Could Elsevier shut down arxiv.org?


They haven’t yet, but they are supporting SOPA, a bill that attempts to roll back Web 2.0 by making it easy to shut down entire sites like wikipedia and craigslist if they contain any user-submitted infringing material. (Here is a hypothetical airline-oriented version of SOPA, with only a little hyperbole about planes in the air.)
I think that appealing to Elsevier’s love of open scientific discourse is misguided. Individual employees there might be civic-minded, but ultimately they have $10 billion worth of reasons not to let the internet drive the costs of scientific publishing down to zero. Fortunately, their business model relies on the help of governments and academics. We can do our part to stop them by not publishing in, or refereeing for, their journals (the link describes other unethical Elsevier practices). Of course, this is easy to say in physics, harder in computer science, and a lot harder in fields like medicine.
There is another concrete way to stand up for open access. The White House Office of Science and Technology Policy has requested comments on the question of public access to federally-funded scientific research. Comments should be from “non-Federal stakeholders, including the public, universities, nonprofit and for-profit publishers, libraries, federally funded and non-federally funded research scientists, and other organizations and institutions with a stake in long-term preservation and access to the results of federally funded research.” That’s us!
But don’t procrastinate. The deadline for comments is January 2.
Here is more information, with instructions on how to comment.
Here is also the official government Request For Information with more details.

Why medicine needs scirate.com

Defenders of the traditional publishing model for medicine say that health-related claims need to be vetted by a referee process. But there are heavy costs. In quantum information, one might know the proof of a theorem (e.g. the Quantum Reverse Shannon Theorem) for years without publishing it. But one would rarely publish using data that is itself secret. Unfortunately, this is the norm in public health. It’s ironic that the solution to the 100-year-old Poincaré conjecture was posted on arxiv.org and rapidly verified, while research on fast-moving epidemics like H5N1 (bird flu) is
delayed so that scientists who control grants can establish priority.
All this is old news. But what I hadn’t realized is that the rest of science needs not only arxiv.org, but also scirate.com. Here is a recent and amazing, but disturbingly common, example of scientific fraud. A series of papers were published with seemingly impressive results, huge and expensive clinical trials were planned based on these papers, while other researchers were privately having trouble replicating the results, or even making sense of the plots. But when they raised their concerns, here’s what happened (emphasis added):

In light of all this, the NCI expressed its concern about what was going on to Duke University’s administrators. In October 2009, officials from the university arranged for an external review of the work of Dr Potti and Dr Nevins, and temporarily halted the three trials. The review committee, however, had access only to material supplied by the researchers themselves, and was not presented with either the NCI’s exact concerns or the problems discovered by the team at the Anderson centre. The committee found no problems, and the three trials began enrolling patients again in February 2010.

As with the Schön affair, there were almost comically many lies, including a fake “Rhodes scholarship in Australia” (which you haven’t heard of because it doesn’t exist) on one of the researcher’s CVs. But what if they lied only slightly more cautiously?
By contrast, with scirate.com, refutations of mistaken papers can be quickly crowdsourced. If you know non-quantum scientists, go forth and spread the open-science gospel!

Does the arXiv Forbid Posting Referee Reports?

ArXiv:1007.3202 is a paper whose conclusions I do not agree with (well actually I do think the original EPR paper is “wrong”, but not for the reasons the author gives!)  The abstract of the paper is as follows:

EPR paper [1] contains an error. Its correction leads to a conclusion that position and momentum of a particle can be defined precisely simultaneously, EPR paradox does not exist and uncertainty relations have nothing to do with quantum mechanics. Logic of the EPR paper shows that entangled states of separated particles do not exist and therefore there are no nonlocality in quantum mechanics. Bell’s inequalities are never violated, and results of experiments, proving their violation, are shown to be false. Experiments to prove absence of nonlocality are proposed where Bell’s inequalities are replaced by precise prediction. Interpretation of quantum mechanics in terms of classical field theory is suggested. Censorship against this paper is demonstrated.

Okay, fine, the paper makes some pretty astounding claims (at one point I believe the author simply rediscovers the detector efficiency loop-hole in Bell inequality experiments), but that’s not what really interests me.  What really interests me is the authors claim of censorship.  In particular the paper reports on the authors attempt to submit this paper to a workshop, QUANTUM 2010, whose proceedings would appear in the “International Journal of Quantum Information” and the rejection he received.  Okay, fine, standard story here.  But then the author gives a synopsis of the referee reports, followed by, I think, a more interesting claim:

I am sorry that I did not put here the full referee reports. The ArXiv admin forbidden to do that. I was told that anonymous referee reports are the subject of the copy right law. It is really terrible, if it is true. The referee report is a court verdict against my paper. Imagine that a court verdict is a subject of the copyright law. Then you would never be able to appeal against it. I think that the only punishment to dishonest and irresponsible referees is publication of their repots. It is so evident! But we see that dishonesty and incompetence are protected. I do not agree with such a policy, however I have nothing to do but to take dictation of ArXiv admin.

