Andrew Jaffe: Leaves on the Line

Some of the biggest issues in science today have to do with the prosaic questions of publishing: How do we disseminate scientific work and the underlying scientific data so that the maximum number of scientists (and members of the public) have access to it? How do we ensure that proper credit is given for work? How do we guard against fraud? The internet provides the infrastructure for solving at least some of these problems, and I'll discuss a few newsworthy aspects of the problem in this and the next few posts.

The Creative Commons is a project to provide a set of licenses that allow creators of works in various media to reserve some rights to themselves, but otherwise allow free access and use of their intellectual or artistic creations -- in the same spirit as free and open-source software. The Creative Commons group is launching a new initiative this year, Science Commons:

The mission of Science Commons is to encourage scientific innovation by making it easier for scientists, universities, and industries to use literature, data, and other scientific intellectual property and to share their knowledge with others. Science Commons works within current copyright and patent law to promote legal and technical mechanisms that remove barriers to sharing.

(Indeed, the Public Library of Science will be using a Creative Commons license.)

Note the intent here: not just scientific publications, but "data and other scientific intellectual property" as well. As I discussed in this post, much of the physics and astrophysics literature is already publicly available through archive servers like arXiv.org, although these don't provide the final versions of articles, usually only accessible directly through the appropriate journals or their web sites (and even then, only with the appropriate personal or institutional subscription). Moreover, a great deal of astrophysical data is indeed freely available online through services like the Hubble Space Telescope archive, NASA's Astrophysical Data System and other related sites. Of course, we astrophysicists are lucky: our science is funded largely by governments who can enforce open access, not by companies who may have a financial incentive for secrecy. And indeed, much of the open-access publishing effort seems concentrated towards the life sciences, where the financial and human stakes are highest.

Still, this won't be trivial to implement, even in astrophysics: scientists work very hard for their data, and they want appropriate control over it -- and they usually want at least some sort of proprietary period before anyone else can see it. (And I've been involved in some projects that, to my chagrin, have never released their raw data to the public.) For example, ESO, the European Southern Observatories enforces the rule that only scientists in member countries will have direct access to the data gathered at its telescopes (although, ESO data will start to become freely available to the international astronomical community in a phased manner). On the other hand, data from US observatories like the Hubble Space Telescope is freely available to all, after a one-year proprietary period.

For the technically-minded, here's an article (via The Role of RSS in Science Publishing: Syndication and Annotation on the Web, by Hammond, Hannay, and Lund of the Nature Publishing Group:

RSS is one of a new breed of technologies that is contributing to the ever-expanding dominance of the Web as the pre-eminent, global information medium. It is intimately connected with—though not bound to—social environments such as blogs and wikis, annotation tools such as del.icio.us [1], Flickr [2] and Furl [3], and more recent hybrid utilities such as JotSpot [4], which are reshaping and redefining our view of the Web that has been built up and sustained over the last 10 years and more [n1]. Indeed, Tim Berners-Lee's original conception of the Web [5] was much more of a shared collaboratory than the flat, read-only kaleidoscope"

Read more...

RSS, which stands for, among other things, "Really Simple Syndication", is a file format based on XML, for quickly promulgating various sorts of summary information through the web; it's used mostly for news headlines and blogs, although it's already being used to list the latest preprints at the astrophysics archive server. Perhaps more importantly, it's also being used to foster discussion of these articles at sites like CosmoCoffee (RSS here) and Physics Comments (RSS here). You can see RSS examples for my blog from the links at the top of this page. (Due to a depressing controversy over the different RSS formats, I can't provide just a single definitive link to a "definition" of RSS, but check the appropriate footnotes in the article above, or the wikipedia.)

(To read RSS, you need a standalone program, although current versions of the Firefox browser and Thunderbird mail reader have rudimentary -- very rudimentary -- capabilities; the next generation of Apple's Safari browser is meant to be RSS-aware, too. Right now, I use the great NetNewsWire on my Mac; I haven't found a really good RSS reader for my Linux machine at work -- does anyone know of one?)

In astrophysics, we are very slowly moving toward various XML formats for data interchange, since XML can very easily be used to not only contain the so-called "raw data" (such as an astronomical image) but also the accompanying (and even more so-called) "metadata", information about the raw data (such as where in the sky the image lies, when it was taken, on what telescope, etc.). In particular, VOTable will be the underlying format for Virtual Observatories such as AstroGrid which I briefly discussed here. ESA's Planck Surveyor satellite, in which I'm also involved, will also likely use some sort of XML underneath.

