MedWorm: Medical Scientists

An egomaniacal drug monkey on demystifying science (scienceblogs.com)

Quote of the Day news feed | Edited by Duncan Hull — Fri, 04 Jul 2008 08:44:39 +0100

Wednesday 02 Jul 2008 (Source: Quote of the Day news feed | Edited by Duncan Hull)

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Ryanair boss michael o'leary on why he loves the smell of recession in the morning (bbc.co.uk)

Quote of the Day news feed | Edited by Duncan Hull — Fri, 04 Jul 2008 08:44:39 +0100

Thursday 03 Jul 2008 (Source: Quote of the Day news feed | Edited by Duncan Hull)

Taste sensation

Sciencebase Science Blog — Fri, 04 Jul 2008 06:36:20 +0100

I wrote about the effect of salt on the boiling point of water recently and Sciencebase reader Derek Burney asked why cooks use salt when boiling vegetables, for instance, if the effect on boiling point and so cooking times is so minimal, as I explained. Well, the small amount of salt (sodium chloride) added to food has very, very little effect on the boiling point and so really does not affect how quickly the food cooks. The fundamental reason we like to cook with salt is that salt has not only its own taste, but also interferes with the bitter-taste receptors on the tongue, essentially blocking them temporarily and so masking the taste of any bitter compounds in the food you eat, therefore emphasising any sweet tastes. It really is purely there as a flavour enhancer. Try it with some raw lettuce, eat a leaf raw and concentrate on the bitterness. Then sprinkle on some salt and eat the second leaf, besides the taste of the salt, you will notice it actually tastes sweeter. Given how bitter and downright nasty some vegetables can taste raw - think Brussels sprouts, spring cabbage, turnip - and perhaps more so in days gone by when quality may have been even lower, it is easy to see why adding salt to the cooking pot would have become standard practice. This was covered in New Scientist a while back. The sodium salt of the glutamic acid, commonly known as MSG (monosodium glutamate) does even more, it has the bitter-blocking sodium ionsbitter-blocking sodium ions. It adds a frissant through the stimulating “deliciousness” (umami, in Japanese, from the word for savoury) of the glutamate. Some research indicates that there are umami receptors on the tongue representing a fifth taste sensation alongside bitter, sweet, salt, and sour. Different research again adds a sixth taste sensation to our tongues, claiming a receptor for fatty acids. Given the highly stimulating effects of salt (as taste and bitter blocker), MSG, and fat (in the form of fatty acids) on our tongues it is perhaps no surprise then that salt-laden fatty foods taste so delicious. addthis_url = 'http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Ftaste-sensation.html'; addthis_title = 'Taste+Sensation'; addthis_pub = ''; A post from David Bradley Science Writer Taste Sensation (Source: Sciencebase Science Blog)

Secret report reveals biofuels causing worldwide food crisis

Living the Scientific Life (Scientist, Interrupted) — Fri, 04 Jul 2008 02:43:21 +0100

tags: politics, pollution, hunger, global warming, environmental destruction, biofuels, overpopulation, birth control, soylent green Image: Matt Groening (The Simpson's). A friend sent a link to an interesting article that was published today in the Guardian. This article reveals that the increased reliance on biofuels by the US and the EU is driving a worldwide food crisis. The confidential World Bank report, researched and written by an unnamed but "internationally-respected economist," has not been published but was instead leaked to the Guardian. Among other things, this report claims that the large-scale diversion of corn into biofuels has driven global food prices up by an astonishing 75 percent. (Interestingly, the International Food Policy Research Institute (IFPRI) estimates that "only" 30 percent of the increase in major grains prices is due to biofuels.) Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

West 34th/penn station subway art 5

Living the Scientific Life (Scientist, Interrupted) — Fri, 04 Jul 2008 01:59:59 +0100

tags: West 34th street Penn Station subway art, Circus of Garden Delights, subway art, NYC through my eye, photography, NYC This is the last artwork from this station that I will show you -- tomorrow I will feature a new (to you) subway station! Circus of Garden Delights. West 34th Street/Penn Station Subway tile mosaic art #5 as seen at NYC's West 34th Street stop at 8th for the A, C and E trains. Artist: Eric Fischl, 2001. Image: GrrlScientist 2008 [larger view]. According to the artist, this subway station artwork "depicts a commuter being drawn into the bizarre and surprising world of the circus, meeting animals, clowns, acrobats and fire-breathers on his way to work." Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Slip sliding away: faster extinctions predicted by mathematical model

Living the Scientific Life (Scientist, Interrupted) — Thu, 03 Jul 2008 22:33:50 +0100

tags: bpr3.org/?p=52, endangered species, estimating extinction risk, demographic heterogeneity, demographic stochasticity, environmental stochasticity, Mechanistic stochastic models, Brett Melbourne The endangered pelagic thresher shark, Alopias pelagicus. More than half of the world's shark species are under the threat of extinction due to overfishing by humans, especially for sharkfin soup. Image: Kevin Markey, 2004 (Pacific Shark Research Center). The International Union for Conservation of Nature (IUCN) released a report in 2007 indicating that more than 16,000 animal species worldwide are threatened with extinction. These numbers translate into one in four mammal species, one in eight bird species and one in three amphibian species that are included on the IUCN's "Red List" of endangered species. However, a paper was just published suggesting that the risk of extinction for many animals and plants has been underestimated by as much as 100-fold. According to the paper's lead author, assistant professor Brett Melbourne of University of Colorado at Boulder's ecology and evolutionary biology department, this underestimation was the result of a mathematical "misdiagnosis." Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

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Norway maple tree

Living the Scientific Life (Scientist, Interrupted) — Thu, 03 Jul 2008 19:59:59 +0100

tags: Norway Maple Tree, Acer platanoides, tree bark, Image of the Day Bark of the Norway maple tree, Acer platanoides. Image: GrrlScientist 2008 [larger view]. Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Update: housing (again)

Living the Scientific Life (Scientist, Interrupted) — Thu, 03 Jul 2008 17:22:21 +0100

I have made several trips to my councilperson's office regarding my weird rent increase so far. The subway trips are getting costly! Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Smells like teen spirit

Living the Scientific Life (Scientist, Interrupted) — Thu, 03 Jul 2008 13:59:58 +0100

tags: Just say Yes, humor, telemarketers, streaming video Since I am a Seattle native, and since Seattle is the home of the grunge rock band, Nirvana, some of my readers are trying to use to get me in a London sort of spirit. In this case, a reader sent me this video of the Nirvana's hit song, "Smells Like Teen Spirit" as played by the Ukulele Orchestra of Great Britain [4:53] Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Collaborative writing

