly, neither of those descriptors actually get to the fundamental issues of privacy, maternal health, and reproductive rights.

That's why, if you listen to the rhetoric, opponents of OA aren't opposing anything at all! They're just for intellectual property rights. But peel back the shiny label and the same malfunctioning product is there. And it's time we turn it right around and demand a full refund. Oppose closed access and contact your representatives about HR801!

Nathan

Knowledge is Water

From Watergate to Downing Street, governments around the world operate on a need-to-know basis in which information is power and ignorance is bliss. This, it would seem, is a necessity for healthy governance, especially when information that could jeopardize national security is at hand. But sometimes, the definition of who, exactly, "needs" to know can call into question the structural integrity of this notion's entire foundation.

The assumption that one is entitled to information while others are not based upon some ambiguous measure of importance is like dumbbell curls of the ego muscles. And, what's more, it perpetuates the status quo of what I call knowledge elitism: I am better than you because I know more than you. Instead of basing exclusivity on geographic location, social status, or family connections, this paradigm establishes a hierarchy of importance based on the sole factor of access to information. And it is a cancer in our society.

Whether this desire to be counted among the knowledge elite stems from some nagging inferiority complex induced by schoolyard bullying or something entirely different, it does not matter. The end result is a system which treats information as a luxury, one reserved only for those who can afford it. Given this entrenched philosophy, it should come as no surprise that water is being bottled and sold for a dollar when it was once freely available in superior quality and quantity from the tap. Water, like knowing, has become a private commodity with varying degrees of access based on how much you are willing to spend.

But this system stands contrary to the desires of nature. According to the natural order, no one can claim ownership of water any more than purview over the stars in the heavens or dominion over the fish in the seas. So too goes for knowledge: it is a common resource, to be shared by, and implemented for the benefit of, the community. The more we lose sight of this truth, the more dire the consequences, because the severe deleterious effects a dearth of water access has on a community's health are analogous to those a lack of open access has on the pace of research. Every stumbling block retards the growth of science, resulting in far reaching consequences that present themselves in the long term.

In other words, knowledge is water. It's good for you and everyone needs it. So let's stop pretending that it's some exclusive commodity for the well-connected or well-paid. Because everyone knows the faucet only runs when it's open.

Nathan

Why is HR801 referred to the Judiciary Committee, when there's a perfectly good one on Science and Technology?

The solution very well may lie in the legal nuance of the bill, but a simpler answer seems obvious to me. As many of you may remember from your High School civics class, most bills die in committee. Therefore, by directing the controversial HR801 to under his own auspices, John Conyers (D-MI), the Chairman of the House Judiciary Committee, can shepard the bill through with a higher chance of success.

In addition, it appears that the bill would have faced fierce competition in the House Committee on Science and Technology, given that its Chairman, Bart Gordon (D-TN), has stated: "Scientific progress occurs when we foster the open exchange of ideas and information." Sounds like a central tenet of Open Access, and seems like Representative Gordon would have little sympathy for HR801.

What we need to do is pull the plug on this bill before it builds momentum, and that means nipping it at its congressional bud: Committee. Here's a list of all the members of the House Committee on the Judiciary. If your representative is on this list, please make a concerted effort to contact them and make your opposition to HR801 heard.

Nathan

Following the money on HR801

Two days ago, I issued an urgent call to action concerning HR801, re-introduced by Congressional Representative John Conyers (D-MI), which would essentially reverse the NIH Open Access policy. I have much respect for Representative Conyers, especially on his health care policies. Thus, I was greatly disturbed upon hearing of this development.

I wanted to know why Conyers would do such a thing, and began investigating the money trail on Conyers' campaign contributions (thanks Alex for the idea!). What I came upon sank my heart. According to Open Secrets, Conyers' third single largest campaign contributor in 2008 was the American Intellectual Property Law Association (AIPLA), whose "Key Bills of the 111th Congress" include HR801. Surprised? Shouldn't be. Money talks, and big money talks that much louder.

