The Winner’s Curse in Scientific Publishing?

The winner’s curse is a concept in economics: often the winner in a competition has paid more for the prize than it’s really worth. An item in the Oct. 9 issue of The Economist describes an analogy to the curse in the area of scientific journal publication. Competition is stiff for publication in the top tier journals, so the tempation is strong to inflate the significance of the article by claiming or suggesting important results beyond what the data support, just to get through the strongly guarded portals of the big journals. But, a study in PLoS Medicine, which the The Economist article summarizes, suggests that the winners in the publication auction also fall foul of the curse, in that subsequent analysis of the results very often shows that the published results were incorrect. Dr. JPA Ionnidis is one of the authors, and we all remember him as the spoil-sport who suggested some three years ago that most published research results are wrong. The authors suggest that the current system of publication distorts the results of scientific research, by conferring an unjustfied cachet on the work published by top-tier outlets, and explore some alternatives. There are two nifty green squares, one cogently stating the paper’s basic argument and the other a numbered list of possible alternatives to the current state.
PLoS

MeSH 2009 in Use.

The National Library of Medicine uses a thesaurus of standard terms to describe the subject contents of the materials it indexes. Medical Subject Headaings, or MeSH, is updated every year and is the only nomenclature which gets this treatment. The other big scientific indexing services, such as Chemical Abstracts, update, for sure, but not annually. MeSH 2009 is in place and is now being used to index articles for MEDLINE and other services offered by NLM. You can read about the new terms in a summary article here:
2009

Letters From Galveston, no. 4.

This week the much-anticipated and dreaded staff cuts were implemented, with all the sorrow, anger, and drama that such an action brings with it. The reductions are being implemented with a certain brisk efficiency…600 a day. Apparently, fewer people were dismissed than had originally been stated, but a large part of the difference may be due to the voluntary change in location on the part of those employees who got good offers elsewhere, or who were tired of dealing with the situation here and simply left, for their own reasons. Head-hunting firms are courting a number of faculty with attractive propositions, in some cases, suspiciously attractive ones, recalling those TV adds about making six-figure sums by working at home part time. But, whatever. Dismissed employees receive salary and full benefits through the end of January, while junior and senior faculty are given a sliding scale of temporary coverage. Out-placement help is supposed to be offered, but the Human Resources staff are very hard pressed, and of course are afraid that, once they have done this job, they’ll be next. It’s oddly reminds you of the accounts if the Moscow Purges of the 1930s… lot of fear, and lots of bitter but hilarious jokes too. The anxiety, anger, fear and bitterness, the averted eyes, the hushed conversations, the attempt to find some reason why X was dismissed and not Y,the relief it wasn’t you, the guilt at the relief, all make the comparison a fitting one, I’m sorry to say. I have also been thinking a great deal about the phrase “storm victims” As the national economy slides, or somersaults, into serious recession those who are losing their wages and benefits have every reason to be fearful and resentful. They did all the right things: signed the pledge of Compassion, Integrity, and Respect, they attended the courses and seminars, got various certifications and degrees, observed the dress code, worried about meeting their Smart Goals, obediently wore their ID badges, and in very many cases took the job home with them, working off the clock via phone, beeper or Blackberry. In other words, they bought in, and how. No matter. Victims, in truth.

UTMB has been losing money for a very long time on uncompensated care given to the uninsured and medically indigent from this part of Texas. Now, other hospitals in the area are having to deal with an influx of patients who used to come here, and in particular, of uninsured patients, who were formerly sluiced to UTMB. And, they don’t like it much. What might come of this is hard to say. Editorials and stories in other papers have been muttering about making this an issue in the new session of the Texas Legistlature, starting in January. UTMB has to make its operations pay; that’s the word. Plans envision opening the hospital with 200 beds, and then expanding as circumstances dictate to 300, 350 or more. A medical educator I talked to was confident that students can be given very good clinical training, but admitted that some residency programs might have to shrink, at least for a while, until the patient base builds up. Some others are not so sure, about the timeline, at least. The seven lean years of Joseph’s dream may be here. It might be seven years, or fewer, or more.

The John Sealy Hospital opened today at 7 a.m. with the foreseen 200 bed capacity. Things went faster in some ways than had been planned, so the facility was declared ready, and patients are being seen. I talked to a surgeon last night who mentioned that he had three procedures scheduled for this morning. Everybody is being cautiously optimistic. There is no point in saying something that will have to be retracted, so better say little or nothing. But this is good news, clearly. How soon things get back to an approximation of normal depends on how quickly the buildings can be repaired, cleaned, disinfected, checked out and returned to service. The upper floors of many buildings were undamaged, but getting them back to work implies some mundane, low-tech services such as reliable elevators and functioning fire alarm systems. Some faculty who had offices facing outwards lost precious hard drives, thumb drives, disks or paper fiiles. These may not have been badly damaged, but they were removed by salvage crews and shipped off someplace to storage. Getting to them can be dffiicult. Many of the clean-up workers have gone, the worst part of the mucking out having been completed. And a lot of the heavy machinery has been removed also,and, I suppose, is stored somewhere to wait for the next disaster.

