LibraryLink

The faculty at Harvard Law decided to follow the lead set earlier this year by their other colleagues, and make their publications Open Access. An institutional server will host the publications, which will be searchable through Google Scholar, and other services. The HLS professoriate voted unanimously to adopt OA release of scholarly work conducted there, and this move increases the visibility of OA archiving as a means of disseminating scholarship. By little and little, the notion is gaining ground that personal or institutional archiving of one’s own academic work is a plus for researchers, since the accessibility of these works rises dramatically when they are placed online. There are a number of unanswered questions about all this, and the roles of traditional publication and online archives will, at the least, need to be revised. But the benefits to individual scholars in having their work known are hard to deny.
The Scholar’s Space has a very useful item on this point which you can read at:
Harvard

Researchers in the life sciences have benefited from the existence of very large biological databanks collecting information on gene structure, taxonomy, protein configuration and similar topics, all available to researchers at little or no cost. By contrast, chemical information, although plentiful and enjoying first-class curation, is expensive to access, since such access depends on subscription to the American Chemical Society’s (ACS) services, and this can run into real money, too much money for many researchers and their parent institutions. Chemspider is the brain-child of Antony Williams, a consultant from Wake Forest, NC. Chemspider is exactly that,a spider;that is, a program launched out onto the web to “crawl” it for specific kinds of information. Mr. Williams’ creation looks at publicly available sites of chemical information and reports on what’s been found. There are more than 5,000 hits on the database in the average day. A great deal of information has been gathered so far. The site has some advertising and the revenue from this helps the small force of volunteers who verify the data. Mr. Willliams hope that Chemspider can be improved and that it will help those scientists who are currently unable to afford the ACS systems.
Chemspider

You can also read comments about the Nature piece by Mr. Williams at:
Willams

For a long time, researchers have been struggling to keep some kind of useful order in their personal collections of reprints, copies and, more recently, PDF files downloaded from electronic journals. Nature reports on a new software program, called Papers, developed by two scientists from the Netherlands, that is gathering some praise as a highly useful tool in managing PDF files. Papers features an interface similar to that of Itunes, the Internet music site, and allows its users to tag, sort and retrieve PDF files that have been collected by the searcher. A previous offering, iPapers was developed by a researcher in Japan and has gained a considerable number of users. There are several other programs which have the same goal, and it’s too early to tell which of them will emerge as the ‘dominant life form”, if any do. People tend to stick with the system they have, in part because of familarity and in part because the task of switching to a new program does not seem worth the time and effort, if the old one is doing the job reasonably well.
Papers

In the bad old days, when medicine really couldn’t do much beyond telling what was wrong and giving a guess at about how much time you had to tell the family, call the priest and the lawyer, physicians used a lot of their spare time in making up classifications of diseases, or nosologies. Some of these sound rather odd to us, but they were all efforts to tidy up and make sense of the welter of direct clinical experience by searching for some common elements that could simplify and “rationalize” the mass of empirical findings into some more comprehensible whole. Much of medical history can be considered as the creation and abandonment of various nosologies, and we like to think that the process has come to an end, and that our classfications are accurate and, in some sense,final. An article in the Science section of today’s New York Times shows that the hunt for a better nosology has in no sense come to an end; in fact, it’s taking on some new and interesting forms. A number of researchers have been tracing the activitiy of genes or gene groups and have found that the same combinations seem to be active in quite different diseases. Duchenne muscular dystrophy and heart attack are apparently quite disparate pathologies, but some evidence suggests a very strong link to the same group of genes in both diseases. A map of putative disease connectivity styled the “diseasome” was published last year in PNAS
Diseasome
The Times piece notes that there are zero drugs available for Duchenne’s but about 40 for various heart conditions, so, if there is some deep similarity, would some or any of the heart drugs work on Duchenne’s? There’s more along these lines, including a little cold water from some in psychiatry who are calling for restraint in expectation. But it all is rather intriquing. It reminds the Grouch of the Cladistics movement in biological systematics, which was effort to re-order the taxonomy of animals and plants by basing it on evolutionary similarities rather than on apparent physical resemblances. There was a good bit of literature on this some time ago, but there seems to be less now.