The AIPLA, like the bill it hawks, has a deceptive name. It seems the association is more interested in limiting public access to research it funded than protecting "intellectual property". Perhaps the AIPLA should consider the fact that, in essence, the research is the "intellectual property" of the taxpayers whose money went into it. But of course this private organization has the interest of its members closest to its mission; I only had hoped that Conyers would do the same for his constituents. Perhaps it is no wonder that the Congressional job approval rating averages less than 30%.

But don't let this news dishearten you. Conyers can't pass the bill on his own, no matter how much money he has behind him. Contact your Representatives and appeal to the better angels of their nature. Stop HR801 now, and in 2010 we can elect responsible persons to represent us.

Nathan

Imaginet

I was listening to the great song Imagine by John Lennon and decided to modify the lyrics for Web 2.0 (if you need help getting the melody in your head, here's a nice music video):

Imagine there's no paper,
It's easy if you type.
We can talk among us
Online, using Skype.
Internet for all the people's
Status on Twitter...

Imagine there's no limits
On what research can do;
Nothing to stop and wait for,
And no payments too.
Imagine all the research
Open for all to see...

You may say that I'm a Digger,
And the internet has won.
I hope Open Access will succeed,
And the world will read PLoS ONE.

Imagine no limitations,
But only if we stand
Up against the greed
In an alliance quite grand.
Imagine all the people
Sharing the knowledge...

You may say that I'm a Digger,
And the internet has won.
I hope Open Access will succeed,
And the world will read PLoS ONE.

Stand for Open Access, Oppose HR801

The most painful defeat is an overturned victory. And this very well may happen if supporters of OA do not respond. Congressional Representative John Conyers (D-MI) has re-introduced a bill (HR801) that essentially would negate the NIH policy concerning depositing research in OA repositories.

The bill's name in no way reflects its purpose: Fair Copyright in Research Works Act. A more apt title would go something similar to Fallacious Companies in Research Win Again, in order to retain its possible acronym. Jennifer McLennan, Director of Communications over at SPARC, issued a letter in which she outlines the five key characteristics of the bill, quoted below:

H.R. 801 is designed to amend current copyright law and create a new category of copyrighted works (Section 201, Title 17). In effect, it would:

1. Prohibit all U.S. federal agencies from conditioning funding agreements to require that works resulting from federal support be made publicly available if those works are either: a) funded in part by sources other than a U.S. agency, or b) the result of "meaningful added value" to the work from an entity that is not party to the agreement.

2. Prohibit U.S. agencies from obtaining a license to publicly distribute, perform, or display such work by, for example, placing it on the Internet.

3. Stifle access to a broad range of federally funded works, overturning the crucially important NIH Public Access Policy and preventing other agencies from implementing similar policies.

4. Because it is so broadly framed, the proposed bill would require an overhaul of the well-established procurement rules in effect for all federal agencies, and could disrupt day-to-day procurement practices across the federal government.

5. Repeal the longstanding "federal purpose" doctrine, under which all federal agencies that fund the creation of a copyrighted work reserve the "royalty-free, nonexclusive right to reproduce, publish, or otherwise use the work" for any federal purpose. This will severely limit the ability of U.S. federal agencies to use works that they have funded to support and fulfill agency missions and to communicate with and educate the public.

In the letter, McLennan goes on to encourage all those involved in and impacted by the OA movement to take action and contact their representatives in order to rally opposition to this bill. A draft letter text is available. I encourage all to participate and take a stand to defend OA and public access to scientific research.

Nathan

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Love in the Time of Closed Access

Romance and courtship, love and loss, life and death. Though these are not characteristics of the OA movement, their presence is ubiquitous in Gabriel Garcia Marquez's classic novel, and no less pervasive globally. And as Valentine's day approaches, I thought I could discuss science's love affair with OA (or perhaps something more?) by considering a few key ways to ensure the establishment of a sound and flourishing relationship.