RRResearch — Thu, 03 Jul 2008 13:32:00 +0100

My bioinformatics collaborator is in town till next Friday, so we can work together to finish up our uptake sequence manuscript. We have done (she has done) a lot of different analyses addressing various questions about how uptake sequence accumulation has affected protein evolution and vice versa, and I'm having a hard time keeping them all straight (partly because I haven't been thinking about this project for a while). The manuscript is mostly written already; but some parts of the Results are still up in the air because they were waiting for some final data. It also needs polishing and some revising to incorporate results from a Neisseria uptake sequence paper that came out a few months ago.To cope with all the data we've been occasionally creating 'Flow of Results' pages that summarize our results and conclusions, in the order we think the paper should present them. Yesterday we began our final push by going through the most recent version of the Flow of Results'. I'm not sure we have everything in the perfect order, but we have an order that's good enough, with each result triggering a question that's addressed by the next result. (Source: RRResearch)

Craig venter’s a life decoded – a captivating read for adult boys (and for historians of the contemporary life sciences)

Biomedicine on Display — Thu, 03 Jul 2008 12:03:08 +0100

Most autobiographies of scientists are terribly boring—soulless accumulations of facts of hardly any interest for others than the near family combined with humourless vindications of the author’s inflated ego—best used as temporary cures against insomnia. When I bought Craig Venter’s A Life Decoded (Viking 2007) more than half a year ago I didn’t have high expectations. A rapid look at the plates—with the usual mix of photos of the subject as a young man hiking with friends and as a mature man meeting other famous men—confirmed my prejudice about the genre and I left the book in the perhaps-to-be-read pile. Not even Venter’s commanding blue eyes on the dust cover could persuade me to open it again. It would probably have remained stuck away if I hadn’t met Joan Leach at the PCST-10 meeting in Malmö last week. We had a short chat about autobiography and popular understanding of science and she mentioned that she had read Venter’s book and had found it “so bad”. Strong opinions use to trigger my curiosity, so I brought it on my summer vacation—and I must admit that I’m captivated by this exciting, elementary well-written story about the maverick who beat them all. J. Craig Venter is probably best known to the public for being the outsider who won the race for sequencing the human genome in the late 1990s. The entrepreneur who invented the so called ‘shot-gun’ method which proved to be faster and cheaper than the official Human Genom Project consortium approach. The bad guy of genomics who left NIH to found two consecutive private research institutes (first The Institute for Genomic Research, then Celera Genomics) and allegedly wanted to make money out of patenting genes instead of giving the code to humanity. Venter doesn’t try to diminish his maverick persona. If anything he inflates it. The basic story-line of A Life Decoded could be the manuscript for a Western movie. Venter portrays himself as the honest, outspoken, no-bullshit guy who was seasoned in Vietnam and who has defended fact-production and efficient science-making against a politically corrupt genomic establishment. He doesn’t try to hide his contempt for the big power players in the game, including Jim Watson, Francis Collins and John Sulston, their (in his view) political maneuvring and protection of institutional interests. His Penguin/Viking publisher has probably toned down some of the most acerbic character assassinations but there is still much left. One of the few scientists in a power position that emerges unscathed is the former editor of Science magazine, Donald Kennedy. There is one important part of the public picture which Venter vehemently rejects, however, namely that he should have had any economic interests in the race for the genome. He argues over and over again that he wasn’t in it for the money; on the contrary, his move from NIH to the corporate world was, he says, the only way he could finance his scientifically and economically superior sequencing methodology and save it from being buried by the HGP politicians and apparatchniks. Accordingly, the villains are not just the HGP officials and Wellcome Trust bureaucrats like Michael Morgan, but also corporate executives who tried to stop him from generously publishing his gene data. The portrait of the profit-hungry head of PerkinElmer, Tony White, is particularly unflattering. Venter has an axe to grind and he grinds it efficiently. After 300 pages, I’m inclined (without having had time to check his sources) to buy the main thrust of his story, from childhood to the present. Especially since Venter is not a lonely rider. He has bonded with other apparently honest, no-bullshit scientists and entrepreneurs who, like him, believe in the power of hard work and attention to detail, and who always put facts before politics. Venter certainly has his share of enemies, but apparently he also has droves of devoted collagues and friends who support his version of the story of the gene wars. His knack for organising others to work for him is also reflected in the production of his autobiography. After having written some 240.000 words, i.e., more than twice the size of an ordinary book, Venter hired a Daily Telegraph journalist to help him trim and reorganise the text and to conduct interviews with other main actors in the story. His current fiancée gave him constant feedback, and several friends and colleagues, not to mention crew members of his famous yacht Sorcerer II, read multiple drafts. This doesn’t mean that Craig Venter has had a ghostwriter—it means that A Life Decoded is as much a team-work as the scientific projects he has led. The professional support-team is probably the explanation for why this is also an unusually well-written book: as literature (don’t forget that auto/biography is as much literature as history) it competes favourably with most mystery novels. One feature of the book that works in favour of Venter’s version is the constant focus on the scientific and technical aspects of the work. True, there is a lot about politics in this book, but compared with many other autobiographies of scientists there is even more about science. Venter goes out of his way to explain the scientific and technical problems he encountered—from his work on the adrenalin receptor in the late 1970s and early 1980s to the jigsaw-like genome assembly in the 1990s. Accordingly, long stretches of A Life Decoded are lucid introductions to bits and pieces of the history of biochemistry, molecular biology and genomics in the revolutionary quarter century from 1975 to 2000; an aspect of the book which in itself makes it obligatory reading for graduate students in the life sciences and for historians of contemporary biomedicine. It’s all told from Venter’s personal perspective, of course, like everything else in this strongly subjective story; but after all this is one of the limitations (and strengths) of the autobiographical genre. (Those who want another side of the story should also read John Sulston and Georgina Ferry’s The Common Thread, 2003.) But first of all A Life Decoded is—personally, politically, scientifically—a book about passion in science. Venter describes his frustration when procedures and machinery didn’t function as planned, and he relates the feeling of exctasy and relief when things worked, results were pouring in, and yet another article—about the Haemophilus influenzae genome, the Drosophila melanogaster genome, the mouse genome, and eventually the human genome—was sent for publication in the most prestigious scientific journals. Venter could have chosen to write yet another boring, self-congratulatory autobiography. Well, it is self-congratulatory and there are many successes in this story to be congratulated. But in addition to the triumphs, Venter also invites the reader to share his emotional ups and downs, even the painful and depressive feelings and (rare) suicidal thoughts. Forget everything you’ve heard about life sciences as boring. Craig Venter’s life in science has been an emotional roller-coaster. The impression of a man who is driven by the passion for scientific success rather than for institutional power is reinforced by the fact that this book, compared with many other autobiographies, leaves most of the dinners-and-meetings-with-important-people stuff out. When, on one occasion, Venter and his second wife Claire were invited to dine at Clintons’s table on a New Year’s Eve dinner, he summarizes the event in four lines, concluding that Hillary was “like a sponge eagerly absorbing what I had to say about the genome”. Me too. I eagerly absorbed Venter’s saga in one reading session and I already look forward to the sequel. The man is only 61 years old and despite having a lot of bad genes (he did of course sequence himself!) and having been diagnosed with early skin cancer, he will hopefully live long enough to write the story about his present work too. His mapping of the microbial genome of the oceans and his new institute’s quest for artifical life promises to put even his 1990s genomic triumphs in the shadow. After these there will hopefully come even more exciting projects out of this man who seems to be genetically determined to live a life of competition. An elementary exciting read for all boys between 15 and 95. So now I believe I understand why Joan didn’t like it :-) (Source: Biomedicine on Display)

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Lie down with pit bulls, wake up with a blogospheric flea in your ear.

