Monthly Archives: June 2006

Two Articles on Drug Tests in Poor Nations.

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Technology Review has an article by Amanda Schaffer which critiques the contents of two other articles. One is “Out of Control” by Celia Farber appearing in Harpers, March 2006, and the other is “A Nation of Guinea Pigs”, by Jennifer Kahn in Wired, March 2006. What they have in common is their subject, which is drug testing in developing or Third World countries, and the practical and ethical difficulties surrounding this enterprise. Schaffer is very tough on Farber, who is, according to this account, an HIV skeptic. That is to say, she does not accept the idea that the AIDS is caused by a viral agent, blaming instead a number of other possibilities, and implicating in the obviously poor health of AIDS victims the very medicines which are supposed to be treating them. Farber is especially critical of HIVNET o12, a drug trial conducted in Uganda, which, she says, yielded results that were spun by industry to exaggerate the benefits and play down the severity and frequency of side effects. The NIH admitted that HIVNET o12 had some flaws and asked the Institute of Medicine for a re-analysis of the data. The IOM agreed that the conclusions were generally valid. Jennifer Kahn’s piece is disturbing, in that it raises some thorny ethical issues about the whole idea of drug testing in poor countries. She writes about India, increasingly popular as a site for drug tests. Can anything like informed consent really be obtained from subjects in such trials? Do the inducements offered to potential subjects, given their circumstances, really amount to coercion? Do the agents tested have any relevance to the actual health needs of the recruits, or are the subjects just canaries in the mine shaft, whose participation is needed to discover toxicities before the agents are really used in an affluent, Western population? Are such studies morally compromised from the very start? No easy questions.

Read more here:
Drug Tests

Bad Fiscal News for PLoS

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The Public Library of Science was founded in an effort to create a “stable” of very high quality life science journals that would also adhere to the principles of Open Access publication, as set forth in various manifestos and declaration. PLoS and other ventures of similar inspiration sought to substitute a different business model. Instead of readers, or their libraries, paying subscription fees to read content, authors would pay a submission fee to cover publication costs and enjoy the benefit of immediate distribution of their work throughout the world via the web. PLoS has fielded a number of very good journals, but it seems that the fiscal side is not working out as well as had been hoped. An “author pays” model was expected to be succeeded by a “funder pays” scheme, in which granting agencies would build into the award enough money to cover release of the paper in an Open Access forum. Nature reports that a review of IRS documents shows that PLoS is losing money, and that support from private philanthropy will be needed for some time to come, if the venture is to succeed. This is discouraging for OA enthusiasts, but the game’s not over yet. Critics were quick to point out that the $1500 submission fee PLoS assesed was far too low to cover real publication costs. Initially, PLoS waved away such objections as simply the predictable sniping of the ensconced and empowered, unwilling to try something new. Since PLoS is raising the submission fee by $1000, the critics may have been closer to the truth. There’s more to the story, by Declan Butler, who has been following changes in scientific publication for Nature.
PLoS

Nature Goes to the Movies

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It’s true. The mag has reviewed motion pictures dealing with scientific topics. Jurassic Park and Contact come to mind, but there were others. The issue of June 22 has another review, one that approaches science from the inside, so to say, in that the people depicted are scientists, doing science “stuff”, and also in that they have more complicated inner lives than the usual Hollywood version of a scientist. That version runs a very narrow range from plaster saint (Greer Garson in Madame Curie, to hopeless nerd (Cary Grant in Bringing Up Baby) through malevolent genius Marlon Brando in Island of Dr. Moreau to maniac( take your pick among any number of candidates, my favorite is Albert Dekker in a Forties turkey Doctor Cyclops). The film in question is a German product Schlaefer or Sleeper, which is described as a “taut moral fable of laboratory life”. In it young scientists work very hard on a research project in a lab run by a martinet. One of them is approached by the Security Services to report on another researcher, a young man of Middle Eastern origins. He refuses initially, but then agrees, for personal reasons, and there are practical, professional and romantic consequences. Schlaefer is also interesting in that the director, Ben Heisenberg, is the grandson of Werner Heisenberg, he of the Uncertainty Principle and the Copenhagen Interpretation and the 1932 Nobel Laureate in Physics. There were lots of other scientists in the family, but Ben went his own way. What are the odds on seeing a German movie about scientists at your local Filmoplex? Answer your own question. What are the odds on seeing ANY complex, subtle, understated drama for grown-ups? One with no explosions or car chases? Yes, that bad. But you can always hope. And there is the DVD. While you’re at it, you can order Dr. Cyclops and watch ‘em back to back. Read Allison Abbot’s account:
Schlaefer
Postscript:
It turns out that the Alexander Kekule mentioned in Dr. Abbot’s account is a relative of another scientific great. He is the great-grand nephew of August Kekule…the German chemist who, according to legend, was trying to figure out how atoms and molecules are arranged, but was getting noplace. That night he dreamed about a serpent devouring its own tail, and in his waking hours parlayed that insight into a description of the structure of the benzene ring. Dr. Abbot was kind enough to enquire after I messaged her and the gentleman himself confirmed the relationship.

