Archive for August, 2010

[2b2k] Open Access articles accelerate science?

A study by Gunther Eysenbach in PLoS Biology suggests that open access articles “are more immediately recognized and cited by peers than non-OA articles published in the same journal.” Therefore, he concludes, “OA is likely to benefit science by accelerating dissemination and uptake of research findings.”

The study consisted of comparing citations among OA and non-OA articles published June 8, 2004 – December 20, 2004, in PNAS: Proceedings of the National Academy of Sciences. (Thanks to Don Marti for the link.)


[2b2k] Nature Mag. vs. Univ of California

Nature and the University of California are in a negotiation that at the moment looks more like a game of chicken. Norman Oder has a very interesting post about it at Library Journal. “UC says it currently pays $4,465 per NPG [Nature Publishing Group] journal, while the proposed cost for 2011 is $17,479. Nature responds that the proposed cost per download represents a very good value.” Nature contends that the current pricing represents and overly-generous discount. Further, Nature points to a per-download cost of $0.56 under the new prices. Keith Yamamoto, a professor and executive vice dean at the University of California San Francisco, is threatening to organize a UC boycott of Nature titles.

It’s all very complex and I don’t claim to understand it. But it is yet one more indication that this system is very broken.


[2b2k] Scientific transparency vs. trust

Last January, Jean-Claude Bradley, an associate professor of chemistry at Drexel, posted about an assignment he gave his students: He asked them to find five different sources for the properties of a chemicals of their choosing. The results were sobering.

For example, in one case a paper that had spent five months undergoing peer review before being accepted by Biotechnology and Bioprocess Engineering got the water solubility of the chemical extract of green tea (EGCG) wrong. The source of the information had it right — caffeine is 21.7 grams per liter and EGCG is 5g/l — but likely through a transcription error, the number for caffeine got appended to the number for EGCG, resulting in EGCG’s solubility being reported in the paper not as 5 but as 521.7. That number is off by two orders of magnitude, and is so high that you’d think one of the peer reviewers or editors would have caught it. The chain of data in this case goes back through several more sources to a published experiment that, unfortunately, does not contain enough information to enable us (well, chemists like Jean-Claude) to fully judge its accuracy.

Jean-Claude’s point is not that all scientific data is wrong. Rather, it is that “trust should have no part in science.” Instead we should be able to check the sources of data, preferably all the way back to the lab notebooks and the raw instrument readings. That’s the impetus behind Jean-Claude’s open notebook science initiative.

Note that in this case, the correction to the published error is likely to come via a blog, but our ecology does not have an obvious or routine way in which good bloggy information can drive out bad published data. But, no nostalgia here, please! As Jean-Claude’s post shows, for all its peer reviewers and expert editors, the old ecology gave errors a stubborn rootedness.

If you accept that humans are more fallible than we’d like, then you build systems that accommodate change. Paper is not very accommodating in this regard. Worse, its fixity has contributed to our false confidence that we can get things right and know when we’ve done so.


[2b2k] Philosophy as writing, science as publishing

I’ve been struggling with a section of my book that maintains that science is a form of publishing. It’s a useful lens, I think, for understanding some of the ways the Net is changing science.

This morning, I went for a book to read on the bus and came across Richard Rorty‘s Consequences of Pragmatism, a collection of essays that I had read half of and put aside about six months ago. And what’s the very next essay I was up to in it? “Philosophy as a Kind of Writing.” Here are the opening paragraphs:

Here is one way to look at physics: there are some invisible things which are parts of everything else and whose behavior determines the way everything else works. Physics is the search for an accurate description of those invisible things, and it proceeds by finding better and better explanations of the visible. …

Here is another way of looking at physics: the physicists are men looking for new interpretations of the Book of Nature. After each pedestrian period of normal science, they dream up a new model …. and then they announce that the true meaning of the Book has been discovered. But, of course, it never is, any more than is the true meaning of Coriolanus or the Dunciad or the Phenomenology of Spirit or the Philosophical Investigations. What makes them physicists is that their writings are commentaries on the writings of earlier interpreters of Nature, not that they all are someow “talking about the same thing,” the same invisibilia Dei sive naturae toward which their inquiries steadily converge.

Rorty’s essay applies the same distinction to philosophy as a way of explicating Derrida … and it is one of the clearest, most sympathetic, and most delightful explanations I’ve encountered.


[2b2k] Mendeley and the ecology of science

Perhaps the coolest thing about writing a book is that you have an excuse to interview people you otherwise wouldn’t get to talk with.

Today I interviewed Victor Henning, the co-founder of Mendeley, a very popular desktop app for researchers that indexes your PDFs, provides social reading and researching tools, and aggregates anonymized information about what researchers are actually reading and annotating. There’s a lot packed into Mendeley, all designed to help researchers find out what they need to know, primarily though social means.

Victor and some friends founded Mendeley as grad students when they discovered that although they were in different fields, their research needs and processes were very similar. In the twenty months since its launch in January 2009, it’s grown to 450,000 users, with 33 million documents in its database.

I’m thinking of using Mendeley as an example of how the scientific landscape has changed. Although it’s hard to find uncredentialed amateurs who, thanks to the Web, have made large individual contributions to science — for most of the sciences, you need lots of training and access to expensive equipment — the Net has changed the world in which credentialed experts work. For example, Mendeley is able to provide a much more responsive picture of the trendlines in scientific research than the “impact factor” by which journals measure their significance; the impact factor looks at the number of citations of the articles in a journal over the prior two years, divided by the total number of articles in the journal. Two to three years is a long time to wait to measure impact. Plus, as Victor points out, Mendeley can be much more granular.

