The Blogging Grouch hopes that all LibraryLink readers returned safe and happy from the hurried exile forced upon us by that bad tempered lady, RITA. We all suffer at the sight of the real victims of the storm’s impact, and the BG is surely not alone in hoping that we don’t need to go any further into the alphabet.
Some years ago there was a book called Adam’s Task, a serious work of animal biology if I recall, the title of which referenced that line in Genesis where God tells Adam to name all the animals. Mark Twain had some fun with that notion, I think…”because it looks like a horse”. All Librarians have a hidden or not so hidden interest in classification schemes. We gravitate to them they way suckers do to TV promo “give aways” that turn out to be swindles. We can’t help it; it’s what we do, as they say nowadays. So, when the Blogging Grouch read an item in the newest Nature about a new resource for animal taxonomy, is it any wonder that his heart raced and respiraton rate soared? The item is actually a proposal for an online system, to be called Zoobank, which would serve as a worldwide registry of animal species and their taxonomic relationships. Andrew Polaszek, of the Natural History Museum in London, writes that many new animal species are identified each year and names are assigned according to the rules of the International Commission on Zoologic Nomenclature (ICZN), the keeper of the Linnean Flame in today’s world, but these identifications are scattered through a welter of specialist journals, academic conferences, letters to journals and other publication outlets. Zoobank would allow new species to be notified to a central registry and allow comments from other experts immediately on “publication”. The obvious analogy is Genbank. Polazek and colleagues assert that something like this is necessary to bring taxonomy up to technological snuff, end duplication of effort and in general move this vital discipline into the new century. A few problems remain, like money, but read the piece and see.
Zoobank
It’s time for a little good luck, don’t you think? The Grouch read an absorbing Op-Ed in Sunday’s NYTimes, written by Dr. Lisa Randall of the Physics faculty at Harvard. In a careful and thoughtful exposition, she states that much of the gulf between scientists and other people trying to understand what scientists are up is traceable to language. Scientists may not always be aware, or may not care, how the public understands words that appear to have the same meaning in both
“domains”, but really don’t. One such word is “theory”. Another, “relativity”. And a nice third, “uncertainty” and in the much-misunderstood Uncertainty Principle. Each of these terms has a very precise “semantic freight” to the scientific practitioner, but that precision often gets lost when discussion leaves the seminar room, or the pages of professional journals, and hits CNN. Lab slang may get promoted to official terminology, leaving the Citizen to puzzle about how subatomic particles can have “flavor” or “charm”, for example. The BG has always harbored a little Lower Class resentment against people who talk like that, wondering if these guys are just laughing at the stiffs who fund their research but who couldn’t follow three minutes of a physics lecture. Dr. Randall covers some of this terrain, and then goes on to talk about some ideas that are really hard to understand, and visualize….extra dimensionality for one. This, as it happens, is the author’s specialty. She has written extensively on this topic and her work has been very widely quoted and cited. The good news, you ask? Well, the BG was trying to find the text online for this week’s LibraryLink but came up dry, until today when Scitech Daily Review made a link available to The Edge, an egg-head zine which has arranged with the NYT to offer Dr. Randall’s remarks online.
The Edge
Google has become the British Empire of the web…the sun never sets on it, or at least it seems that way, since it’s hard to open the morning paper or login to a favorite news site without tripping over a Google story. One of the products Google has launched recently is Scholar, which aims at bringing to the web the contents of scholarly/academic publications in the learned disciplines. At issue here is the uncomfortable fact that a lot of web content is completely useless for anything resembling serious academic work. Since Google, as a search engine, trawls the web and since there are no editorial or methodological controls on who can publish what, the hit list on any given search is likely to bring up gems and trash in a very lopsided ratio. Scholar aims to fill this quality gap. System users can invoke this search module and be reasonably sure that the sources retrieved in response to any query will be limited to serious academic works. The Blogging Grouch has been a bit neglectful of Google Scholar, frankly, but has resolved to keep playing with it. The system has both basic and advanced search modes, and the Grouch prefers the latter, but results with the basic operation were OK. There is some background information, but it’s rather sketchy, especially on how documents get into Scholar in the first place. Some items in the results list open to full text but others so not. They take the searcher to a page with ID/password challenge. Viewed from this chair, Scholar is leagues away from the way established literature search services such as MEDLINE or CAS operate. But, Google gets roses from the BG for even trying to make academic work more generally available. More on Scholar later.
Connect to Google, and Select Scholar from the choices above the query line.
The Christian Science Monitor (CSM) gave a nice review to a new book by Peter Watson called IDEAS: a history of thought and invention from Fire to Freud. The CSM scribe, Merle Rubin, contrasted a certain American timorousness in expressing opinions and drawing in bold strokes with a British willlingness to go out on a limb and make judgments, even if somebody may not like it. Peter Watson seems to represent this strain of independence admirably. The mere title tells you that this guy is no wimp when it comes to staking a claim. You can expect opinions and judgments, by the bushel, and some of them will probably be very annoying. The Blogging Grouch is writing this one down in the Little Black Book. Cooler weather is coming (it is, isn’t it?) and wrestling with IDEAS might be a good way to spend a couple of those long winter evenings.