Columbia Chemist Pulls More Papers

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Science reports that the leader of a team of chemists at Columbia University has announced the retraction of four papers which had appeared in Organic Letters and the Journal of the American Chemical Society. This move follows on the earlier retraction of three other papers issuing from the same laboratory. In both cases, post publication efforts to replicate the experiments described in the papers proved impossible, and the laboratory director found himself constrained to withdraw the documents. Improved methods of manipulating chemical bonds were the topics in all the papers, and this area is considered to be both difficult and extremely rewarding for successful investigators, since the commercial payoff could be great. Now, however, the exact state of the question may be hard to assess, since the problem papers might have mislead other researchers into pursuing false trails. Dr. Dailbor Sames of Columbia and university officials would not discuss the case in detail, since the investigation is continuing.
Papers

Principia Mathematica Simpsoniana

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The Blogging Grouch enjoys kicking back with a glass of vino and a small dish of olives to watch Homer, Marge and the crew, but there was always that nagging feeling of alienation, a sense that the guys behind this are seriously weird. And now, the proof emerges. It wasn’t the wine or the olives. The show’s writers are mathematicians!!! That explains it, and very nicely too, without remainder. According to a piece in Science News, a number of the folks who write the scripts for the comdey series have advanced degrees in science, math, computer technology and related fields. Over the years, the crew have delighted in tossing mathematical jokes, pranks, problems, and similar mathematical arcana into the shows, largely to see if anybody gets them. They also take a few whacks at the low level of mathematical awareness among the general population. To be fair, they can be just as caustic with their own tribe, when they satirize mathematicians or academic nerds generally. To get some idea of the lengths the writers will go to stick in a gag, read the section on the equations appearing as background elements, seeming to show that Fermat’s famous theroem is wrong, since the equation provides a counter-example. Yeah, a real leg-slapper. Still , in the small but dedicated and enthusiastic community of number freaks, I’m sure it was the source for endless mirth. It would be the same group who went to see the movie Pi fourteen times.
Math Among the Simpsons

Nature Debates Peer Review, and Experiments.

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Nature has launched one of its periodic debates, which are efforts to take the mind of the scientific community on this or that pressing issue. This time, it’s a doozy: peer review. Hooray, says the Blogging Grouch, it’s about bloody time. Peer review is considered the cornerstone of quality in modern scientifc, or even general academic, publication. Publishing in outlets that don’t offer peer review is the career equivalent of jumping from a speeding train. Survival is possible, but not very likely. On the other hand, peer review has plenty of critics. Some dismiss it as merely another way for the Established Insiders to torment the next generation. Others see it as mechanism to guarantee that nothing interesting, exciting or upsetting will appear in the august pages. And, finally, others think it’s simply not working, since too much material of dubious quality gets published, including an embarrassingly large number of phoney papers. Them as wants to have a say on the matter can contribute to the debate:
Debate
Nature is also offering, on a three month trial basis, the chance for authors whose manuscripts are being reviewed in the traditional manner to also allow the posting of their submissions for open review on a website. Persons familiar with the field will be allowed to comment on the submission, provided they identify themselves. The journal will analyze the experience and report to the readership.
Experiment

Access to Research in Senate Bill.