I can’t supply my link to the Times, since it won’t work for most of our readers, but the curious can find it in the paper issue of May 6, and probably on the Times web site.

Things have been happening. People are writing new books. Smart folk are coming up with new gadgets, processes, and ideas. It’s hard to keep abreast with everything. But, we’ll try to review some of the more interesting developments.
The NIH policy on mandatory deposit in PubMed Central of final manuscripts reporting research funded by public money is in place. The sun is still rising and setting, people seem to be getting on with their lives pretty much as before, and the somewhat creaky machine of Academia has, apparently, absorbed this innovation without much difficulty. It’s early days yet, though.
The geniuses at Palo Alto Research Center (PARC) have come up with re-useable paper, or more accurately, vanishing ink. You can read about it at Concurring Opinions , a blog for law school profs. The post describes the technology and raises some legal points, as a law blog should.
Ink
How did we get Science? Or, where did Science come from? Tons of paper and gallons of ink were used in explaining this, but maybe we have some of it wrong. One investigator says we’ve got a lot of it wrong. The experimental tradition of craft and alchemy, yes alchemy, was very stong in the Islamic cultures of the Mediterranean and in late medieval Europe, so there was a very broad base of equipment, process and technique on which emergent Science could be based. William R. Newman has written Atoms and Alchemy: Chymistry and the Experimental Origins of the Scientific Revolution
(U of Chi Press, paper, $30) to explore the intellectual and technical background of the alchemical contributions to what became modern Science. There’s no bigger insult to hurl at a scientist that to say “alchemist”. It connotes fakery, ignorance, pseudo-mysticism and did I mention ignorance. But those guys padding around their laboratoria did learn a lot about distilling, heating metals and cooling them again, acids, etc. And these techniques lay ready to hand, or better, there wasn’t anything else to make use of when the pioneers came along and said: “Hey, let’s make Science!”. There’s a good review in Books and Culture
Review
The UK’s Guardianhas a special supplement called Libraries Unleashed: colleges and universities confront the digital challenge. The slant is definitely Over the Pond, but the variety of topics considered is enought to make this worth reading: ebooks, library buildings, open access publishing, digitization and preservation all get a hearing in this overview:
Guardian

Several web sites are reporting the news that a big German publisher, Bertelsmann, is planning to issue part of the German portion of Wikipedia as a printed volume, to go on sale in September. The price is 19 Euros, and the Wikipedia foundation will get one Euro from each sale. Some folk are scratching their heads, but this move may not be as retro as it sounds. Germany can rightfully boast of a health publishing industry, and the publication of Nachschagewerke or books you look up stuff in, is an important segment of the total effort. The printed WP will feature about 25,000 articles and 1,000 photos or other illustrations, and a team of editors from Bertelsmann is working to select the entries and pare them down to a couple of paragraphs at most. Some have noted that Bertelsmann made some rude remarks about the quality of WP materials, but it seems all has been forgiven and after all, a Euro is a Euro. Is there a market for something you can get more of somewhere else, and at no charge? Well, yes. I can’t vouch for this personally, but I have read that the German WP is less prone to silliness, pointless vandalism and Wikipedia pollitics, and the volunteers’ contributions are of high quality. In the printed version, the WP articles are going to be pared and polished up, and facts will be checked with Teutonic thoroughness (Bertelsmann is a major publisher of reference books, and their editorial/technical staff is very good). I’d buy one, and I’d use it with confidence. I think other people will also.