People who lived on the Island or the Bolivar peninsula, or the shore line of Galveston Bay of course had the worst of the surge. The relatively low wind level (Category II) and the relative dryness of the storm didn’t cause massive damage on mainland communities, and some people may be drawing the wrong conclusions from this. A Cat.IV surge and a Cat. IV wind would spread the destruction envelope much further inland, so conclusions that this place or that is “safe” may not be supported by events.

Many residents have temporary quarters on the mainland, and their drive to work should be made a little easier by the opening of the new Galveston Island Causeway, which has been under construction for the last several years. Crews are linking up the bridge roads with the main road onto the Island (I45), moving barriers and laying pavement. There are still boats to be seen tossed up onto some section of land, and after such a while, the fact that a boat is so far out of its natural element doesn’t really excite comment or interest. We have gotten used to them. What might be called the “second wave” of debris is starting to appear in quantity on streetsides, as more contractors get started on repairs. The “first wave” was due to what I’m calling “mucking out”…removing damaged or destroyed materials to stabilize the buildings and prevent further loss. The “second wave” comes from restoration efforts. The City has set a deadline of Nov. 30 for contractor pick up, so removal of these new piles will be somebody else’s job.

Last night the Galveston Symphony Orchestra played it’s first concert of the season, not in the Opera House, but in the ballroom of the Moody Gardens Hotel. There was a good crowd, and the GSO was in form, with music by Rossini, Rimksky-Korsakoff and Berlioz…the stomping, thundering Symphonie Fantastique. GSO Board president Mike Hughes spoke to the audience, saying that this was the first arts event on the Island since the storm.
He also noted that the badly damaged Opera House will reopen on Jan.4. So, the place which has heard the voices of Caruso, Nelly Melba, Fredericka Von Stade, Samuel Ramey, Denise Graves, Mel Torme and countless other performers, in all forns and genres from Grand Opera through Country, Rock and Jazz, will host the GSO again in its February concert. It’s another sign of life.

People here are resentful and angry at the “hands off” attitude taken by the state, most particularly with regard to the failure to help out UTMB. And they are aware that, despite the obligatory pilgrimages to the Island by various legislators, no significant rescue package was ever contemplated, much less planned. This, and the dismissal of staff at UTMB, are putting the Island’s economic future under a cloud, and some are trying to chase away the cloud by listening to the seductive siren song of casino gambling. To Islanders, this is old stuff. Galveston used to be “wide open” to use a somewhat old-fashioned phrase. There was gambling and fast night life. That was the reason big show biz names came down here in the first place. So there is nostalgia for what seems like Better Times Than These. Some people are convinced that gambling here will turn the trick: money, jobs, prosperity, and the rest. Others say that such a move is Death to the image of Galveston as a “family resort”, and that where gamblling goes, drugs, hookers, the Mob will surely follow. To me, the old saying is true: there’s no such thing as easy money. Casinos bring their own people and don’t hire locally,except for the lowest paid jobs. They try their best to keep the suckers at the tables, so there’s no incentive to visit the local shops, restaurants and businesses. Then, there’s the ethical question: is this the best we can do? Fleecing suckers? It may happen. We’ll have to see.

I was at my house yesterday, working on some things, when I looked out the patio door into the back yard. It’s pretty desolate and very sad looking. All that brown, against a grey sky, was a mood-buster. I also went out west a little, to the airport, Scholes Field. It was built during WWII as a training facility for navigators, I think. Lots of buildings were left over, and, while many of them were torn down, others were taken over by small businesses and kept going over the years. Helicopter services that fly to and from the oil rigs in the Gulf, form the bulk of the air traffic now. IKE hit the place very hard. Many of the old WWII era buildings are in ruins, as are many of the newer metal sheds. You can see a debris line on the cyclone fences, up about 6 or 8 feet from the ground, where leaves and grass were deposited by the surge, as a reminder, if you needed one, about what happened. It’s all pretty ghostly and empty, at least on a Sunday. The trailers the chopper crews and rig staff used to sleep in are gone, either moved, or swept away. Not many machines were to be seen, either. I don’t know where they went, or if they’ll be back.

Beautiful Science.

