PS. More seriously, I've come to feel that only a non-profit organization can solve the "walled garden" problem in academic publishing. We need something like a "Mozilla Foundation for Science" -- an organization dedicated, not to maximize profits for shareholders, but to keep power over scientific research in people’s hands.
That's why we have governments.
No, I'm not being sarcastic. The public sector is there to serve the public good, and this is quite obviously a public good. I'm not anti-privatization either. Private exploitation under public laws and guidelines is a common strategy to solve these issues.
What has undermined public/private solutions is not public opinion or political ideology, but greed, lobbying and corruption. A foundation is nothing but a workaround, and foundations have a history of getting corrupted by the greed and delusions of grandure of its administrators.
It's time we address the real problem. The legacy of thousands of years of civilization is being stolen from us.
The open source movement has shown that there's a third way, and I suspect that that's the way to go. It's fault tolerant: if a group of people are detracting from its mission, the others can very easily go on and continue as is.
Science is more expensive than software, though, and therein lies the rub.
Palin is a sock puppet for those with the money, and the people voting for the likes of her have been deliberately deprived of a decent education. This is a symptom of the same corruption.
The open source movement is a workaround, exploiting a flaw in a corrupted system. It should serve as an example of how much better things can be, not as an excuse to never address the problem, especially not when millions are being criminalized by exactly the same copyright system for the simple act of sharing.
It's not fault tolerant: changes in the copyright law (the laws bought and paid for) can kill copyleft, and whatever license one may prefer, copyleft upholds some of the essential pillars of the open source ecosystem.
Don't get me wrong: I'm all in favor of pragmatically using these workarounds.
But I'm also in favor of keeping our eyes on the prize: the knowledge accumulated over millennia should not be allowed to be monopolized and exploited by the few.
Open source is not a "third way". It's a necessary detour.
I really wish this were the case, but political views remain relatively static in the face of increasing levels of education. (see: http://www.nytimes.com/2012/03/04/opinion/sunday/college-doe... )
Unfortunately, even if we sent all the Palin-voters to college, they would still probably be convinced that Obama is a muslim, earth is 5,000 years old, etc etc. It's rather depressing to think about, since there appears to be no cure for it.
Science needs to be transparent and made available in real time. This is the whole purpose of science, to freely distribute knowledge for the well being of humanity. I honestly believe that and I'm working to bring that transparency to science as we speak.
Yes, this needs to happen. NIH already requires that publications arising from NIH-funded research be made publicly available 12 months after publication (http://publicaccess.nih.gov/). Other funding organizations really need to do this. IMHO, they should also require that publications be made publicly available immediately upon acceptance and provide incentives for "gold" open access (where the article is immediately made available on the publisher's website).
You can't fork funding the way you fork source code though. It's not just more expensive, but fundamentally different.
The real problem is that some companies manage to exploit a monopoly granted to them by the government in ways that are not pleasing to the public. The government is the entity which created the problem. Granted, while solving another but it will still be the government agents who break down your door and arrest you if you build an unauthorized competitor or even just try to release that "legacy" (vide Aaron Swartz), not Elsevier's.
It's hard for me to understand how you can blame a company that puts up a paywall more than people using violence (or at least credible threats of it) who enforce the rules stopping others from competing.
Because we're not 15 year olds who just read Atlas Shrugged?
Laws happen because a variety of agents (lobbyists, legislators, public interest groups) push for them. They're not enacted by some amorphous specter of 'government'.
I don't think anyone here blames companies for putting up a paywall or doing something else to maximise their profits; it's why they exist. However, we do recognise that this is not always an ideal state of affairs. A public sector body is one way to remove the profit requirement; private-sector not-for-profit organisations are also a possibility (but have to worry more about where their funding comes from).
And it acts as an extension of "the people" as the entity providing oversight and regulation in this example as well. That it doesn't happen in real life is evidence of subversion of an ideal, rather than some inherent truth.
Additionally, I think that until academic publishing has a standard browser-based solution (MathML, MathJax + Pandoc + LaTeX) outside of PDF that the costs will be prohibitively expensive.
JSTOR is not a publisher--agreed. They are, however, a central repository who charges an arm and a leg for research that, often, has been funded on the taxpayer's dime.
There is obviously a difference between making academic research available to universities at reasonable prices and making academic research available to everyone for free. The latter is obviously better, but to happen, the money would have to come from somewhere. For a publisher, the obvious answer is publication fees (which is what PLoS does). This is not an option for JSTOR, since most of their material has already been published. I suspect that JSTOR would happily make everything in their collection open access if they had a sufficiently large endowment to do so.