Open Reading Frame — Thu, 03 Jul 2008 09:40:46 +0100

This clumsy hatchet job from Nature reporter Declan Butler is beneath him, a poor excuse for journalism and an affront to the respect with which many of his colleagues are regarded by the research community. Let's start with the title: "PLoS stays afloat with bulk publishing". Loaded rhetoric, anyone? The clear implications are that PLoS is floundering (Butler's own numbers show otherwise!), and that "bulk" is somehow inferior (to, one presumes, "boutique" or some such). PLoS is "following an haute couture model of science publishing" sniffs our correspondant, who goes on to clarify: "relying on bulk, cheap publishing of lower quality papers to subsidize its handful of high-quality flagship journals". This emphasis on "quality" and the idea that the same somehow equates with scarcity continues throughout: "the company consciously decided to subsidize its top-tier titles by publishing second-tier community journals with high acceptance rates", "the flood of articles appearing in PLoS One (sic)", "difficult to judge the overall quality", "because of this volume, it's going to be considered a dumping ground", "introduces a sub-standard journal to their mix". The intent is obvious, and the illogic is boggling. Where does Butler think the majority of science is published? Even if you buy into this nebulous idea of "quality" (one knows it when one sees it, does one not old chap? wot wot?) there can be no "great brand" journals without the denim-clad proletarian masses. All the painstaking, unspectacular groundwork for those big flashy headline-grabbing (and, dare I say it, all too often retracted) Nature front-pagers has got to go somewhere. It gets much worse, though, when we get some measure of what Butler thinks "quality" means: Papers submitted to PLoS One (sic) are sent to a member of its editorial board of around 500 researchers, who may opt to review it themselves or send it to their choice of referee. But referees only check for serious methodological flaws, and not the importance of the result.That, along with an earlier remark about "a system of 'light' peer review", is a blatant and serious misrepresentation of PLoS ONE's review process. Here's the actual policy: The peer review of each article concentrates on objective and technical concerns to determine whether the research has been sufficiently well conceived, well executed, and well described to justify inclusion in the scientific record. [...] Unlike many journals which attempt to use the peer review process to determine whether or not an article reaches the level of 'importance' required by a given journal, PLoS ONE uses peer review to determine whether a paper is technically sound and worthy of inclusion in the published scientific record. [...] To be considered for publication in PLoS ONE, any given manuscript must satisfy the following criteria: Content must report on original research (in any scientific discipline).Results reported have not been published elsewhere. Experiments, statistics, and other analyses are performed to a high technical standard. Conclusions are presented in an appropriate fashionand supported by the text. Techniques used have been documented in sufficient detail to allow replication.Reports are presented in an intelligible fashion and written in standard English.Research meets all applicable standards, including the Helsinki Declaration, with regard to the ethics of human and animal experimentation, consent, and research integrity.Report adheres to the relevant community standards for research, reporting, and deposition of data. (Standards PLoS promotes across its journals).Which is to say that PLoS one holds authors to exactly the same scientific standards that every journal should follow. Which is to say that any methodological flaws, not "only... serious" ones, will see a paper revised, or rejected if the flaws can't be overcome. Which is to say that PLoS ONE uses peer review to do what it was designed to do, not to create an artificial scarcity from which to milk profit with scant regard for the integrity of the scientific record. That's not "light" peer review, it's real peer review. With this scurrilous parroting of anti-OA FUD, Nature makes pretty clear where its interests and its allies are. Well, you know what happens when you lie down with pit bulls... There's a lot more, but that was the issue that pushed my buttons the hardest. See Bora for a roundup of responses; here's a quick outline of some of the key issues: Jan Velterop, responding to Butler's last "investigation" of PLoS finances two years ago, pointed out that it's ridiculous to expect a new journal with a new business model to break even in a few years, when new journals from established publishers take up to a decade to achieve the same goal; DrugMonkey also mentions the "so what" nature of this complaint. Jonathan Eisen remarks that somehow Butler gets from "PLoS ONE is doing well and making money" to "PLoS is a failure"; go read Jonathan to see how twisted your logic has to be to make that particular trip. (Jonathan also provides an important reminder, that we should not confuse Nature Publishing Group as a whole with their many talented and well intentioned employees!) Grrlscientist observes that, while Butler's piece makes it sound as though PLoS' reliance on donations were a bad thing, all journals rely on the donation of time and expertise by unpaid reviewers. Drugmonkey, Jonathan and Grrlscientist all make the point that Nature has its own stable of "second tier" journals with "lower barriers to entry" -- the same mechanism for which Butler criticizes PLoS. Stevan Harnad is famous for making the point (here, for example) that if the funds currently draining into subscriptions were used to pay OA costs, there would be an immense improvement in the utility of the scientific record even if there were no financial saving. Finally, pretty much every commenter has pointed out the glaring lack of any "conflict of interest" statement on the Nature piece -- having said which, I'd better make one of my own. It's well known and obvious at a glance at this blog that my favorite drink is the Open Access Kool-Aid. I have personal friends who work for PLoS, and I've previously applied to work there myself. (Source: Open Reading Frame)

Drug monkey on demystifying science (scienceblogs.com)

Quote of the Day news feed | Edited by Duncan Hull — Thu, 03 Jul 2008 08:54:59 +0100

Wednesday 02 Jul 2008 (Source: Quote of the Day news feed | Edited by Duncan Hull)