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Members of the two parties reached across the Senate aisle to iniatiate a measure that would compel Federal agencies granting more than $100 million per annum to insist that award recipients make the results of their funded research more generally available. Sens. Joseph Lieberman of Connecticut and John Cornyn of Texas are the co-sponsors of the legistlation, named the Federal Research Public Access Act of 2006. The bill would require that reports of research funded by the agencies in question be made available in the form of electronic versions of the manuscripts approved for publication in scientific journals. There is not much chance that the bill will be passed without ammendments so there is no point in going into particulars which might not survive in the final act. But it does show what the BG has alluded to before: the rather esoteric and even exotic topics of research and scholarly publication have hit Capitol Hill, and are not going away. I think it’s also fair to say that the new measure shows impatience and frustration in Congress at the poor compliance record of researchers with the kinder, gentler voluntary submission policy which was announced in May of 2005. Only about 4% of NIH award recipients deposted their approved manuscripts with the NIH’s electronic archive, PubMed Central. Unhappy with this track record, the Congress apparently will move to a more forceful policy. Members of Congress see this as a can’t lose issue with voters, but apart from the facile politics, there is real concern that Federal research dollars are not producing the results they should because the research reports are blocked by subscription and affiliation barriers. We’re a long way from the final form that Congress will vote on, but the process will be interesting to watch.
Here’s an FAQ from SPARC about the proposed legislation:
Federal Research Public Access Act, 2006 ( Remember that SPARC is an “advocacy” body, and very much in sympathy with the measure’s intention. I’m sure they’ll give the basic facts correctly, but may not be as vigorous in noting drawbacks)

PLoS Clinical Trials Debuts

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The Public Library of Science (PLoS) has launched another in its projected series of open access journals. In May, PLoS Clinical Trials appeared with the intention to provide an “unbiased, peer-reviewed venue for clinical trials results in all fields of medicine and public health”. Although I looked quite carefully at the journal’s web page(s), I couldn’t find any statement about publication frequency. The other PLoS journals are monthlies, so it’s a fair bet to say that this will be a monthly too, but there is no direct statement to this effect. Adding Trials brings the PLoS stable to a total of six titles, a very nice increase which seems to support the organization’s plan to go slow and add new items only when everything is ready. This blog takes a moment to wipe its sweaty brow and welcome the new entrant to the world of scientific publishing.
Plos Clinical Trials

Research Fraud in China

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Nature, in an editorial about research in China, asks, who is looking out for faked results? The same question could easily be asked about other places, but, that’s bye the bye. The concern centers on the emergence of China as a major factor in the total world scientific endeavor, with some brow wrinkling about the absence of those structures which at least allow for the orderly investigation of suspect conduct. The importance of ‘face’ in the cultures of the Orient also makes it difficult to accuse colleagues of less than proper conduct. And the absence of protection for whistle blowers is said to obstruct frankness about fakery. Again, I had that head-swimmy feeling that everything being said could go just as well in Cambridge (either Mass or UK), Palo Alto or San Antone, so why pick on the Chinese? Maybe more things over there are more immediately political than they are over here, and anything involving a state structure, such as a university, involves the authorities, with all the bad memories of exactly how very wrong that can go. And anonymous denunciation from below, whistle blowing of a rather primitive sort, also has rather unpleasant historical associations with the terrible events of the Cultural Revolution. Nobody is anxious to have that back, even on a modest scale. So the Chinese will just have to work this out as they may.
Fraud
A couple of days after I wrote this, NPR had a story on ALL THINGS CONSIDERED about the topic of scientific fraud in Chinese research. OK, so it was a slow news day, thank heavens.

Numerology Follies

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OK, we went along with the crowd on the DaVinci Code thing, and found out that abandoning all standards can be kinda fun. So we’ll continue on the downward path with a nod to the numerology crowd. June 6, 2006 is the date that set the number-freaks atwitter, since, when “translated”, it writes out as 666, or the Sign of the Beast, in the Apocalypse. LiveScience has a nice little precis of the current goofiness, along with a little historical background and some sociological theorizing. Numerology has been around for a long, long time and boasts some illustrious practitioners, a certain I. Newton for instance. And let’s not forget the Kaballa tradition, which got some screen time in the creepy, but gripping “PI”, an art house movie of a few years ago that showed New York to be an even weirder place than most of us thought. So, those three digits in that combination have been shunned by the pious and by those who don’t believe in making enemies for a very long time. On the other hand, some scholars have noted that at least some manuscript sources suggest that the “correct” number is 616.
Numbers
666 Math