Is it really true that the arXiv forbids publishing referee reports?  Do referees really retain copyright on the referee reports?  And if so, should it be this way or should referees have to give up copyright on their reports?  Inquiring minds want to know!

Cost of Nearly All of Physics Since the 1990s? 30 Bucks.

Via the arxiv API google group, I see that the arXiv now has made available process PDFs for bulk download from Amazon’s Simple Storage System.  I haven’t had a chance to play around with it, but according to this webpage, the cost is about 15 cents per gigabyte downloaded and the complete set of PDFs is about 200 gigabytes.  Cool, all of physics (and some math and CS :)) for 30 bucks.  (It would be nice to have the source as well as the PDFs, but this is a good change over their prior policy of zero bulk access to the entire corpus of PDFs.)  Anyone had a chance to play with this?

Portrait of a Reviewer as a Young Man

Science is dynamic. Sometimes this means that science is wrong, sometimes it means that science is messy. Mostly it is very self-correcting, given the current state of knowledge. At any given time the body of science knows a lot, but could be overturned when new evidence comes in. What we produce through all of this, however, at the end of the day, are polished journal articles. Polished journal articles.
Every time I think about this disparity, I wonder why different versions of a paper, the referee reports, the author responses, and all editorial reviews aren’t part of the scientific record. In an age where online archiving of data such as this is a minor cost, why is so much of the review process revealed to only the authors, the referees, and the editors?

Detexify Squared

A friend sent me a link to Detextify2:

What is this?
Anyone who works with LaTeX knows how time-consuming it can be to find a symbol in symbols-a4.pdf that you just can’t memorize. Detexify is an attempt to simplify this search.
How does it work?
Just draw the symbol you are looking for into the square area above and look what happens!
My symbol isn’t found!
The symbol may not be trained enough or it is not yet in the list of supported symbols. In the first case you can do the training yourself. In the second case just drop me a line (danishkirel[[[at]]]gmail.com)!
I like this. How can I help?
You could spare some time training Detexify. You could also look at the source on GitHub and if you want to contribute you’re welcome.
Who created Detexify?
Philipp Kühl had the initial idea and Daniel Kirsch made it happen.

Pretty cool. One step closer to the day when I write an equation on a piece of paper and the LaTeX just automagically appears for this at equation.

Film Reviews in Nature Physics?

What in the world is a review for Star Trek doing in Nature Physics? (Thank to reader W for pointing this out.) I mean, at least the review of Angels and Demons has references to physics, but the review of Star Trek, is, well, just a review of Star Trek with no reference physics or science or, well, anything that I could see the audience of Nature Physics relating to.
I’m not saying I don’t appreciate the review, or the book/art section of Nature Physics, but doesn’t this seem a bit out of place. It is too bad, indeed, because the movie does contain time travel, and as Cosmic Sean demonstrated their is ample fodder for a review of Star Trek that at least pulls in some fun physics.
In a related note, Nature physics now requires a statement of author’s contributions. (“Dave Bacon’s contribution was to sit around and crack jokes all day while we worked hard and tried not to get distracted.”)

Comments?…I Don't Have to Show You Any Stinkin' Comments!

One of the more interesting “problems” in Science 2.0 is the lack of commenting on online articles. In particular some journals now allow one to post comments about papers published in the journal. As this friendfeed conversation asks:

Why people do not comment online articles? What is wrong with the online commenting system[s]? I think this is one of the central issues in Science 2.0.

Or as Carl Zimmer commented on comments appearing at PLOS One a few years back:

What I find striking, however, is how quiet it is over at PLOS One. Check out a few for yourself. My search turned up a lot of papers with no discussion attached. Many others had a few comments such as, “This is a neat paper.” There’s nothing like the tough criticism coming out about the new flagellum paper to be found at PLOS One.

Continue reading “Comments?…I Don't Have to Show You Any Stinkin' Comments!”

arXiview: A New iPhone App for the arXiv

Over 9 months ago I decided to apply for teaching tenure track jobs. Then the economy took what can best be described as a massive, ill-aimed, swan dive. Thus creating an incredible amount of stress in my life. So what does a CS/physics research professor do when he’s stress? The answer to that question is available on the iTunes app store today: arXiview. What better way to take out stress and at the same time learn objective C and write an iPhone app that at least one person (yourself) will use?
Continue reading “arXiview: A New iPhone App for the arXiv”

Deleting arXiv References?

A while back, Aram commented on how he had trouble trying to get arXiv links into a paper he had written (read the further comments for a comment indicating that it was not the policy of the journal to do this.)
Which reminded me: I believe I’ve submitted papers with arXiv references to Physical Review A, but looking back over the papers I don’t see any such references unless the paper was never published. Does anyone know Physical Review’s policy on this? A quick scan of the guidelines didn’t yield anything. Shouldn’t Physical Review be allowing these links? Sure if I want to be careful about a paper I’ll check out the published version, but many times, having the preprint around is extremely useful.
Which reminds me even further: am I the only one who finds it extremely annoying that references in Physical Review don’t include the titles of the papers? (Unless, of course I’m writing a PRL, in which the silly four page limit makes me wish I could use doi’s for references alone.)