Lay a strong foundation. On this point, we've succeeded rather well. Two key publishers including Public Library of Science and BioMed Central have emblazoned a suitable path to the golden destination of OA. But already cracks are visible. Questions concerning the peer review process, academic validity, and publishing guidelines have been raised concerning those publishers that do not charge for OA publication. These imperfections must be addressed, and constant inspection ensured.

It takes two to tango. It's all about cooperation, and that often means compromise. The world isn't going to change in a day, but through strategic partnerships among and between academia, publishers, and government, progress can, and has, been made. Without this elemental teamwork, no relationship (whether it be personal or philosophical), can be maintained.

Keep the flame alive. The period of honeymoon, infatuation, novelty, call it whatever you will, the meaning changes none at all: something that is new is exciting, and as that newness fades, the excitement often follows suit. And in the end, complacency is much more comfortable than action. Though difficult, avoiding this rut is exactly what must be done in order to guarantee the healthy longevity of the OA movement.

Nathan

New Blog!

I started a new blog entitled Social Justice Science. It's opinion on two topics that are very dear to my heart: Social Justice and Science. Also, I examine instances when these two ideas come together. With the power of technology and science ever increasing, it is important to consider the moral compass that guides the direction of progress. This is what I attempt to do with the new blog. I titled my most recent post Ghostwriting the R.I.P. examining the sticky issue of ghostwriting (not attributing authorship) in today's medical publishing paradigm. I encourage all of you to go check it out.

Nathan

PLoS ONE Introduces Collections

On January 30th, PLoS ONE tried something new. While the pioneering OA journal had always categorized all of its research articles into subject areas (physics, mathematics, biochemistry, etc.) and publication date (PLoS ONE publishes on a daily schedule now in order to facilitate the high volume of research it processes), a new option in the Browse Articles menu was introduced a few days ago.

Collections they are called, and fascinating they are certainly. The idea is similar to the concept-driven magazine issue, with a coherent focus on the theme or topic of the week/month. The only difference being that the articles represent novel research as opposed to journalistic reporting. As PLoS ONE is a formidably large journal, collections will help simplify the organization of research into accessible units.

Not all of the PLoS ONE articles will be published into collections. Instead, according to its website PLoS ONE will "from time to time" develop a collection in order to "highlight specific topics." Though not stated explicitly, it may be a reasonable guess to think that new collections may be a monthly addition, similar to the publishing schedule of its more prestigious sister journals, PLoS Medicine and PLoS Biology.

The first collection is entitled Stress-Induced Depression and Comorbidities: From Bench to Bedside and tackles a research field of growing interest to many neuroscientists. This body of work comprises two Overviews and eleven Research Articles, the collective results produced from several international research institutes. I encourage all of you to check it out.

Nathan

Science of the Common Man

Closed access publishing is an artifact of the bygone era during which it was largely believed that only a few, great men were the pioneers of knowledge, and the masses of the "common man" were mere spectators along the river of science. In the past, every effort was made to limit the demographic diversity of university and professional populations. Notions of racial and gender superiority encouraged institutionalized discrimination. Women were only able to become full members of the University of Oxford in 1947. US law allowed public schools to remain segregated until the US Supreme Court case of Brown v. Board of Education in 1954.

Now, I am by no means comparing closed access publishing with racial or gender discrimination. I am noting, however, that the basic result (that of limiting participation within a certain arena of academic pursuit) remains the same. In fact, closed access publishing is blind to the color, creed, and nationality of those whose quest for knowledge it inhibits. And although the matriculation barriers of the past took the form of laws, monetary and reproduction restraints are little different in my mind.

One of the beauties of scientific publishing is that there is no educational, socioeconomic, or gender prerequisite for contributing to the body of scientific knowledge. All that is required is a novel idea. On the surface, at least. Here, the distinction arises between what is de jure (of set requirements, i.e. law, standards, directives, etc.) and what is de facto (of fact).