Here’s the CSM review:
Ideas
The article in PLoS Medicine ,which stated that many reports of research results are false, has drawn some comments which summarize the paper’s conclusions, while pointing out that many of the pitfalls hightlighted by the author are well-known already, and that problems inherent in medical research might be more strictly dealt with in the literature of other other disciplines. Medical researchers must contend with pesky humans and their odd behavior, like not taking their meds, for one thing. On the other hand, if these dangers are well known, how come authors are writing and editors accepting papers that feature small samples, weak effects, poor study design, etc?
Reviewers and editors are supposed to be guarding against exactly that. Are there too many journals publishing too many articles?
New Scientist
Economist
Ben Goldacre, a UK physician, owns a blog called Bad Science in which he talks about, well, you know. He published an article in the GUARDIAN in which he attacks the British media, print and broadcast, for their utterly execrable explanations of stories about science. Not only do they fail to explain science stories interestingly, or even correctly, they use them in some perverse ways of their own. Dr. G creates a simple taxonomy for the way the “press” handles items of scientific character. Some are treated as wacky stories: a “slap- your- forehead- in -astonishment- at- those -weirdos ” approach. Another favorite is the scare story in which some actually existing risk is magnified into an imminently threatening catastrophe…the “Flesh-Eating Bacterium” is the Grouch’s favorite. Lastly, there’s the “breakthrough” story, in which some interesting, perhaps promising line of investigation is inflated in importance well beyond any reasonable, or even sane, expectation. Goldacre gives examples of each kind. He’s very tough on the press, and tougher on the “science editors” who let these abuses continue, but suggests that maybe the editors don’t know enough science themselves to see the problem. The Grouch took a look at the Bad Science blog. I guess we can take comfort, of a chilly sort, in knowing that pseudoscientific flummery and scamming are flourishing across the Pond at least as well as they are here. The posts on Penta Water are funny. What is it about water, anyway?
To read the Guardian piece, go to Scitech Daily Review. It’s in the middle section, Books and Media
Scitech Daily
The blog can be found:
Bad Science
Along with millions of others, the Grouch watched in astonishment as the intricate complex of communications technologies seemed to collapse during and after Hurricane KATRINA. Survivors were reduced to the most primitive methods of asking for information about missing relatives or friends, such as scrawling messages on wreckage…methods that differed little from those used by survivors of bombing raids on German cities 60 years ago. Technology Review reports on several new techniques which might survive such events more robustly. Various WiFi linking methods and an approach called “mesh networking”, which de-emphasizes the role of network nodes in forwarding messages might offer more secure and survivable communications in natural disasters. Well, OK, it’s worth a try, but the Grouch is a bit skeptical. Spiffy communications networks of whatever character will need power, or batteries, or both. Nobody has figured a way around that one. From early reports, it seems that both fuel for generator power and batteries for devices were not on hand in adequate amounts, since pre-storm planning didn’t foresee more than a few days of operation off the grid. Read it and see what you think.
Networks
The BMJ reports on the use of novels written especially to present ethical problems that can occur in different areas of clinical practice. Brian Hurwitz edits the Living Literature Series, which contains the novels designed to serve as “igniters” for discussion in ethics classes and seminars for health professionals. Paternity and Double Trouble profile questions arising from assisted fertility technologies, while Vacant Possession is concerned with difficulties arising in decision making for the mentally handicapped. Judging from the review, all three books stress the role of unintended consequences and how things can go wrong despite everyone’s best intentions. The Grouch found the BMJ piece preachy and tiresome. While medical triumphalism needs to be resisted, so does gloom. And, the Grouch has to mention that courses in the Institute of Medical Humanites here were using Tolstoy’s Death of Ivan Ilyitch in the same role some years ago. But, writing and publishing stories specifically for this role does seem to be something new.
Read the BMJ article:
Fiction
Flannery O’ Connor thought so, and she gave that title to one of her novellas*. In an article appearing in the web zine First Monday, John Willinsky explores what he calls the unacknowledged convergence of open source, open access and open science. The piece resists easy summarization, but the author sketches the history of the open source phenomenon in software, the advent of open access publishing and the idea of open sciences, that is, the attitude that research findings should be freely shared, in the hope that fellow members of the guild will take the ideas and in some fashion make them more interesting and useful. Willinsky is a professor at UBC in Vancouver, whose interests include studying the history of technology, and he hopes to trace the correspondences existing among these three apparently disparate phenomena, which he regards as “resistance movements” to the improper and destructive extension of intellectual property rights. The author points out what he regards as strong similarities in motivation and in the mechanics of reward between those who create open source code and those who conduct scientific research, namely the desire to work on interesting problems and to solve them, elegantly. The article has a large bibliography and many interesting notes. The message is that these three streams of action share common goals, and that society would benefit more if they could find ways to work together more effectively.
Three by Flannery O’Connor: Wise Blood/the Violent Bear It Away/Everything That Rises Must Converge (Signet Classics (Paperback)) (Mass Market Paperback)
Read the First Monday article:
Convergence