Leveraged knowledge management

Sciencebase Science Blog — Thu, 03 Jul 2008 08:32:48 +0100

Several years ago, I was called on by a multinational producer of hygiene, food, and cleaning products to pay a visit to their research and information centre. My role was to play editorial consultant for content for their new Intranet. You see, the company had lots of researchers in one building who were working hard on non-stick ice cream and insect-deterring shaving gel, while the information team were in a separate building trawling patents and fishing for pertinent technology news. Unfortunately, the two teams worked a different shift system and rarely met, and even when they did meet, they didn’t have much to say to each other. One group were more concerned with the latest formulation change that might result in a shift in rheological properties for a new cheese-and-chocolate pie filling or a non-grip floor cleaner, while the other group were interested only in assessing prior art or working out Boolean strings for searching databases. The new Intranet would, however, bring the two groups together. The system would provide regularly updated news and information about what each team was doing, forums for discussing ways to improve efficiency and, most importantly, offer them an area where ideas might be mashed up to help each see the possibilities of the other’s efforts. It would be pretty much an internal version of what we now know as online social networking. And, as with many mashups we see these days would, the reasoning went, allow the company to come up with novel products and marketing strategies based on the two sides of their knowledge. At the heart of the solution was the concept of knowledge management. Indeed, the person in charge had KM somewhere in his job title and, unfortunately, the word leverage was also in his job description. [This post's title is meant to be ironic, in case you didn't spot it, db] Now, before this consultancy work, I had not come across the abbreviation KM, nor the phrase knowledge management and had certainly never wittingly used the word leverage. To my mind it sounded like nothing more than market-speak. Nevertheless, I quickly worked out what it was meant to mean and undertook the task with my usual level of workaholic diligence. Apparently, I’m not alone in my perspective on KM. But, more to the point many people are unaware of the fact that the stuff with which they work is labelled knowledge and that they can manage it nevertheless. In fact, that’s the main conclusion from a paper entitled: “Dimensions of KM: they know not it’s called knowledge…but they can manage it!” published today in the International Journal of Teaching and Case Studies recently (2008, 1, 253). In that paper, Sonal Minocha a senior manager at Raffles University, Singapore, and George Stonehouse of the Napier University Business School, Craiglockhart Campus, in Edinburgh, UK, have explored how for business students the concept of knowledge is a fascinating one as most of them wonder what is encompassed within “knowledge management” for it to be a subject. Yet these same students, can manage knowledge almost without needing to know precisely what KM is. Perhaps that finding extends into the workplace too. Indeed, following a case study involving the fall and rise of a major vehicle manufacturer the researchers come to the following conclusion: Competitive advantage, however, depends upon the creation of new knowledge, based upon this learning, centred upon the development of new business, new ways of doing business, improved customer and supplier relationships, and the development and leverage of new knowledge-based core competencies. Aside from the use of the word leverage and phrases like core competencies, that seems to be a fair conclusion. Well, by now you may be wondering what happened to that proto-social network pioneered by the manufacturer of anti-shark surfboard wax and child-repellent screen cleaners. My consultancy work lasted a week during which time, I’m not proud to say, I taught the management team a thing or two about how not to flip a flip-chart and almost blinded the team leader with a laser pointerI taught the management team a thing or two about how not to flip a flip-chart and almost blinded the team leader with a laser pointer. At the end of the week, we had a fairly solid outline for how to proceed with the new networking system. Unfortunately, the staff member in charge of the KM project to bring the research and information people together was leveraged out of the company soon after; for reasons unrelated to the incident with the flipchart and laser point, I should add. A post from David Bradley Science Writer Leveraged Knowledge Management (Source: Sciencebase Science Blog)

Foreign accent syndrome

Bayblab — Thu, 03 Jul 2008 04:00:00 +0100

Foreign Accent Syndrome is a rare condition that can occur after brain injury. With this condition, a patient speaks the same language, but with a different regional accent (for example, a person from the American midwest may adopt a British accent). Recently at McMaster University, and published in the Canadian Journal of Neurological Sciences [press release] a Canadian case was reported. In this instance, a woman from Southern Ontario suffered a stroke and began speaking with a Newfoundland accent, which continues even two years after the original brain injury:"Rosemary's speech is perfectly clear, unlike most stroke victims who have damage to speech-motor areas of the brain," says Humphreys. "You wouldn't guess that the speech changes are the result of a stroke. Most people meeting her for the first time assume she is from out East. What we are seeing in this case is a change in some of the very precise mechanisms of speech-motor planning in the brain's circuitry." (Source: Bayblab)

Pubmedfight

Bayblab — Thu, 03 Jul 2008 04:00:00 +0100

This is how respectable scientists resolve disputes and settle their dominance. Your argument carries so much more weight when you demolish your opponent at pubmedfight! If only it could take into account impact factors then we would be set.... [found on scienceroll] (Source: Bayblab)

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Sleep

Bayblab — Thu, 03 Jul 2008 04:00:00 +0100

This is such a massively broad topic but I ran across a review of the literature on why we sleep in PLoS Biology. Check out the above table of the leading reasons why we need to sleep and the pros and cons of that arguement. Previously I had thought that it known that sleep was necessary for learning and thus just plain necessary, but it turns out that it is just one of three leading theories. The most convincing to me according to the review is the theory that we require sleep to restore some key macromolecules. The article also contains many other interesting aspects of sleep research including some conjecture on why evolution favoured sleep as such a prevalent behavior, but I didn't understand much of it. (Source: Bayblab)

Nature versus open access

Living the Scientific Life (Scientist, Interrupted) — Thu, 03 Jul 2008 02:51:26 +0100

tags: bpr3.org/?p=52, open access, publishing, life science research, Declan Butler Wow, have you read Declan Butler's nasty little hatchet job that was just published in Nature about the Public Library of Science (PLoS)? My jaw hit the top of the table in my little coffee shop where I am ensconced -- why would Nature demean their journal by publishing such a snotty little screed where they attack the normal, but probably painful, financial ups-and-downs of a new journal? Because Nature represents the old way of doing things, so Nature is afraid of those upstarts, PLoS, whom they (rightly) view as competitors, that's why. Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

West 34th/penn station subway art 4

Living the Scientific Life (Scientist, Interrupted) — Thu, 03 Jul 2008 01:59:59 +0100

tags: West 34th street Penn Station subway art, Circus of Garden Delights, subway art, NYC through my eye, photography, NYC Circus of Garden Delights. West 34th Street/Penn Station Subway tile mosaic art #4 as seen at NYC's West 34th Street stop at 8th for the A, C and E trains. Artist: Eric Fischl, 2001. Image: GrrlScientist 2008 [larger view]. According to the artist, this subway station artwork "depicts a commuter being drawn into the bizarre and surprising world of the circus, meeting animals, clowns, acrobats and fire-breathers on his way to work." Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Only nature could turn the success of plos one into a model of failure