I was listening to NPR the other day, in the car I guess, while they played a segment on the science books and manuscripts that are kept in the Huntington Library, in San Marino, not far from Los Angeles. First, if you have never been to the Huntington, put it down on one of those Ten Things to Do Before I Die lists. It’s a private research library, but open to the public. Rare books and manuscripts are the specialty, with the focus on British and American Literature. They have goodies such as the manuscript of Dickens’ A Christmas Carol . And there are two art museums. a very nice restaurant and a Japanese Garden. It’s all set in a beaurtiful park too. But the NPR segment focused on the Dibner Hall of the History of Science. Dibner’s curator, Daniel Lewis, is a real enthusiast, but not a bore. He managed to convey a lot of his own pleasure and excitement at the beauty of the books he deals with. But he underlines that the books are not there just “for pretty”. Each of the items on display was significant in the progress of fields such as astronomy, medicine, biology or optics. The point is to help the visitor understand where the book in question fits in the history of discovery. It doesn’t hurt of course that the books themselves are visually splendid and worthy of respectful consideration, simply from the aesthetic standpoint. In a marriage of art and science that has long since gone on the rocks, scientific ideas were transmitted in books that were, simply but inadequately put, beautiful. They pleased the eye, and engaged the senses. Today’s texts with their boring illustrations and pages of equations may be closer to the ideal of “objectivity” science supposedly strives for, but it’s hard to avoid the notion that somewhere along the way, something has been lost.
Here is the link to the Dibner Hall website. Take a look at the rest of the Huntington as well:
Dibner

PS I should point out that the Blocker Historical Collections here in the Medical Library building stand right up there in the front rank of major assemblies of scientific rarities. We have some of the items showcased in the Dibner display, such as a first edition Vesalius De Fabrica of 1543 AND a copy of the corrected edition of 1555. The Huntington has Newton’s own copy of the Optiks, and that’s hard to beat. But we’ve got Harvey’s De Motu Cordis, so game, set and match!

How Gray’s Got That Way?

Not long ago, we noted the appearance of The Anatomist: A True Story of Gray’s Anatomy, by Bill Hayes, Ballantine, 304 pp., $24.95, which described the genesis of Gray’s Anatomy, one of the basic tools in the med student’s bag. Well, it seems that the show biz motto has some truth in it: “if they liked it once, they’ll love it twice”, because there is another recently published full length treatment of Gray and the coming to be of the famous text, now in its 4oth edition. The new book was well-reviewed in The Economist and while it obviously covers a lot of the same ground as the Hayes work, there is sufficient new material and some different interepretations to make it worth a look. Gray wrote the text and lived up to his rep for clear explanation but the illustrations were prepared by Henry Vandyke Carter, a physician from poorer circumstances than Gray, who had dough and moved in high circles. Carter’s drawings give the book it’s punch, and there is no doubt that he was very gifted. The new item is:The Making of Mr Gray’s Anatomy: Bodies, Books, Fortune, Fame
By Ruth Richardson. Oxford University Press; 322 pages; $29.95 and £16.99

Ps. The “Mister” in the subtitle is not a mistake. It’s practice over there to refer to surgeons, which Gray was, as Mister. I think it’s kind a reverse snobbery thing. For a long time surgeons were looked down upon as mere “practitioners”, who didn’t have the dubious advantage of university education and the sheepskin saying Doctor. And the surgeons kept the style of address, as a kind of nyah, nyah to the MDs, even though their professional and social status had altered completely, with the advances in anesthesia, infection control, and so forth.

11.11.11.

I don’t know how I missed it, but Nov. 11 marked the 90th anniversay of the end of WWI. “At the eleventh hour, of the eleventh day, of the eleventh month, the guns fell silent”. I think that’s how it goes, and I shouldn’t have used quotation marks if I only think it, but I’m pretty sure. The Great War, the War to End All Wars, to Make the World Safe for Democracy, etc, etc. Millions lay dead, four empires came to an end, scores of new countries were created, such as, oh, Iraq, and the world’s first Communist state. All the bloody strings of our current history lead back to these events and one good way to figure out what’s going on now is to trace it back to what happened then. There has been a lot of new scholarship about WWI and its aftermath, some of which we have talked about here. If there are “lessons”, I don’t know what they are, other than this: Events almost always upset the best plans and calculations; things war especially, can take on a logic of their own, and are a lot harder to stop than to start. Not much to take with you, is it, when you count what the lessons cost. 11.11. used to be Armistice Day, which morphed into Veterans’ Day because, since 1918, there had been more wars.

Amazonia Before Columbus.