On one point, all can agree: there are few to no de jure limitations to contributing to science. While these were present in the past (with specific references in the first paragraph), they have all but died out in today's age. Unfortunately, de facto barriers, some of which inescapable, remain. The average American (lets call him Alvin) does not have access to a well-equipped lab, not by the virtue of any federal, state, or local law decreeing it (as would be in the case of de jure) but rather by the virtue of Alvin's not being employed (and not having the qualifications necessary to be employed) by a university or company with said facilities. This widely acknowledged situation is quite acceptable by all standards. However, the fact that Alvin cannot read the latest research on dark matter because it was published in a closed access journal and not self-archived in a free repository IS a problem.

Now Alvin may have been able to contribute, at least in some small way, to the understanding of dark matter. But instead he was frustrated, and in general turned off, by the constant presence of pages demanding payments he cannot afford with his sub-median salary, and thus he abandons his scientific pursuit.

While I am sure many of you will scoff at this notion that closed access snowballs into lost contribution to science. But even those who doubt that de facto problems are problems, or even that people like Alvin can offer any valuable insight, I have to ask: is continuing along with the status quo worth the risk?

It is clear that barriers in science remain from those older times, the only difference being that they have successfully hidden themselves within the paradigm of social acceptability. They have shed their ostentatious de jure robes and have chosen instead the de facto ghillie suit. Their purpose remains unchanged.

Nathan

Misfortune Strikes

Hi all,
I have some bad news. Hosting problems have required me to relocate to Blogger, hence the new format. All of the post dates are gone as well. Unfortunately, no comments were able to be transferred over. However, I will continue posting on the pertinent issues concerning Open Access. I am working diligently to restore OAB to its full potential.

Nathan

PLoS ONE @ Two

In a recent PLoS ONE paper, The Role of Medical Language in Changing Public Perceptions of Illness, Meredith E. Young and her colleagues investigated the effects of disease label on perceived seriousness. Two general categories of label were used: “medicalese” (the technical term for the disease used in the medical community) and the lay language. The researchers based their assessments on a survey of 52 McMaster University undergraduate students.

The researchers also considered the effects of the point in time at which the medicalese label was introduced, separating the diseases into two categories of recently medicalized disorders and established medical disorders based on data from Lexis Nexis. The results of this investigation demonstrate a significant difference in perception depending on the label attributed to the disorder.

This research defines inter-disciplinary. It touches upon the fields of medicine, linguistics, statistics, and even a subset of philosophy. That subset being epistemology — the theory of knowledge. Epistemology recognizes that language (including names for medical disorders) affects what we perceive to be true, what we believe, and what we know. This paper quantifies that epistemic phenomenon, and helps answer the question: how do different labels affect our perception of the same thing?

Nathan

External Pressure to Produce Internal Change

Some stalwarts of the anti-OA camp remain unwavering in their opposition. Chief among these are the likes of Nature, which produced editorials highly critical of the OA movement. While OA has made significant strides, especially with the great success of OA publishers such as PLoS and Biomed Central, its progress is slow.

The forces at work are in a near stalemate, locked in an internal struggle within the scientific community. We find ourselves at a tipping point, perched upon the peak of the mountain of choice. On one side we are presented with the barren desert of the closed access status quo; on the other we have the verdant forest of OA progress. However, neither combatant can generate sufficient momentum to surge over the edge.

Into this quagmire must the public come. Take, for example, a plumber (whom, according to Sarah Palin, represents the American “Common” Man). Now this plumber, lets call him John to avoid any confusion with the “real” plumber, he hears a mention of the OA debate and is overwhelmed with apathy — an expected result. Not only does the topic initially seem uninteresting; to him, it is like a war between the Zorgons and Blastothons on the planet Marsas. (This shabbily written example is purely fictitious. Any resemblance to actual aliens is incidental and does not express the views of the author on what surely are peace-loving creatures.)

However, John might well find a certain Quote of a certain Doctor from a certain Civil Rights Movement quite interesting: “Injustice anywhere is a threat to justice everywhere.” In other words, it DOES matter. The OA discussion DOES matter to John, not only for the sake of justice itself, but also for the improvement of science as a whole, which will inevitably improve John’s life in one way or another.