The Tree of Life — Wed, 02 Jul 2008 22:03:00 +0100

Now, mind, you I like Nature as a publishing unit. They publish some very fine journals. Now, most of them are not Open Access, so I choose not to publish there if I can avoid it. But I still like them. And many of the editors and reporters there are excellent - smart, creative, insightful and such. But Nature the publisher can also be completely inane when it comes to writing about Open Access and PLoS. In a new article by Declan Butler, Nature takes another crack at the PLoS "publishing model"The problem with PLoS now is ... wait for this ... the success of PLoS One. PLoS One it turns out is publishing a lot of papers (including one by me, today). And bringing in a decent amount of money to PLoS apparently (note for full disclosure - I am involved in PLoS Biology as "Academic Editor in Chief" and PLoS Computational Biology as an Academic Editor ... although I should note I am not involved in financial discussions at PLoS in any way). So why is the success of PLoS One a problem? Well, because it allows Nature to do the old good cop bad cop routine and to write, again, about the "failings" of the PLoS publication model. Now, mind you, the article does not quote a single source for what the PLoS publication model is. But they do say it has failed. From what I can tell here is the logic of the failure argument:Nature believes PLoS' model for success revolved solely around PLoS Biology and PLoS Medicine and some of the other other PLoS journals being self sustaining after a few years.Analysis of some financial information suggests that PLoS Biology and Medicine currently are not breaking evenPLoS One is apparently wildly successful and thus is brining in some money to PLoS.PLoS One publishes a lot of papers (they discuss this a bit and imply that this is a bad thing because some of the papers must be bad. Note - they do not back this up with any evidence. Silly for me to ask a science journal to use evidence)Therefore, the entire PLoS Publication model is a failure.The problems with this logic are, well, large. Here are some:Does Nature really think that there ever was a single "model" for how PLoS should be evaluated? If so, where is the documentation of what this model actually was?Even if there was a PLoS model and even if it turns out to be not exactly what PLoS is doing now, what is the big deal? If you were a stockholder of any company and they told you "we are never going to change our business model no matter what happens in the world around us" I would recommend you not buy their stock. It is simply farcical to expect any entity to stick to a single simple model forever. Does not Nature supplement some of their bigger journals with their higher volume other journals?Most companies these days use high profile entities such as PLoS Biology and PLoS Medicine to attract attention to other portions of their company in order to help bring in money. Is this somehow not allowed by PLoS? Doesn't Nature do the same thing?If you look at the figure Nature shows of PLoS $$$, it shows income rising in 2007 and expenses going down. How did that get turned into a bad thing?So - I still do like Nature publishing because much of the time it has high quality stuff. It even has high quality stuff commenting/criticizing the Open Access movement and pointing out some of the challenges with it. But this article by Butler is not an impressive piece of work. I really wanted to give him an award but could not think of what to give.See also (thanks to Bora for pointing out a bunch of these links)FrontalBlogotomy Drug Monke: Nature offers a completely objective and unbiased review of PLoS. GnxpGreg LadenGrrrlscientistVanyaPeter SuberLiving the Scientific LifeAlex Holcombe/Ceptional Nature targets financial weakness of PLoS journalsThis is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist at the University of California, Davis. (Source: The Tree of Life)

Pin oak tree

Living the Scientific Life (Scientist, Interrupted) — Wed, 02 Jul 2008 19:59:59 +0100

tags: Pin Oak Tree, Quercus palustris, tree bark, Image of the Day Bark of the pin oak tree, Quercus palustris. Image: GrrlScientist 2008 [larger view]. Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

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The plight of the penguins predicts the coming plight of humans

Living the Scientific Life (Scientist, Interrupted) — Wed, 02 Jul 2008 17:03:59 +0100

tags: bpr3.org/?p=52, global warming, climate variation, climate change, penguins, El Nino, marine zoning, P. Dee Boersma Adélie penguins, Pygoscelis adeliae, and chicks. (a) Adélie penguin chicks may get covered in snow during storms, but beneath the snow their down is warm and dry. (b) When rain falls, downy Adélie chicks can get wet and, when soaked, can become hypothermic and die. Images: P. Dee Boersma. According to an article that was just published in the journal BioScience, penguin populations are declining sharply due to the combined effects of overfishing and pollution from offshore oil operations and shipping. Dee Boersma, professor of biology and the Wadsworth Endowed Chair in Conservation Science at the University of Washington in Seattle, has been studying Patagonian (magellanic) penguins, Spheniscus magellanicus, at Punta Tombo, Argentina, for almost 30 years. In her paper, she reports that their numbers have declined by 22 percent since 1987. Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

My first plos one paper .... yay.

The Tree of Life — Wed, 02 Jul 2008 15:45:00 +0100

Well, I have truly entered the modern world. My first PLoS One paper has just come out. It is entitled "An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)" and well, it describes automated software for analyzing rRNA sequences that are generated as part of microbial diversity studies. The main goal behind this was to keep up with the massive amounts of rRNA sequences we and others could generate in the lab and to develop a tool that would remove the need for "manual" work in analyzing rRNAs. The work was done primarily by Dongying Wu, a Project Scientist in my lab with assistance from a Amber Hartman, who is a PhD student in my lab. Naomi Ward, who was on the faculty at TIGR and is now at Wyoming, and I helped guide the development and testing of the software. We first developed this pipeline/software in conjunction with analyzing the rRNA sequences that were part of the Sargasso Sea metagenome and results from the word was in the Venter et al. Sargasso paper. We then used the pipeline and continued to refine it as part of a variety of studies including a paper by Kevin Penn et al on coral associated microbes. Kevin was working as a technician for me and Naomi and is now a PhD student at Scripps Institute of Oceanography. We also had some input from various scientists we were working with on rRNA analyses, especially Jen Hughes MartinyWe made a series of further refinements and worked with people like Saul Kravitz from the Venter Institute and the CAMERA metagenomics database to make sure that the software could be run outside of my lab. And then we finally got around to writing up a paper .... and now it is out.You can download the software here. The basics of the software are summarized below: (see flow chart too).Stage 1: Domain AnalysisTake a rRNA sequenceblast it against a database of representative rRNAs from all lines of lifeuse the blast results to help choose sequences to use to make a multiple sequence alignmentinfer a phylogenetic tree from the alignmentassign the sequence to a domain of life (bacteria, archaea, eukaryotes)Stage 2: First pass alignment and tree within domaintake the same rRNA sequenceblast against a database of rRNAs from within the domain of interestuse the blast results to help choose sequences for a multiple alignmentinfer a phylogenetic tree from the alignmentassign the sequence to a taxonomic groupStage 3: Second pass alignment and tree within domainextract sequences from members of the putative taxonomic group (as well as some others to balance the diversity)make a multiple sequence alignmentinfer a phylogenetic treeFrom the above path, we end up with an alignment, which is useful for things such as counting number of species in a sample as well as a tree which is useful for determining what types of organisms are in the sample.I note - the key is that it is completely automated and can be run on a single machine or a cluster and produces comparable results to manual methods. In the long run we plan to connect this to other software and other labs develop to build a metagenomics and microbial diversity workflow that will help in the processing of massive amounts of sequence data for microbial diversity studies.I should note this work was supported primarily by a National Science Foundation grant to me and Naomi Ward as part of their “Assembling the Tree of Life” Program (Grant No. 0228651). Some final work on the project was funded by the Gordon and Betty Moore Foundation through grant #1660 to Jonathan Eisen and the CAMERA grant to UCSD.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist at the University of California, Davis. (Source: The Tree of Life)

Just say 'yes'!

