Monthly Archives: August 2005

New Study of Lysenko

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The story of T.D. Lysenko has often been used as the textbook example of what can go wrong when ideology, particularly political ideology, interferes with science. Lysenko’s ideas on genetics were made into the official Soviet doctrine in 1948, even though his theories were largely rejected elsewhere, and the view is that this could only have happened through police-state methods triumphing over the crucial self-corrective measures of real science. Well, maybe. A new study by Nils Roll-Hansen shows that the true story is rather more complicated, and that the received version, at least in the West, needs some updating. Rolls-Hansen has studied Lysenko’s scientific publications and other materials in Russian archives, and his version of the Lyseneko story has more facets and is more interesting than the generally received story of an essentially talentless but well connected and politically correct boob triumphing over genuine scientists through threats and bullying. There is a long review in NATURE of
The Lysenko Effect: the politics of science
Nils Rolls-Hansen
Humanity Books, 2005, 335 pp. $25
Read the NATURE review
Lysenko

Social Bookmarking

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Frankly, the Blogging Grouch thinks that we already have more than enough tools and gimmicks to indulge the human propensity to yak, and that we would all be a lot better off with less communicatin’ and more, a lot more, silence. That jaundiced view is not shared by others, it seems, since the parade of gadgets never stops. Hot on the heels of Instant Messaging, we have “social bookmarking”. We’re all familar with the “bookmarking” part. Web browsers let us select and store the addresses of nifty sites, so we don’t have to remember them, or write them down. One click, and you’re back to Nifty Site. But the new wrinkle comes when this familiar method is extended to allow the posting of search engine results, say, or a list of scientific papers you have found useful. Users assign “tags”…descriptive character strings…to their postings. The tag has to be one word, but more than one tag can be assigned. If you wish, you can “publish” your list of tagged sites and so share them with a larger community. In effect, it’s a quick way to compile , store and share addresses of electronic resources in a distributed environment. NATURE staffers, more precisely, the New Technology team at Nature Publishing Group, created an in-house tagging/sharing program which they call CONNOTEA. But there are others, such as cite.u.like and del.icio.us. An article in NATURE describes the phenomenon, which it somewhat breathlessly describes as a “social revolution”. Not another one! The BG is still reeling from the loss of vinyl LP recordings, but decided to try CONNOTEA and see what the fuss is all about. Those who can’t wait for the BG’s verdict are welcome to poke around on their own, to see what’s what.
Revolution
Connotea
CiteULike
Del.icio.us

Most Published Research Findings False?

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PLos Medicine published in its August issue an analysis claiming that most published research findings are not correct. This rather surprising, not to say shocking, position is set forth and defended by J.P.A. Ionnidis, of the Ioannina School of Medicine in Greece, and Tufts University Medical Center in Boston. The author, an epidemiologist, is concerned that many research studies are too small, have effect sizes that are too small, have too many possible relationships, allow too great flexibility in design, definition, outcome and analytic methods. Conflict of interest and competition in a “hot” field are also factors that can decrease the probablitiy of a reported finding’s being true. In fact, the author asserts: Most Research Findings are False for Most Designs and Most Fields. He concludes with some recommendations for improving the situation.
Read the article here:
Research

PubMed and Old Medline

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The National Library of Medicine (NLM) has been working to extend the range of computer-controlled searching of the biomedical literature. MEDLINE coverage begins with citations from 1966, for a number of procedural and technical reasons. Any effort to search the literature prior to that date required manual approaches in a number of different printed tools, each somewhat different from the others, and each covering different time spans. NLM has been trying to broaden access to the pre-66 biomedical literature through a series of projects collectively known as OldMedline, in which the contents of the predecessor printed searching tools are digitized and added to the PubMed database.
You can get to older material in this way: Conduct a PubMed search, setting whatever limits you care to, such as language of publication, human studies, etc. Then, on the same limits screen, click on the Subsets selection arrow, and from the pull down menu, select OLDMEDLINE for Pre-1966. Click on GO, to launch your search. Your results should all come from the period before the start date of MEDLINE. OLDMEDLINE contains only citations, since abstracts were added to the records only from 1976 onward.