So now I make my plea. I call on all the Johns of the world, all of the Jills, all of the non-scientists and all of the public. This fight is your fight as well. Make your voice heard and throw your support in for the OA movement. Disregard the myopic assumption that not caring is for the best faring. Call your Representative, write a letter to the editor, throw a fundraiser for PLoS, do ANYTHING. Just don’t do nothing at all.

Nathan

Obama and Open Access

With Barack Obama’s historic election to Presidency of the U.S. on November 4th, new opportunities for advancing OA arise. With fresh faces and new insights in the White House and Congress, further critical legislation either supporting or mandating OA can come about.

The mandate concerning NIH-funded research represents the first step in a very long journey toward complete OA for all. The interconnectedness between government and research is quite tangible. Therefore, government policy can be a major impetus for greater momentum for the OA movement.

For this reason, I encourage all of you to contact the President-elect to demonstrate your support. If we can bring OA into the spotlight in Obama’s science policy, these next four years may bring many great victories for the movement.

Nathan

PubMed Central and arXiv

PubMed Central (or PMC) is a digital archive of biomedical research that makes these papers freely available to the public. It is owned and operated by the U.S. National Institutes of Health and thus is a public resource.

PMC lends itself to comparison with arXiv: both are free digital archives of research papers helping advance the cause of OA. However, the differences abound. Firstly, PMC emphasizes the biomedical aspects of research while arXiv focuses upon the physical and quantitative sciences. Secondly, PMC is a resource funded by taxpayer dollars (through the NIH) but arXiv is operated by the private Cornell University.

Thirdly, papers are added to PMC by the journals that publish them; manuscripts are uploaded onto arXiv by the authors themselves. Finally, PMC ensures that the papers it archives have been subjected to thorough peer review (thus making Indexing by PMC a mark of validity). In contrast, arXiv does not impose any sort of review onto uploaded papers.

PMC and arXiv offer unique strengths and limitations and emphasize different fields of scientific endeavor. However, it appears clear that they are two very different approaches to the same ultimate goal: increasing access to scientific literature.

Nathan

Spotlight on arXiv

In my most recent post, I noted the disproportionate emphasis of OA publications on the biomedical sciences. However I failed to mention one critical player in the field of open scientific publishing: arXiv. The X represents the greek letter chi, thus making the pronunciation of the site “archive,” which is exactly what it is. Researchers may deposit e-prints of their manuscripts on arXiv in order to make them freely available for all to see.

While this is certainly a great positive, the more interesting aspect of arXiv is its emphasis. Its focus encompasses those areas often not found in many OA publishers, such as mathematics, physics, computer science, and statistics. It does not impose any sort of peer review, it truly is an archive of e-prints, a very successful one at that. According to its homepage, as of the 3rd of October arXiv has posted over 500,000 articles online under open access.

Cornell University currently owns, operates, and largely funds arXiv, however it does recieve some funding from the National Science Foundation. Paul Ginsparg established arXiv in 1991, and it was originally hosted by Los Alamos National Laboratories.

Nathan

OA Emphasis on Biomedical Research

I could not help but notice, in my perusal of the internet wealth of OA, that the majority of OA publishers emphasize either biological or medical sciences. The evidence abounds. BioMed Central, an OA publisher, makes no attempt to obfuscate this focus — its very name demonstrates its approach. Of course, while BioMed Central also has PhysMath Central and Chemistry Central, these two wings constitute a total of four journals. Compare this to 194 under the BioMed name. The emphasis is clear.

However, BMC is by no means the only OA publisher with such an approach. The Public Library of Science clearly leans toward the biomedical sciences as well. PLoS currently publishes seven journals, six of which are biomedical and one is general. However, while on its face it may be general, PLoS ONE in fact publishes the great majority of its papers in the biomedical fields. In fact, only 184 papers have been published under the categories of Chemistry, Physics, and Mathematics combined. To put this in perspective, PLoS ONE has published around three times that many in Neuroscience (551 papers) alone.