Living the Scientific Life (Scientist, Interrupted) — Wed, 02 Jul 2008 13:59:59 +0100

tags: Just say Yes, humor, telemarketers, streaming video Just a little fun for all those people who are tired of being tortured by telemarketers [1:20] Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Art and the biomedical invisibles (why do museums want to bring art and science together? — part 4)

Biomedicine on Display — Wed, 02 Jul 2008 12:07:15 +0100

As I wrote in the last post, our co-operation with the Danish Museum of Art and Design in 2004 was the founding rationale for our pilgrimage into art, design and science. Then things went rapidly. In 2006 we engaged Canadian-British artist-curator Martha Fleming to help us organise a workshop on ‘Biomedicine and Aesthetics in a Museum Context’, followed by a public conference on ‘Art and Biomedicine: Beyond the Body’ hosted by the Royal Academy of Fine Arts in Copenhagen. We also began experimenting with different kinds of art exhibitions and installation, for example the street exhibition ‘The Face of Disease’, the photo collage exhibition ‘100 Light Years’, and the installation ‘Labyrinthitis’, a medical technology-inspired installation by Berlin-based sound artist Jacob Kirkegaard. In this process, we were, in my ideal-typical reconstruction, entertaining another rationality for bringing art and science together, namely that art is a way of representing the new biomedical invisibles (see Martha’s article ‘The huge invisibles’). Medical museums have traditionally dealt with visible artefacts at a phenomenologically accessible macrolevel. The audience loves to see all these highly evocative objects: amputation saws, trepanations sets, pickled tumours, and so forth. But the armamentarium of contemporary biomedicine (HPLC columns, gene chips, etc.) are not particularly evocative, and the body they help researchers to represent is invisible (mainly protein interactions). Hence another reason why art enters into the strategy of medical museums these days. Art is considered a way of bridging the everyday world and the invisible cellular and molecular domains. This is what the annual Wellcome Image Awards are about: “the winning pictures”, they say, “show a wide variety of subjects, normally invisible to the naked eye, revealing new layers of complexity and making the ordinary extraordinary”. They probably mean making the extraordinary ordinary, though :-) [the next post will be about art as a great cross-disciplinary integrator] (Source: Biomedicine on Display)

Mathematicians robert adler, john ewing and peter taylor on lies, damned lies and statistics (mathunion.org)

Quote of the Day news feed | Edited by Duncan Hull — Wed, 02 Jul 2008 09:16:23 +0100

Tuesday 01 Jul 2008 (Source: Quote of the Day news feed | Edited by Duncan Hull)

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Health benefits of indium

Sciencebase Science Blog — Wed, 02 Jul 2008 08:23:12 +0100

Yet another health supplement hits the streets, this time in the form of indium sulfate. Never heard of it? Apparently, it “is a rare trace mineral that supports several hormonal systems in the body. Indium may strongly elevate immune activity and reduce the severity and duration of a myriad of human conditions.” That’s according to the NaturalHealthConsult.com website, which goes on to claim that the element will “normalize the hypothalamus and pituitary gland in the brain.” The site explains, that “As the conductor of various studies on indium, Dr. Schroeder (the scientist best known for inventing the means to take lead out of gasoline) found that possibly the most important function of Indium is to normalize the hypothalamus and pituitary gland in the brain.” Well, the late Henry A. Schroeder of Dartmouth Medical School, a leading toxicologist, spent years highlighting the problems of lead toxicity, but did not as far as I know despite the wording of the quote above, develop a method for removing lead from gasoline. Why would you need to do that? The petrochemical companies used to add tetraethyl lead as an antiknocking agent, so the simplest method for its “removal” is just not to add it in the first place. Tetraethyllead was first added to gasoline in 1923 and it quickly became obvious that workers at the three manufacturing plants were becoming psychotic and dying from its toxic effects. The issue was essentially hushed up and “research” between 1926 and 1965 claimed a consensus that lead was only a problem at high exposure levels and atmospheric lead from vehicle exhausts was not a problem at all. We now know different, thanks partly to the efforts of Schroeder. Meanwhile, back to indium. Elemental discoveries are a boon to any marketeer, especially if you can convince consumers to buy, buy, buy. A document entitled: “Patented Indium Trace Element in Marketing Form Available for License” suggests how this can be so There are 3 questions that a company should ask when considering the addition of a new product for its product line: What is it that I can sell abundantly, at a high profit and worldwide, exclusively? Why will my customers want to continue to use it, daily, for the rest of their lives? How will my customers be able to afford to use it daily, all of their lives, continuously? It then tells us how these pertain to indium (In, element 49) and how a clever marketer might exploit the patent on the health benefits of indium. So, where do the supposed health benefits of indium come from or is it just a marketing scam and what about those claims to affect the activity of glands in the brain. Well, indium is an element in the same group of the periodic table as boron, aluminium, and gallium, oh and thallium, so one would not expect it to be particularly beneficial or even essential to health. Indeed, aluminium is a neurotoxin. However, Schroeder, towards the end of his life, wheelchair bound with muscular dystrophy, included indium in some of his last few experiments. He apparently, demonstrated that lab animals, on lifetime indium, had fewer cancers than controls. Other than references to the use of indium in imaging agents, I can find nothing in the medical literature regarding the positive health benefits of daily supplementation with indium, not then, not now. Yet, the web is littered with so-called health food sites selling indium sulfate to unwitting consumers, presumably, exploiting that marketing guidance I found on at least one site. However, there is one site to which I shall refer you and that is the webelements site from Sheffield University’s Mark Winter. the entry for indium explains that depending on dose: All indium compounds should be regarded as highly toxic. Indium compounds damage the heart, kidney and liver, and may be teratogenic So, who do you trust most, a health website hoping to get repeat sales based on your fears of poor health as you get older, or a well-respected site from a leading research team at a top university? I’m pretty sure I don’t want to be ingesting an indium compound daily for the rest of my life in the vague hope that represents some undiscovered panacea, that would just be bad medicine This item originally published July 25, 2005, was overhauled and updated at the request of a Sciencebase reader on July 2, 2008. A post from David Bradley Science Writer Health Benefits of Indium (Source: Sciencebase Science Blog)

Badass scientist of the week

Bayblab — Wed, 02 Jul 2008 04:00:00 +0100

I couldn't pass on the opportunity for a new installment in this series, and to share this news of a biologist who jumped into the Golf of Mexico to save a 375 pound bear from drowning. I mean look at the picture, this may be the most badass scientist yet... "Mr Warwick kept one arm underneath the bear gripped the scruff of the bear's neck with the other to keep its head above water as he dragged the animal back to shore." (Source: Bayblab)

Science blogging 2008: london

Nascent — Wed, 02 Jul 2008 04:00:00 +0100

We at Nature Network are putting on a science blogging conference in London on 30 August 2008. More than 100 bloggers, scientists and science communicators will gather at the Royal Institution to discuss topics such as how science blogging can change (improve?) the public’s perception of science, how blogging can boost your creativity and be used as a teaching tool, how scientists can be more open with their primary research data, and what the future holds for online scientific communication. Click here for the programme. A few sessions have been set aside to be ‘unconference’ sessions, meaning that the topic and the speakers will be proposed and decided on the day of the event. Click here for more details about the conference. There’s already been quite a bit of discussion about the event in the conference’s forum on Nature Network. Registration is free. Just email us (network at nature.com) with your name, affiliation, and a link to your blog if you have one. (Source: Nascent)

West 34th/penn station subway art 3 [detail 2]

Living the Scientific Life (Scientist, Interrupted) — Wed, 02 Jul 2008 01:59:59 +0100

tags: West 34th street Penn Station subway art, Circus of Garden Delights, subway art, NYC through my eye, photography, NYC Circus of Garden Delights. West 34th Street/Penn Station Subway tile mosaic art #3 [Detail #2] as seen at NYC's West 34th Street stop at 8th for the A, C and E trains. Artist: Eric Fischl, 2001. Image: GrrlScientist 2008 [larger view]. According to the artist, this subway station artwork "depicts a commuter being drawn into the bizarre and surprising world of the circus, meeting animals, clowns, acrobats and fire-breathers on his way to work." Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Calling all bioinformaticians...