I agree with your point. But you are ignoring another major expense that the fees go to:
Paying the actual publishers and rights-holders licensing fees. JSTor is not a publisher. Most of what they distribute, there is a copyright holder, usually the original publisher, that will not let them host and distribute without a fee.
This is obviously not something JStor has a whole lot of control over.
I agree that JStor are the 'good guys'; their fees are more reasonable than most of their for-profit competition, AND their service is _just plain better_ than most of their for-profit competition.
It would be interesting to see how much of JStor's budget goes to paying licensing fees to the rightsholders; I don't know if that information is public.
This is why I've given up trying to work in the field or found a company in the sector... Anyone with an idea and need a technical cofounder? ;)
In the long run I see such system emerging and being successful, and eventually replacing everything else. Needless to say it will take a lot of time though to popularize it.
What do you think? Could this be done?
The real tragedy is the general reference, social science, and humanities journal diaspora where the usage and demand has skyrocketed with the increased access online resources allow to lay researchers. The science journal communities are way ahead in self-sufficiency in adapting, and are increasingly open to the corrupt state of publishing and alternate community publishing platforms.
I'm way more interested in informal discussion of interesting papers and news than anything else.
As everyone else has mentioned, the big issue is getting a large community. So what would be really cool would be to figure out how to do something like HN or SO without active involvement by a large community. In my field there's a lot of discussion/review/etc of working papers and published results, but it's all scattered across different blogs and commenting systems. Plus papers build on each other and some are clear replies to other research. If you could take that sort of dispersed discussion and put it into an HN or reddit style threaded view that was available at one spot (or an SO style question and answer format, if you prefer), that would be awesome.
Arxiv even has a paid fellowship, but it is postdoc wages, not professional wages.
So there's an ongoing transition now by researchers/editorial boards/etc to move to a system with lower access costs (some of which involves taking back journal ownership, some doesn't). There's some logistical overhead and fixed costs, but those are falling. It seems like in 20 years (conservatively) all new research will be available to whomever wants it no matter what Elsevier or other companies do in the meantime (the papers may not be literally free, but affordable).
So, like I said initially, I can see how some software for logistics or communication would be helpful, but the main issues don't strike me as technical.
Is it a "technical issue"? No, but neither is booking your flight via phone, that worked just fine.
Could it be made much better, more accessible, cheaper, and overall better via technology. Yes.
Maybe you could give details about what you mean by "antiquated idea behind publishing" because I'm pretty sure what I described is not 1970s speed. Now, if your point is that what I've described is not common practice, I agree completely. But that means that people need to be persuaded to use existing technical tools -- I can't see a specific step that's going to be a significant pain point (I'll grant that not everyone can/will use github, but uploading a zip archive of the paper's directory to a personal webpage is easy and is almost as good for code and data dissemination).
Other anecdotes are blogs that announce and discuss new research:
That is legitimate academic discourse, put out by an extremely established and credentialed economist, almost instantly. On blogger.
My viewpoints are limited to life sciences, where people have no idea what FTP means, let alone GIT. Also, what you did is not typical, people (at least in my field of neurobiology) have no intention of doing something like that in fear of being scooped.
The antiquated idea behind publishing is the concept of doing an experiment, filtering out all the negative data, and then submitting their positive data to a journal that they think will publish their data. We've been waiting for 7 months now for a paper to get published in PNAS due to this antiquated process. 7 months to do what you did in a few minutes uploading your data online and making it public.
Meanwhile, 'search' as we know it rules the world and is the driving force enabling the entire tech industry. It wouldn't be hard to throw a little effort in building out their platforms, but there's no competition to force further development in their products.
Elsevier in particular is spending ridiculous amounts on internal research & acquisitions for its platform (called SciVerse, http://www.hub.sciverse.com/), following the latest advancements in machine learning and NLP for data mining, etc etc.
They also host competitions for start-ups and developers to produce new apps for their platform.
These businesses may be unethical and not to everyone's liking, but they are not stupid.
This would add real value to the scientific publishing and simply help the researchers to find what they need.
I don't think this is a technical issue. Journals make mistakes on which papers to publish all the time, even when the referees work hard and take the review seriously, so this is hard for committed people to do well.
There are some arguments for both approaches, but I believe that the double-blind approach is much better.
Project: Very briefly, I'm working on collecting raw data (positive AND negative), indexing it, and making relationships between datasets. For example, my neuroscience study has relationships to cancer biology, so the data presented to the user would include results from both.