Most of the world uses the metric system to weigh and measure. We do not, here in the States; it’s not ‘Murican and we ain’t a gonna do it, nosiree! We prefer our own customary measures which are so much easier and not awkward at all…hand me that
13/32 wrench, not that’s an 11/64, yeah, there you go! The metric system was introduced by the First Republic in Revolutionary France, to replace the thousands of traditional measures existing all over the country, so that when you bought liquid or bulk goods, you could be sure that you got the same amount, whether in Paris or Lyons or anywhere else. The zealots not only wanted to get rid of the paralyzing complexity of the older customary measaures, they also wanted to establish new ones that were based some natural standard, one that everybody could understand. So the meter is one forty-millionth of the earth’s circumference. Once you have established a standard like the meter and the kilogram, you isolate a copy of it in a vault someplace where nobody can mess with it, and compare all other copies to it. Simple. Well, no, it’s really not. The reigning assumption about the reference copies was that they wouldn’t change, much or even at all, if kept tucked away. And exactly that seems to be the problem, or at least one of the problems. Scientists have demanded, and obtained, ever more precise ways of determining the value of the constants they use in their work. But, we still use the reference copies of the meter and the kilo, both kept in secure locations in Paris, to check how well the other national copies of the standards, well, I guess “measure up”. And this is where things get weird. It seems that either the refrence copy of the kilogram, called le grand kilo or some of the globally distributed copies, or some of them or all of them are gaining/losing mass. Nobody has a really good explanation for this, but one of the outcomes of efforts to solve the mystery has been a resurgence in efforts to find a natural reference so that everybody can know exactly what a meter and a kilogram really “are”. All this is detailed in a very interesting article appearing in the Los Angeles Times and called The International Kilogram Conundrum. The piece describes some efforts to create a better measure of the kilogram, which might not be so susceptible to variations, but I think the bigger story concerns why is this “mass drift” happening at all?
I have an LA Times link, but I don’t think all our readers can use it, so I recommend that you read the story on 3 Quarks Daily.
Kilo

The blog Concurring Opinions is written by and for law profs. It’s worth looking at, because, law being law, odd and interesting things show up on it, often with even more interesting analysis. Recently, some of the posts there have been dealing with a new book by Jonathan Zittrain called: The Future of the Internet and How to Stop it.. There is also a sort of debate among the posters about some of the arguments in the book, but that’s OK. Scott Fitzgerald said that there are no second acts in American life. While that’s a great line, it’s not really true. We all are curious about the Internet’s second act, quite apart from the technology. If you are interested you can read more at:
Future

John A. Wheeler, Dean of American physicists, cosmologists and other types who try to understand the universe, died at his home in Hightstown, NJ of pneumonia. JAW is the person responsible for the coinage in 1967 of “black hole”, a concept with a very specific technical definition, but the term has come to be applied broadly. JAW was professor of Physics at UT Austin, which is certainly one reason for this blog to pay respects, but he was also the son of a family of librarians, and that’s definitely another. JAW knew and worked with, or opposed, all the big names:Einstein, Bohr, Oppenheimer, Dyson, and Richard Feynman was one of his students. The surviving Wheelers are numerous and I’m sure they miss their paterfamilias who liked gunpowder and things that go bang.
This is the NYTimes obit:
JAW

It’s been a while since we peeked over the shoulders of the Lab Lit folks, and it’s about time we brought you up to date on what they’re doing. One of the things they are up to is building The List… not the Little List in The Mikado but an enumeration with brief notes of novels and plays and movies and such that deal with science and scientists, but not SciFi stuff, and not productions that descend into caricature, and the writer has to get the science right. So on those counts alone the bar is set pretty high. I was led to The List by a note on Lab Lit about a nomination, apparently made in perfect seriousness, of the Patrick O’Brien sea stories about life on a Royal Navy warship during the Napoleonic Wars. The science part emerges in the character of Stephen Maturin, the surgeon aboard HMS Surprise, the ship of war commanded by his friend and characterological opposite, Jack Aubrey. The person nominating the O’Brien novels, a professor of physics at a Uni in the UK, makes a very strong case for Maturin as a kind of scientist in the way that was understood at the time in question, and marshalls evidence from the books to show the doctor as an avid naturalist, busily investigating plant and animal forms in whatever part of the world Admiralty orders send Surprise. Maturin gathers specimens, dissects, classifies, keeps detailed note and forwards his contributions to learned societies, and just does all the scientisty stuff you would expect. Naval fiction is not everybody’s thing, and the O’Brien books make special demands on the reader in that their author was at great pains to get all the details of ships, shipboard life and battle at sea in the age of fighting sail exactly right. So there’s plenty of talk about mainsils and capstans and cutlasses and all the rest of it. The editors at Lab Lit seemed impressed at this elucidation of Dr. Maturin’s other self as scientist, and the O’Brien books may be allowed onto The List. You can read the nominating essay at:
Maturin
You can also look at the rest of The List and mutter to yourself about what’s there:
List