Open Reading Frame — Wed, 02 Jul 2008 01:08:05 +0100

Mike of Bioinformatics Zen is looking for information; please help him out if you can, by taking the survey either here or at BZ. Take particular note of the following: The raw data entered into this questionnaire, along with any interpretation will be released into the public domain under a creative commons attribution license. If you are unhappy with answering any of the questions please leave them blank. By completing this questionnaire you consent to your answers being released. (Yes, I know it's repeated at the top of the survey: it's important.) Loading... (Source: Open Reading Frame)

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Update: planning my london visit and scienceblogging conference appearance

Living the Scientific Life (Scientist, Interrupted) — Tue, 01 Jul 2008 23:17:04 +0100

I just had to let you know a few details about my London visit. First, my renewed passport arrived in snailmail, with no problems at all! The new passport is quite fancy, by the way, with all sorts of aphorisms about democracy and how wonderful it is printed at the top of each page. Too bad they didn't include anything about the lack of health insurance, the housing crisis and the absolutely crappy employment situation for people with "too much education". Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Natural selection turns 150 years old today

Living the Scientific Life (Scientist, Interrupted) — Tue, 01 Jul 2008 21:10:00 +0100

tags: natural selection, evolution, Alfred Russel Wallace, Charles Darwin, Darwin Year, Linnean Society of London Image: Gary Larson. This morning, I was pleased to hear National Public Radio was celebrating the 150th birthday of Natural Selection, the mechanism whereby evolution occurs. Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Playful green-naped rainbow lories

Living the Scientific Life (Scientist, Interrupted) — Tue, 01 Jul 2008 19:59:59 +0100

tags: Green-naped Rainbow lory, Trichoglossus haematodus haematodus, birds, Image of the Day Last in a series of ten images of lories by this photographer. A playful group of green-naped subspecies of the Rainbow lory, Trichoglossus haematodus haematodus. There are 15 subspecies of rainbow lories occurring throughout the islands of the south Pacific Ocean. This subspecies is primarily found along the east coast of Australia. Image: John Del Rio [larger view]. Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

One aesthetically corrupted, always corrupted (why do museums want bring art and science together - part 3)

Biomedicine on Display — Tue, 01 Jul 2008 14:04:11 +0100

Which were Medical Museion’s reasons for going into art and aesthetics? The first on my list of ideal-typical rationalities is what I call “once-aesthetically-corrupted, always-corrupted”. The argument goes like this: As Sepp Gumbrecht pointed out in his seminal 2004 book The Production of Presence: What Meaning Cannot Convey, most humanities scholars, including historians, are engaged in interpretative and hermeneutic practices. But rarely in aestethic practices, i.e., what he calls the ‘production of presence’. Same for historian-as-curators in the world of science, technology and medical museums: Most STM-curators see their museums as sites for historical narration, interpretation and contextualisation, but rarely as sites where visitors are engaged in sensual and aesthetic experiences, in presence-production. What changed our minds, from seeing our museum as an institution for meaning-production only, to an institution involved also in presence-production was when our neighbour, the Danish Museum of Art and Design in Copenhagen, was setting up an anniversary exhibition in 2004. Since we were, and still are, good neighbours, their curators went over to our place to take a close look at our collections, and they went back with over 60 artefacts which we had, until then, routinely classified as historical objects. But they decided these were aesthetic objects. That was our aesthetic epiphany, our moment of entrance into the aesthetics of medical objects. And since then our museum has never really been the same. Suddenly we saw things that medical historians have never really seen. And more generally speaking, I believe that this is one of the rationales for why STM-museums in the last 15-20 years have, more or less by default, begun to incorporate aesthetic approaches and art in their exhibitions: Once you have tried it, there is no way back. Once the discursive rationality of the historian has been corrupted by the irrationality of aesthetic judgement, you cannot really undo it. More and more of us, former science, technology and medical history museums, are becoming fallen historical angels. (Photo: Snowrunner 2006, from Flickr; creative commons) [next post will be about biomedical invisibles] (Source: Biomedicine on Display)

Underwater astonishments

Living the Scientific Life (Scientist, Interrupted) — Tue, 01 Jul 2008 13:59:59 +0100

tags: Underwater Astonishments, marine biology, evolution, streaming video David Gallo shows jaw-dropping footage of amazing sea creatures, including a shape-shifting cuttlefish, a pair of fighting squid, and a mesmerizing gallery of bioluminescent fish that light up the blackest depths of the ocean. He focuses on the work of two scientists: Edith Widder at the Ocean Research & Conservation Association, and Roger Hanlon at the Marine Biological Lab. [6:01] Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

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Richard creightmore on glastonav and gps at glastonbury festival (guardian.co.uk)

Quote of the Day news feed | Edited by Duncan Hull — Tue, 01 Jul 2008 08:47:55 +0100

Festive Sunday 29 Jun 2008 (Source: Quote of the Day news feed | Edited by Duncan Hull)

Scrabble® inventor alfred butts on his spelling (guardian.co.uk)

Quote of the Day news feed | Edited by Duncan Hull — Tue, 01 Jul 2008 08:47:55 +0100

Monday 30 Jun 2008 (Source: Quote of the Day news feed | Edited by Duncan Hull)

Carbon tet and paradigm shifts

Sciencebase Science Blog — Tue, 01 Jul 2008 07:32:02 +0100

Since tetrachloromethane is banned as an industrial solvent avoiding its formation as a byproduct of other chlorocarbons is important, this week, The Alchemist learns that a lanthanum chloride catalyst could help with the cleanup. A paradigm shift in drug discovery could be approaching as researchers working with proteins involved in Alzheimer’s disease have discovered an apparently novel approach to inhibiting disease. In organic chemistry, the Alchemist hears that molecules are not quite as diverse as we first thought, while an Olympic analysis could help sports officials spot dopey athletes. Princeton scientists are focusing on a new approach to making microchips and, finally, an astronomer with a chemical bent has had a cometary mineral named for him. More on this and all the links in my Alchemist column on ChemWeb A post from David Bradley Science Writer Carbon Tet and Paradigm Shifts (Source: Sciencebase Science Blog)

Why do museums want to bring art and science together? — part 3

Biomedicine on Display — Tue, 01 Jul 2008 06:31:49 +0100

Scienceblogs to take over the world

Living the Scientific Life (Scientist, Interrupted) — Tue, 01 Jul 2008 02:46:18 +0100

tags: Seed Media Group, ScienceBlogs, ScienceBlogs.de I have been made privy to a special 1 July 2008 press release from Seed Media Group, the parent organization for ScienceBlogs, which hosts my blog. The news is good. Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