As Victor says: “My personal opinion is that some form of credentials will always matter. It’s a heuristic to decide if some other person can be trusted. But credentials will not just be that someone is a tenured profession or is at a top isnstution or is published in Science or Nature. In the Mendeley context it may be that his paper has lots of readers, or lots of rankings or tags.”

The old authorities and credentials are still there and are likely to continue to have weight. But the ocean in which they swim is now filled with a lot more fish.


[2b2k] Suggestions wanted: Amateur scientists

For the section of my book I’m currently writing, I’m looking for examples of contributions to science by amateurs in the Age of the Web. These can be crowd-sourcings, individuals with ideas or data that pushed a science forward, or some category I am not yet considering. (I’ve already briefly noted Make and Maker Faire. I’ve also spent some time in the book on Innocentive and other contests, but if you have a particular good example don’t assume I already know about it!)

I’d be grateful for any ideas or suggestions. Thanks!


[2b2k] Books: The early years

I ‘m reading The Coming of the Book, by Lucien Febvre and Henri-Jean Martin (1958), who explain the arrival of printed books with an impressive attention to fact-based detail. Amazing scholarship.

Here are some of the points that struck me because of my own peculiar interests in this topic, in page-number order.

The “points ” by which we measure fonts were adopted in the 18th century. They are 144th of the length of the foot of the king of France at that time. (p. 60)

“…the Arab writer Mohammed Ibn Ishaq remarked in 989: ‘The Chinese write their religious books and their works of scholarship on sheets of paper which open like a fan. ‘ ” (p. 73). [If that 's how the West had written books, we wouldn 't have taken long-form thinking as the pinnacle of human reason.]

The book brought about a standardization of script. “Regional styles were the first to disappear. Then, more slowly the major forms of script were standardized until eventually the new roman type triumphed in the greater part of Europe… ” (80). Roman script was a simpler face that emulated the style of the classical Romans.

Gutenberg invented the printing press in 1440. Before 1500, about 20 million books were printed. (248) The population of Europe at that time was under 100 million. (249)

“Like their modern counterparts, 15th-century publishers only financed the kind of book they felt sure would sell enough copies to show a profit in a reasonable time. We should not therefore be surprised to find that the immediate effect of printing was merely to further increase the circulation of those works which had already enjoyed success in manuscript, and often to consign other less popular texts to oblivion. ” (249) [No long tail here!]

Of the books printed before 1500, about 77% were in Latin. 45% were religious books. 10% were on law. 10% were on scientific topics. (249) That meant there were about 3,000 different science titles printed. (258)

The initial effect of the printing press was to make the most popular books — the traditional classics — more popular, and to drive less-popular classics into non-printed oblivion. (253-4) “Especially often printed were the great medieval compilations in which …the sum total of available knowledge on all subjects was thought to lie… ” (258) The classics that “were already being read in the 15th century became even more widely known. ” (265)

Most of the science that was published was “of no lasting interest. ” Many of the science books were about “practical astrology. ” “So, printing does not seem to have played much part in developing scientific theory at the start, though it seems to have helped draw public attention to technical matters. ” (259)

“…at the outset…printing brought about no suddden or radical transformation ” although it did force the publishers to decide which books to print and which to ignore. (260) Many works we now treasure were ignored by printers during the 15th century and had to be rediscovered, including the Letters of Heloise and Abelard, most of Roger Bacon ‘s works, and the Chanson de Roland. (261)

“A desire for typographic accuracy and the constant search for the best manuscript version of a text … provided an immense stimulus for philological studies. ” (261) It also had printers searching for the authors of works that were frequently anonymous. Only now did artists begin to sign their works. (261)

By 1550, hand-written books were rarely used. (262) 30,000-35,000 different editions were printed befor 1500. Between 1500 and 1600, about 150,000-2000,000 different editions and between 150-200 million copies were printed. (262) By 1550, private collections of 500 books were common. (262)

To increase their markets, printers started commissioning and publishing translations. (272)

French only became the official language of France in 1539. (273)

Although printing helped some scholars, “on the whole it could not be said to have hastened the acceptance of new ideas or knowledge. In fact, by popularising long cherish beliefs, strengthening traditional prejudices and giving authority to seductive fallacies, it could even be said to have represented an obstacle to the acceptance of many new ideas. ” For example, printing didn ‘t help the public absorb or accept the geographic discoveries made in the 16th century. (278) [Printed books are echo chambers! :)]
TAGS: -berkman


Two tweets worth

1. A show at the Des Moines Art Center is featuring works overstuff and overcrowded over the ages.

A year or so ago, Des Moines Art Center curator Amy Worthen noticed a pattern in the things the museum was adding to its permanent collection. Many of the new paintings and prints were crammed with imagery, top to bottom, side to side.

“There was just a lot stuff going on in the works,” she said. “I mean, insanely packed.”

She wondered why, especially since the artwork was created by artists with entirely different backgrounds and styles.

Cool idea for a theme.

2. I like AKMAs calm-but-stern commentary on Anne Rices decision to depart a Christianity that she has defined for herself in the worst possible way. AKMA has a great last line, although I suspect a person not as kind would have substituted “Anne Rice” for “Flannery OConnor.”