Last November we blogged a little about 1491, a book by Charles Mann, which summarizes the research being done on the state of the Americas in the time before the arrival of Europeans. The burden of Mann’s book can be summed up thusly: There were many more Indians (a term Mann used deliberately), they were here a great deal longer, and they affected the land much more intensely, than had previously been thought. Mann continues his reporting on this topic in Science in the issue of 8.29.08 There is an interesting article on the archaeolgy of Amazonia, which place, you might think, shouldn’t have any at all. The previous understanding was that apart from tribes of hunter-gatherers, human settlement there was pretty thin, and there was hardly anything suggestive of permanent structures. Once the region began to be cleared for agriculture and grazing, the picture started to change. It seems that there was quite a lot permanent human settlement in the Amazon, and there is a great deal of material left over, a lot of it in the form of construction. Raised plots for agriculture and a very large network of causeway-like linear elevations, which seem to have been used for movement during periods of the year when the area was being flooded by runoff from the Andes snowmelt. So far, no one has come up with Lost Cities or anything, but the scale of what remains is impressive, and points to a very strong degree of “social integration” and political control. Some of the structures may have served religious or ritual purposes. Just when you think you have it all figured out, something new comes along.

arXiv Now at Half-Million Mark.

arXiv is the online repository of original papers in physics, math, computer science and related fields. In October, the site loaded it 500,00th paper, and that is surely something of a milestone for a project that was deemed highly specialized and frankly experimental. The idea behind arXiv was a relatively simple one: use the Internet as a publication vehicle to cut costs and speed up dissemination. Paul Ginsparg, working at Los Alamos national laboratory, was the guiding spirit launching the site in 1991 and high-energy physics was the concept domain on which this “pre-print server” was grounded. It proved so successful in attracting contributions and providing commentary for authors that all of physicis was soon included as “in scope” and the other subject areas accreted to arXiv in rapid succession. When Ginsparg moved to Cornell in 2001, so did arXiv, and the Cornell University Libraries and the Department of Information Science sharre responsibilities for managmenet. The site is still ‘physico-math’ in character, very largely, and one of the mysteries is why other disciplines have not either started posting their preprints on arXiv, or set up pre-print server systems of their own. There doesn’t seem to be anything like arXiv in chemistry, and certainly not in biology or medicine or “biomedicine”. Initially there was concern that a really successful arXiv would spell the end of physics journals, but that does not seem to have happened. Authors, reviewers, and publishers seem to have learned to live with the newcomer, and the switch to electronic publication of journals has made everybody less nervous, since the edges between these forms of dissemination have been smudged a bit. Open Access publication advocates want everything to be more like arXiv and the fact that it’s not can be explained in different ways. A lot of heavy breathing about “culture” usually starts here, and that’s when I leave. At any rate, hats off to arXiv and good luck with the next half-million.
This is the press release from Cornell:
PR
This will take you to the arXiv site:
arXiv

New UT Blog Discusses Books by UT Authors.

ShelfLife@Texas is a new blog devoted to discussions of new books by UT authors, eg alumni and current faculty. Here is some of the press release boilerplate: ShelfLife will offer readers an inside look at the university’s vibrant community of authors. Our contributors will write about books by faculty and staff members, students and alumni of the university, on topics ranging from the arts, history and the humanities, to business, law and politics.

There will also be interviews with authors and contributions reporting on trends in the publishing, academic and literary worlds. I spent some time with it today and it looks promising. The page is nicely set up, the selections are interesting, the style is lively, and I suffer from the prejudice that there can’t be too many blogs about books. I was surprised to see another major FDR bio appearing, but there is one, written by UT history professor H.W. Brands: Traitor to His Class: The Privileged Life and Radical Presidency of Franklin Delano Roosevelt” (Doubleday, 2008)

Take a look:
ShelfLife

Michael Crichton Dead at 66.

More bad news keeps on coming for writers. The author of numerous best-selling scientific thrillers, including Jurassic Park and The Andromeda Strain , Michael Crichton, died yesterday at the age of 66. The cause of death was cancer, from which he had suffered for several years. A native of Chicago, Crichton was very tall, 6’9”, and somewhat awkward in his youth, so he escaped into writing. Deciding that he wasn’t good enough for either serioius writing or serious basketball, he decided on medicine as a career, and attended Harvard College and the Harvard Medical School. He continued his writing, using various noms de plume, and found some success. The Andromeda Strain, his first major hit, appeared in 1969, while he was still in medical training. The book became a best seller and was shopped to Hollywood for a nice sum. Crichton did not practice medicine, and now established as bankable, he continued his career with hits such as Disclosure, Rising Sun and the blockbuster Jurassic Park. Writing for the movies and for television was another path, and in 1994, he created the long-running TV show ER. Crichton was a very disciplned writer, who worked hard every day, and used his medical and scientific training to feed his lively imagination. Many people not only liked his books as recreations, but also learned something about science and medicine from them as well.
Here’s the AP obit via Yahoo!
Chrichton