Regardless of the specific reason, it is clear that OA has in general focused heavily upon publishing biomedical scientific research. Perhaps in order for OA as a movement in general to succeed, we must expand its base of support to include more completely the entire spectrum of scientific inquiry.

Nathan

Education and Open Access

While most Universities around the U.S. contain a plethora of scientific journals freely available to their students, the vast majority of U.S. public high schools do not. While some (those students uninterested in research pursuits) are not directly impacted by this problem, many student researchers feel the squeeze of being limited to a small fraction of the vast scientific body of knowledge.

In fact, this issue extends beyond those high school students engaged in research. Many instructors assign their pupils research reports that must cite published papers. Being directed to a payment page after reading an exciting abstract can be a very frustrating experience for a pre-college student, or any person in general for that matter. This frustration may even turn some students off from scientific research in general, especially if their only experiences with it have involved pulling out their hair.

In other words, the lack of OA has far reaching consequences, extending far beyond the relatively limited scope of academia. In order to continue scientific advances, young budding researchers must be exhilarated and enthralled by science, not annoyed and frustrated by its pecuniary red tape.

Nathan

Spotlight on Directory of Open Access Journals

The Directory of Open Access Journals (DOAJ) represents a very important resource for researchers seeking to publish in or peruse OA journals. It contains a directory including 3686 OA journals and 211516 OA articles according to its home page.

DOAJ is especially helpful to authors with limited funds as they search out OA options that do not require publication fees which sometimes fall beyond their limited means. The DOAJ For authors page allows prospective OA contributors to search out journals based on field and whether or not publication entails a fee.

By centralizing all of the OA journal information, DOAJ allows researchers dependent upon OA papers to quickly and effectively search through 1263 OA journals with the Find articles engine by keyword. With this streamlined approach, OA researchers can avoid wasting time being turned away by incessant payment pages.

The directory also seeks to ensure that the reader can attain a quality piece of OA work through two primary requirements delineated in the About page:1) the paper must satisfy the OA definition promulgated here, 2) the journals must exercise quality control through either peer review or editorial selection. Overall, the DOAJ is an invaluable resource for OA authors and readers around the world.

Nathan

Varying OA Business Models

In my most recent post yesterday (Spotlight on Internet Scientific Publications), I briefly discussed the method through which ISPUB generates revenue as compared to the business models of BioMed Central or Public Library of Science. However, I believe we have only hit the tip of the iceberg with regard to this critical topic, as business model is one of the most defining features of the entire OA movement.

There are two major types of OA publishers: for-profit or not-for-profit. These can often be identified with a simple glance at the URL — for-profits usually have a “.com” domain name, while not-for-profits will end with “.org”. However, even these distinctions are not sufficient in order to fully understand the entire spectrum of OA publishers. In order to simplify the approach, I will discuss each major model individually using specific and well known examples.

The Public Library of Science operates under a not-for-profit model that draws revenue from several sources, including membership fees, publishing fees, and some advertisements. BioMed Central is quite similar, drawing resources from publishing fees and advertisements, differing primarily due to its for-profit approach. Finally, ISPUB funds its operations entirely through online advertisements, sparing both the readers and authors from fees.

Despite the obvious differences, one commonality that unites the business models of all OA publishers is their lack of any sort of cost to read the material, thus facilitating the dissemination of information and the acceleration of scientific advance. In order to display the material online, one must have a website.

Nathan

Supporting PLoS

As many of you well know, publishing and maintaining high quality scientific journals is quite expensive. The Public Library of Science (PLoS), the publisher of several OA journals, achieves this end primarily through publication fees paid by the authors or their institutions.

Unfortunately, sometimes the cost of operation exceeds the revenue, and PLoS must rely on charitable support from private individuals such as you and I. Some great ways to support PLoS include becoming a member or making a donation. Of course, these private contributions in no way affect the final decision concerning a submitted paper. However, they most certainly support the noble cause of making scientific research more available to all those interested. And for that, I encourage all of you to do your best to help support the OA movement through monetary contributions.