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West 34th/penn station subway art 3 [detail 1]

Living the Scientific Life (Scientist, Interrupted) — Tue, 01 Jul 2008 01:59:59 +0100

tags: West 34th street Penn Station subway art, Circus of Garden Delights, subway art, NYC through my eye, photography, NYC Circus of Garden Delights. West 34th Street/Penn Station Subway tile mosaic art #3 [Detail #1] as seen at NYC's West 34th Street stop at 8th for the A, C and E trains. Artist: Eric Fischl, 2001. Image: GrrlScientist 2008 [larger view]. According to the artist, this subway station artwork "depicts a commuter being drawn into the bizarre and surprising world of the circus, meeting animals, clowns, acrobats and fire-breathers on his way to work." Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Looming news

The Tree of Life — Mon, 30 Jun 2008 23:27:00 +0100

Just having some fun with/at Carl Zimmer who claims he has some news to post very soon. SeeSome News...Almost Ready...This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist at the University of California, Davis. (Source: The Tree of Life)

Help profauna stop indonesian parrot smuggling!

Living the Scientific Life (Scientist, Interrupted) — Mon, 30 Jun 2008 22:48:07 +0100

tags: smuggling parrots, poaching parrots, ProFauna Indonesia, endangered species, conservation, politics Indonesians protest the illegal wildlife trade. Image: ProFauna Indonesia. You know that I am passionate about the parrots of the south Pacific Ocean -- I devoted my life to researching them, in fact. So it is my responsibility to bring a very important and tragic issue to your attention. Indonesia, home to many of the birds that I love so much, is killing its endemic parrots through poaching and smuggling. Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Update: housing

Living the Scientific Life (Scientist, Interrupted) — Mon, 30 Jun 2008 20:17:21 +0100

I called the landlord's office (again) last Friday to find out what this "rent increase" is about, and the people in the landlord's office had no ideas. As most of you know, I have been trying to find out about this "rent increase" for the past three months, by writing and calling my landlord, but he refuses to explain. Since I live in a rent stabilized apartment, all rent increases must be approved by the city before they are enacted, according to my sources. Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Portrait of a blue mountain rainbow lory

Living the Scientific Life (Scientist, Interrupted) — Mon, 30 Jun 2008 19:59:59 +0100

tags: Blue Mountain Rainbow Lory, Swainson's Rainbow Lory, Trichoglossus haematodus moluccanus, birds, Image of the Day Eighth in a series of lory images by this photographer. Rainbow Lory, Trichoglossus haematodus moluccanus. This subspecies of rainbow lory is also found in Australia, along the east coast. Image: John Del Rio. [larger view]. Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

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Eye on carl (zimmer, that is)

Living the Scientific Life (Scientist, Interrupted) — Mon, 30 Jun 2008 18:37:00 +0100

My friend and colleague, Carl Zimmer, has some news that he is going to tell us about today at 5pm ET, so be sure to pop in to his blog at that time to see what's happening. Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Birds in the news 137

Living the Scientific Life (Scientist, Interrupted) — Mon, 30 Jun 2008 16:59:59 +0100

tags: Birds in the News, BirdNews, ornithology, birds, avian, newsletter Ruby-crowned Kinglet, Regulus calendula, with insect egg or pupa in its beak. Image: Dave Rintoul, KSU [larger view]. Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Ovulation

Living the Scientific Life (Scientist, Interrupted) — Mon, 30 Jun 2008 13:59:59 +0100

tags: Ovulation, medicine, technology, streaming video Recently, human ovulation was captured on video for the first time ever. Two researchers, Stephan Gordts and Ivo Brosens of the Leuven Institute for Fertility & Embryology in Belgium, performed transvaginal laparoscopy, which involves making a small cut in the vaginal wall and observing the ovary with an endoscope. "This allows us direct access to and observation of the tubo-ovarian structures without manipulation using forceps," reports Gordts. Below the fold is part of their video. [0:55] Read the rest of this post... | Read the comments on this post... (Source: Living the Scientific Life (Scientist, Interrupted))

Why do museums want to bring art and science together? — part 2

Biomedicine on Display — Mon, 30 Jun 2008 05:59:55 +0100

Why has art and aesthetics then entered the science, technology and medicine (STM) museum sector? This was not the case 15 or 20 years ago. What has happened in the last two decades? I will not attempt to give any historical, sociological or political explanations for the flow of art and aesthetics into STM-museums; that’s a topic for a serious research project and even a book. Instead I will take on a more preliminary task: I will try to reconstruct a handfull of ideal-typical rationalities for why STM-museum curators around the world are engaged in bringing art and the biomedical sciences together. I hasten to add that I haven’t done any fieldwork, or asked curators to fill in any questionaires. The reconstructions that follow in the next couple of posts are based primarily on websites and occasional discussions, and especially on my own experiences as the director of Medical Museion in Copenhagen. Sizewise, Medical Museion is somewhere between the Jurassic midgets and the contemporary Power giants. We are placed in an old 18th century palace-looking building (the former Royal Academy of Surgeons) in the Copenhagen inner city area, with approx 4000 square meters of storage, exhibition and office space. Our biggest asset, besides the building, is a huge collection of medicotechnical artefacts, wet specimens and hard human remains — actually one of the biggest collections in northern Europe — ranging from 18th century medical curiosities to 20th century everyday medical care objects. We believe we have a total of around 200.000 objects plus another 60.000 images. Like many other similar medium-size traditional medical history museums around the world, our museum was – until recently, when it was still called the Medical History Museum at the University of Copenhagen – content with taking care of and displaying the old treasures. Some medical history museums are in fact still quite satisfied with such a role; they are not interested in becoming engaged with the rapidly changing biomedical landscape, i.e, all these revolutionary things that are happening on the interface between postgenomic cell biology, pharma production, medical technology, biotech industry and computer science. It’s a messy world, so I think it’s perfectly legitimate (and probably even quite wise) to stay away from it. But we decided to jump on the life science bandwagon, to engage with the hurly-burly of the contemporary life science world. So in the last four-five years we have turned both our research efforts, our acquisitions of new artefacts, and our temporary exhibitions towards investigating and displaying contemporary developments in the biomedical field. And a few years ago, a private Danish research foundation, the Novo Nordisk Foundation, decided that this approach was worthwhile supporting. So now we are in the midst of a combined research and curatorial project called ‘Biomedicine on Display’. I say ‘combined’, because we seek to integrate research, the acquisitions of the material and visual culture of biomedicine, and the creation of exhibitions. And we do indeed have a great interest in bringing art, aesthetics and medicine together. So in a sense, we are not just a medical history museum anymore, but a medical museum. That’s one of the reasons we changed our name to Medical Museion. So, which were our reasons for going into art and aesthetics? [I’ll be back tomorrow or the day after tomorrow]. (Source: Biomedicine on Display)