The article discusses how RSS is currently being used in science publishing (although it emphasized publishing via already-extant paper journals rather than services like the archive), in particular at Nature, where the authors are employed, what sort of protocols for metadata may be needed, and other scientific uses of RSS such as data exchange and even podcasting. (I think the article gets many aspects of the RSS version history incorrect; I also feel it's worth explicitly mentioning the name of alpha-blogger Dave Winer, who more or less invented RSS and much of the blogging infrastructure we know of today.)

On its own, all this is just boring techie jargon. However, when combined with the Science Commons ideas from the last post, we begin to get a full model for disseminating scientific information: data and publications freely exchanged on the web, with open standards so authors and publishers don't have to continually re-invent the appropriate wheels, with appropriate metadata so other scientists know what they're getting, and know how to properly reference it.

Finally, my colleague Sean Carroll writes about David Politzer's Nobel-prize speech, and giving credit where it's due.

There's a lot to criticize about the US campaign system, and the politics that it supports, but there's no denying that both Democrats and Republicans knew that something big was at stake in the 2004 elections. Here in the UK, the Tories -- thankfully no longer the "natural party of government" -- are showing what they really think of the political process with their exciting new campaign slogan: "Value for Money and Lower Taxes".

To be fair, Labour's back-to-the-sixties faux-psychedelia campaign is only marginally better. And in the interests of equal time, the Liberal Democrats show themselves to be serious, if dour -- although "The Real Opposition" may not even be a realistic goal. (Some day, I'll remember to blog about what "liberal" means here and back in the US).

It almost makes me wish for the evil Swift Boat Veterans. And Dan Rather...

Creationist Textbook Stickers Declared Unconstitutional: "An anonymous reader writes 'MSNBC reports that a judge in Atlanta, GA has ruled that a sticker placed on all textbooks in Cobb County stating that 'Evolution is a theory, not a fact,' is unconstitutional, and ordered that all stickers be removed.'" (Via Slashdot.)

Meanwhile, here in the UK, not only does the government refuse to condemn the teaching of creationism, it still actively encourages rich creationist demagogues' control of schools.

According to the BBC, Oxford University (where I've heretofore been proud to be a long-term part-time visitor in Astrophysics), presently the fourth largest consumer of green electricity in the UK is considering moving back to fossil fuels. More specifically, it's hired `"energy-purchasing consultants" Epal' (whom I can't find anywhere on the web, strangely) to investigate its options. Despite all the talk about top-up fees and science funding in the UK, Oxford (and especially its Colleges) is one of the wealthier entities in the UK, and it should use its cash to worry about the long term, not the bottom line.

From The New York Times:

The president of Harvard University, Lawrence H. Summers, who offended some women...

[and men!]

...at an academic conference last week by suggesting that innate differences in sex may explain why fewer women succeed in science and math careers, stood by his comments yesterday but said he regretted if they were misunderstood.

Economists, like (other?) scientists, have a hard time shaking the illusion of their own rationality -- they don't really understand how their own decisions can be based on anything other than the truth. So (according to The Guardian):

During Dr Summers's presidency, the number of tenured jobs offered to women has fallen from 36% to 13%. Last year, only four of 32 tenured job openings were offered to women.

Of course this must be due to real differences, not, say, unconscious discrimination. Really, every day we all see bias and prejudice at work, insidiously: we are more comfortable with colleagues like us (whether it's gender, race, education, geekiness, whatever), so we unconsciously make tiny choices showing those preferences, tiny choices that in the end add up to real differences in the way people are treated.

Meanwhile, other US universities from MIT to Princeton and Duke are actually making changes -- and seeing the effects. Like Harvard, most of the UK is lagging behind.

Following up on my a previous posts about the future of the Hubble Space Telescope and on manned and unmanned space exploration: By now the web has discovered that the Bush administration has decided to remove funding for Hubble Space Telescope servicing (robotic and human) from the next budget. Of course, the purity of the Administration's motives leave plenty of room for doubt. As DavidNYC puts it in Daily Kos:

But ... the choice is not between $1 bil for Hubble vs. $1 bil for schools or healthcare. Rather, the choice is between $1 bil for Hubble vs. $1 bil for Bushco's insane, cockamamie Martian scheme - a scheme which some commentators believe is just a ruse for the Bushies to proceed apace with their desire to militarize space.

But there's another point, too: it's between $1 billion for Hubble and all the other ways NASA could spend that money -- or all the ways it would be spending it if it weren't for Hubble or Mars (not to mention the more or less useless -- and dangerous -- International Space Station). In particular, it could be for the sputtering Origins Program which could still produce a series of unmanned missions over the coming decades to find planets, image the early universe, and trace the evolution of Black Holes. I'd rather see these missions go forward than eke a few more years out of Hubble, frankly.