PubChem Provokes the ACS

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The National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, has been working for some time on enhancements to current information systems that will allow easier passage between the bibliographic information contained in MEDLINE and the biosystematic and biostructural databases which are also accessible from PubMed. One important strand in the ties connecting the various sites is the database of small molecules known as PubChem. PubChem is actually composed of three separate subfiles: PubChem Substance, PubChem Compound and PubChem Bioassay. NCBI sees the PubChem resources as important aids in helping researchers mine the published literature more effectively for useful information, as a contribution to the NIH Roadmap. This effort is supposed to accelerate biological discoveries and fast-track them into clinical trials, and eventual treatments. But the American Chemical Society(ACS) has been upset with the emergence of what it sees as a publicly funded competitor to its own well established chemical information systems such as Chemical Abstracts, and has issued statements detailing the grounds for its opposition.
Check these sites:
NIH Roadmap
PubChem

Medical Journals Flacking for Big Pharma?

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Yes, says Richard Smith, and they may not even be aware that they have been co-opted, which makes it all the sweeter from the Candy Man’s point of view. Smith edited the BMJ for over 25 years, and has recently joined the growing number of critics who are worried about the influence drug companies exert over scientific publication. In an article in PLoS Medicine, Smith discussed several methods companies use to see that the results they want get published. Actual fudging of data is too crude and too easy to detect, Smith says. It’s better to run studies that ask the “right questions”, and he gives some examples of how this is done. Peer review can’t be relied on, since the individual article seen by an editor and sent out to reviewers is probably pretty good. The fact that the article itself is only one piece in a large and adroitly designed marketing plan is generally not something an editor could detect. Smith has some suggestions for possible ways out.
Companies

Congress Moves to Support Open Access

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Both houses of Congress have supported measures that call for comprehensive reports on the success of the voluntary manuscript deposit program introduced by the NIH on May 2. Lawmakers are interested in seeing data about the level of compliance on the part of those receiving NIH awards, and have issued requirements for detailed reports, due in Feb. 2006 on the project. The Association for Taxpayer Access (ATA) surmizes that the success of the voluntary form of the project will be judged by the number of manuscripts submitted to PubMedCentral (PMC), and the embargo date selected by authors. Now, in mid-summer, the total number of submissions is said to be rather low, and the number of manuscripts available from PMC, small. Congress may not like this situation at all, and unless the numbers start to look better, and fast, researchers may find themselves facing a tougher set of requirements.

Web Pioneer Praises Blogging

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Sir Tim Berners-Lee, regarded as the Father of the Web, was interviewed by the BBC recently. He has some definite ideas about blogging, which he regards as something much closer to the original vision which guided his efforts in launching the World Wide Web. Blogging allows people do be more immediately and directly creative, since they don’t have to craft long, complicated packages of HTML. With blogging software, they just write text, which is what humans have been doing for millenia. Berners-Lee anticipates that the Web will become more stable, as he puts it, and more a part of the life’s daily background, like electricity. People won’t think about doing things “on the Web”…they’ll just do them. The Blogging Grouch is a little miffed at the vapidity of some of the interviewer’s questions, trying to elicit from Berners-Lee an expression of “responsibility” for various excesses and abuses of web technology. A low ” B” for the Beeb on that score.
Interview

Changes to PubMed

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The National Library of Medicine (NLM) will be making some changes to the PubMed system interface. First, the HELP link now located on the blue sidebar to the left will be surpressed. HELP information will be available only from the BOOKSHELF. A link called NLM MOBILE will be added to the sidebar, to direct searchers to a source of information about products and services that are compatible with various handheld devices.
Then, the SINGLE CITATION MATCHER utility has been enhanced in two ways. There is a checkbox on the form to restrict the search results to those citations in which the author in question is the “first author”. Then, the list of author names has been modified to allow searchers an “autocomplete” function when searching in Citation Matcher.
Bookshelf

NLM Mobile

Single Citation Matcher

Blogging, in Historical Perspective

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The Grouch stumbled on this piece while hacking through the Internet undergrowth in search of new material for LibraryLink. “Nothing new under the sun” as the wise man said, and the old guy may have had a point. Blogging, for instance, is sometimes presented as an absolute novelty, made possible only now by the wondrous technology of the Information Age, or whatever Age we are said to be in. And, the putative implications of this “movement” in shaping society, culture and politics are suggested to be enormous. Imagine the disappointment the Dedicated Blogger feels, when somebody, a humanist yet, cuts the blogging movement down to size by saying that blogging is nothing new at all, just a continuation by other means, of the pamphleteering effort that goes back to the first days of the Republic. If you want to , you could even trace this willingness to yack across the water to the Mother Country, in the blizzard of broadsides, pamphlets, booklets and other occasional controversial lit that accompanied the religious crisis and the eruption of the English Civil War in the 1640′s…Charles I, Cromwell, Puritans, Parliament and all that. Consider the life and career of Henry Clarke Wright, a man with a lot on his mind and willing to say it, anytime, anywhere.
Henry Clarke Wright