Nathan

Numbers Speak Louder than Words

In this blog, I have discussed extensively my position that OA is superior to the closed access model in numerous ways. Most of my assertions have been derived from logical deduction, personal experience, and general trends. However, I have yet to present perhaps the strongest evidence supporting the OA model — numbers.

In a 2006 paper in PLoS Biology entitled Citation Advantage of Open Access Articles, Gunther Eysenbach investigated how publishing approach (either OA or closed access) affected the number of citations a paper received. This number of citations is a definite reflection of the dissemination of the paper through the scientific community.

Eysenbach found a definite quantitative citation advantage for OA papers over closed access papers. He wrote,

We found strong evidence that, even in a journal that is widely available in research libraries, OA articles are more immediately recognized and cited by peers than non-OA articles published in the same journal. OA is likely to benefit science by accelerating dissemination and uptake of research findings.

With similar evidence mounting, I feel that the scientific advantage of publishing OA will build, encouraging ever greater numbers of researchers to join the OA movement.

Nathan

OA Obstacles

It is approximated that there are over 20,000 legitimate peer-reviewed scholarly journals in existence today. Unfortunately, only around 10 to 15 percent of these journals are open access. This frequency is much too low, and quite frankly disappointing.

One possible cause of this is the existence of an option through which one may engage in “open access lite” as I call it. That is, depositing the paper or abstract in a central open access repository such as PubMed. This method is in fact very popular, and while it does offer some access to all, it simultaneously limits the ability of purely OA publishers to proliferate and prosper.

One logical antidote to this problem would be to encourage researchers to go 100% OA and actually publish their papers in an open access journal. Of course, this and similar assertions will be perpetually countered by those journals which profit off of the closed access model, as they lobby continuously to prolong the longevity of closed access publishing.

Nathan

Open Access in the News

One of the most exciting signs of progress in the Open Access (OA) movement is the widespread lay media coverage of discoveries published via OA. On my last post, I touched briefly on the subject, however it is clearly a topic that requires in-depth discussion and analysis.

Over at PLoS ONE there is an In the News section, with a different paper highlighted each week. The currently spotlighted paper has clearly received extensive coverage, with discussion popping up in places such as BBC News, The Guardian, and The New York Times. However, this is merely the tip of the iceberg, as media coverage of OA articles has been quite extensive. Science News discusses on average two to three papers published in PLoS ONE alone every single issue. The total number of OA papers discussed in this periodical is even higher.

This brings us to one of the key advantages of OA. Suppose that a scientist reads an exciting article in a periodical concerning a recently published paper, and hurries online to find its location. With closed access, the potential reader must jump through a series of hoops, such as creating a profile, logging in, purchasing the article (the list goes on) and very well may abandon the pursuit. In stark contrast, if that paper is OA, the potential reader nearly immediately becomes an actual reader who can spread the word or advance the research.

Nathan

Nature Monkeys Around

While perusing PLoS ONE recently, I noticed something that was quite frankly surprising. Under the New and Noted section of the front page, I saw an interesting article entitled Preference Transitivity and Symbolic Representation in Capuchin Monkeys (Cebus apella).

The research team, led by by Elsa Addessi , found that Capuchin monkeys could comprehend symbolic representations of food. A different “token” gained a different treat, and soon the monkeys began to synthesize this mental association. Each monkey had individual tastes, and chose the item that represented its preferred treat. This is surprising news, given the significant evolutionary divergence between humans and Capuchin monkeys and is all in all a profound discovery.

Despite the ground-braking nature of the work, I found that its most interesting aspect concerns its coverage in NatureNews of Nature Publishing Group, publisher of the journal epitomizing closed access elitism (Nature). In fact, Nature had recently published a letter disparaging the entire open access (OA) philosophy, declaring it harmful and counterproductive. I could not help but notice that Nature Publishing Group nearly simultaneously prints a scathing attack and a subtle affirmation of the merits of OA. Perhaps they should make up their minds.