Re: Publishing, I'm going to provide raw data to scientists and create a venue for them to "blog" about these datasets. I think science needs to move incrementally (at internet speed) and get away from taking 3 years to produce a study and publishing a big paper of only positive data. Also, I'd like for the "peer review" portion to be more transparent, so that we can avoid the insane bias that goes into peer review.
Goal 2: Create "big data" by combining small academic science results into a big ass database. Meta data could be the new preliminary data for academic grants.
So yeah, if anyone is interested in playing with this, let me know.
klg2142 @t columbia.edu
A couple years ago, I spent many nights and weekends working on the academic publishing problem. The effort culminated in a massive hypermedia-style XML schema for distributed and inter-connected publishing, referencing, archiving, etc. There were hundreds of elements just in the common metadata model before I even got around to defining content modules.
Then something hit me like a ton of bricks. I think it was seeing backbone.js for the first time. I realized how quickly web technology was moving forward, how easy it was becoming, and, by contrast, how absolutely shitty it was going to be to write mountains of XSLT on top of my huge DTD. Even in my attempt to create something really different, my approach was still totally clouded by the prevailing anti-wisdom of the academic publishing technology community.
I realized I was on the wrong path. It was a great thought exercise that contributed immeasurably to my day work, but I had to move on.
Happy to share more information if you like, though I'd need to dig the files out of deep storage.
There a perfectly viable alternatives, Open Source and free to use e.g. Zotero et al.
But it does add another example of why we should be wary of even well-meaning for-profit companies, without some kind of more solid guarantee that they won't sell out in the future. For stuff like this, either a nonprofit foundation, or at least a forkable open-source version of the platform, seem like necessary prerequisites if you want to ensure that Elsevier-and-co can't buy it out. I guess a company 100%-owned by a strong open-culture advocate could be reliable also, but it gets more complex when investors are in the mix.
Also a reason I don't trust academia.edu compared to, say, the arXiv.
Nothing we've done over the past 4 years should give you reason to worry and there's plenty of reason to believe that Elsevier doesn't want to piss off our community.
Choice quote: "For that reason then I co-founded PeerJ, an Open Access journal, with one aim of never being in the position to take shit ever again from a closed publisher."
I'm not 100% behind the Mendeley hate right now, but they're against all odds. While everything I've heard from the team so far, including on the prominent HN threads, has been reassuring and positive, it's still just words.
People are making predictions about the future right now, and no words will be able to sway public opinion. Only action, and time. It seems Mendeley (or, as of now, Elsevier) are betting on the latter, because there has been no action, only PR.
It means that a week ago CEO could make the same promises and be heard seriously, but the same CEO promises right now are not worth the paper they're not written on.
Now at any point in the future all the Mendeley 'openness' promises can be easily broken by Elsevier, so they either know that all the promises they're making now are empty (i.e., lying intentionally) or they don't know that (then they're naive and incompetent as general managers).
Promises can be made by those in control. Leaders in public companies can be considered in control. Leaders in privately held companies can be considered in control if their public vision and roadmap is aligned with the owner. But if the owner has a clear interest to change the roadmap - then it would be imprudent to rely on such a roadmap. Elsevier has a reputation of intentionally sabotaging projects (say, gov't initiatives) that should bring openness - if they fool you twice, shame on you.
And for broke, internet saavy students, free stuff with a promise of a new groundbreaking trend in science was enough to lure them.
That started being enforced for .edu in 2001, but previous registrants were grandfathered in. The registrar did manage to evict a bunch of the questionable .edus in 2003, by stepping up enforcement of technical requirements, such as the requirement to have accurate whois information, and to be responsive via the whois-registered email address. But presumably academia.edu survived that purge. I can't actually think of any other prominent for-profit company that still retains an .edu. The registrar also now prohibits transferring them, so you can't buy one even if some others have survived (though maybe you could lease it).
Even right here on HN there have been many posts about such situations some time after acquisitions; and Elsvier reasonably does have practical motivation to interfere here and there.
Such arms-length separations are often published in mergers&acquisitions PR and practically never happen in practice, they all get abused - should we really believe that Elsevier is so exceptionally more etchical than most other companies?
They have that "remote" in their hands. They have promised not to use it. Will they?
Or build it yourself if so inclined/able:
I chose it a few months ago over mendeley because it allowed me to search in the PDF annotations, which isn't possible with mendeley. I recall mendeley could search notes added to a PDF file (one text area for the whole file), but not within sticky notes attached to specific pages, so it was impossible to search the annotations I made and also have those annotations appear on the relevant part of the PDF.