Nathan

Spotlight on PLoS

PLoS, or the Public Library of Science, was born in 2000 as the brainchild of Patrick Brown, Harold Varmus, and Michael Eisen. It originally took the form of an online open letter that was supported by tens of thousands of scientists from around the world. This radical idea gradually took the form of a full fledged and prestigious scientific publisher. It currently has a whopping seven journals, including: PLoS Biology, PLoS Medicine, PLoS ONE, PLoS Computational Biology, PLoS Pathogens, PLoS Genetics, and PLoS Neglected Tropical Diseases.

PLoS Medicine and PLoS Biology have reached the pinnacle of their respective subject areas, with ISI impact factors of 13.8 and 14.1 respectively. This profound success simply demonstrates that open access and prestige are anything but mutually exclusive. Overall, PLoS has published thousands of excellent papers that are made available for all interested.

The Public Library of Science is a 501(c) nonprofit organization that relies upon both publication fees and private donations to continue in its mission to throw open the locked doors that once hid scientific research. Recognizing its foundation upon the internet, PLoS encourages participation in the online community, including its very own blog. PLoS ONE, in fact, allows online users to rate and discuss content. In a way, PLoS is the American Revolution of 21st Century science, returning the power to the people in a uniquely noble manner.

Nathan

Open Access Building Momentum

Effective 7 April of 2008, the National Institutes of Health (NIH) initiated a ground-braking policy that requires all research funded by NIH to be deposited in an open access repository, such as PubMed Central, upon acceptance for publication. This policy ensures that research funded by taxpayers is readily available to those taxpaying funders.

This OA breakthrough came relatively soon after Harvard University’s Faculty of Arts and Sciences (FAS) unanimously approved a measure that will deposit all scholarly papers produced by members of the FAS in an open access repository produced and maintained by Harvard. This move represents simply another victory for the OA movement. The professors at FAS hope that other centers of higher learning will follow in the OA path.

These recent advancements reflect the inexorable trend toward OA that has permeated the scientific community. With the increasing availability of research to all, it seems that the resulting increased academic exchange and discussion will accelerate the process.

Nathan

Open Access and Developing Nations

Academic research is often described as the act of “standing on the shoulders of giants.” However, those in impoverished and developing nations without access to the funds required by closed access publishers are often denied access to critical background research, thus snuffing out an important source of scientific illumination.

The dawn of the internet has been a key player in helping to level out the global economic playing field. The onset of the Open Access (OA) movement has extended this equalizing power to the realm of academia. Now the brilliant minds of poor nations can have unrestricted access to the information they need to advance science.

Some may argue that the publishing fees of OA publishers (sometimes thousands of dollars) in fact limit the ability of researchers in the developing world to share their research. However, this attack is clearly unfounded. Every single OA publisher I have found to date offers fee waivers for those without the funds and ensures that ability to pay in no way affects the peer review process.

I think the benefits far outweigh the perceived drawbacks with regard to OA and its effects on those researchers in developing nations. As more and more capable minds begin contributing to scientific literature via OA, the inevitable result is nothing less than human advancement.

Nathan

PLoS ONE Ratings

One of the most innovative features of PLoS ONE is the ratings system. As the papers published in the journal are primarily selected based upon scientific rigor and communication, PLoS ONE encourages the rating of the papers in order to identify the most interesting and significant results as judged by the scientific community.

Unfortunately, it appears that the ratings system has not been used as much as had been hoped. There are several possible reasons for this, including

1) The time crunch that affects nearly all participants in academia,

2) A lack of expertise in the field of the paper, preventing an adequate review,

3) An unwillingness to criticize those papers one deems unimportant.

While these setbacks are most likely simply the birth pains of an emerging application, I encourage all of you to rate articles after reading them in order to expedite the process of fully integrating the ratings system into the academic mainstream.

Nathan