The other thing I like about qiqqa is that it allows us to have a shared library on our local server, instead of having to send all our data to the cloud.
Both are great desktop tools for full text search across many PDF files, even those that need OCR. Before I was using google desktop for this function, and qiqqa is definitely a step up.
And yet, people are continually surprised and disappointed when a company takes a profitable course of action, rather than ignoring profits for altruistic reasons.
Likewise, I could be surprised that a fancy restaurant replaced all their silverware with disposable plastic. It would maximize their profits that night, but destroy their reputation and hence long-term profits.
I think this is a fairly recent phenomenon, that's gone hand in hand with the development of the Internet.
First, we had companies without business plans (or profits) that peaked in the 90s. That bubble burst, but the reputation of "something for nothing" has lingered.
Companies have since found new ways to monetize users (e.g. targeted advertising) in a way that's mostly transparent to the users. This has perpetuated the sense of "something for nothing" associated with online products and services.
Please don't lecture me about capitalism. I had enough of that when I took a degree in economics.
But none of that is because Elsevier has suddenly decided to support open access. It's because buying and developing Mendeley is an affordable way for Elsevier to launder its godawful reputation. All the smiling emoticons in the world don't change that.
AFAIK, the open source tools cannot much the maturity of Mendeley, am I wrong? In this age and time, how hard can it be to clone a service like that?
> I think Mendeley had more advantages over Zotero than the social aspect
> (which I never used). Mendeley could automatically incorporate your
> folder of orphan PDFs into your library
> automatically fetching the bibliographic info.
(Those two repositories are the greatest things about Zotero, in my opinion. Holy crap.)
> It had a nice dedicated desktop client for searching your library
Is the standalone client decent? Is the meta-data retrieval as good as Mendeley?
I think the standalone client is actually based on Gecko SDK and possibly xulrunner, so calling it standalone might be a little unfair of me. However, it certainly doesn't require Firefox itself...
Here's to hoping that Elsevier wont revoke your pdfs!
(Disclosure: I'm part of the Mendeley team)
There is no mention anywhere of any other way of using it except on the download page.
The first time I went there I didn't click on the download button because I didn't want a browser-based app.
Instead of just telling someone they're wrong, explain why. How is Zotero not a browser-based application, and how does it do everything OP described?
Zotero retrieves PDF metadata using a Google Scholar lookup, a method that Mendeley later adopted:
This process can also be applied to a watch folder using the third-party add-on ZotFile (Zotero supports extensions):
Zotero has always allowed all kinds of searching of metadata and content:
Zotero also includes notes (and these notes can be pulled from PDF annotations using ZotFile):
shoot me an email if you want to chat more (it's in my profile)
elsevier's business practices are well documented and the protest is not just manned by some fringe people but has support from prestigious institutions and scholars.
with each new round like this people will educate themselves even more about open access and contemporary free and open source tools for academic work.
zotero probably will win this out and be pushed to mimic mendely features soon enough. zotero already is pretty good but its social features need to developed or integrated with other platforms like arxiv or academia.net.
last not least given googles science-bias and foothold in academia not least with google-scholar and google docs I wonder why they haven't made a move with respect to citation management.
Change will happen once open access journals get A level status. If there's enough that are sufficiently peer reviewed a simple legislative fix (for state funded/supported education which is the case for most forms of education) would be to treat open access publications preferential when it comes to hireing new academic staff.
As someone with the long term vision of massive changes in education towards e-learning I think the way to attack this is to actually couple OA initiatives with sites like coursera, edx etc.
How deep are the Buffet/Gates pockets, maybe just buying up a bunch of content and freeing it might be the easiest path.
There's no sign of freeing it, though.
As mentioned in this blog it would seem the wisest thing would be to switch for the moment and keep an eye on mendeley.
Who knows, maybe they really will change Elsevier, I doubt it but you never know.
After all, given the backlash Elsevier know this is their ONE (long-haul) chance to redeem themselves. Screw this up and they are totally beyond hope (For those who might not think they already are)
Papers purchased by Sinauer in early 2013
part of Thompson-Reuters
free and open, backed by a major non-profit organization
Hopefully this will be good news for zotero which is open source.
And hopefully it will be really bad news for endnote which is one of the worst commercial programs I've ever tried to use.
It's a real bummer. There's so much good stuff locked up in these publishing houses.
However, more likely, it wants to be able to say, "See, we are committed to being open", and continue with its primarily closed practices.
The same will happen here.
Sounds about right.