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Cal Academy Butterfly Collection [video] (from Grrl Scientist's blog)

Fri, 04/27/2012 - 4:00am

SUMMARY: A glimpse at Cal Academy’s butterfly collection and a discussion about why these butterfly collections are important to science Do you like butterflies and moths? I certainly do. When I was a graduate student, part of my graduate training was invested in studying moths. So captivated by moths and butterflies was I that I seriously considered devoting my professional career to studying them. But butterflies and moths — the lepidopterans — are more than just pretty insects that pollinate plants. They are important research subjects that provide valuable glimpses into evolutionary processes. They provide scientists with important insights into sexual selection, speciation, and the relationship between ecology and evolution and between genetics and evolution.

Kitty and Phineas: Always print the legend? (from Suzi Gage's blog)

Thu, 04/26/2012 - 8:02pm

Phineas_Gage_Cased_Daguerreotype_WilgusPhoto2008-12-19_Unretouched_Color.jpgRecently I feel a little like the rug has been pulled out from under my feet. I’m referring to revelations (uncovered by speaking to friends and when ‘researching’ (read: looking on Wikipedia) an answer for ’I’m a Scientist’ last year) about two of my firmest held beliefs from my psychology studies. Specifically, two case studies so well known they are simply referred to by their names. Kitty Genovese and Phineas Gage.These are stalwarts of (I’m willing to wager) almost every undergraduate Psychology degree in the country, if not the world. Kitty Genovese was the New York lady who was brutally murdered in 1964, as 38 neighbours and bystanders did nothing. Phineas had an unfortunate accident with a tamping iron whilst building a railway, the rod passed through his frontal lobe, and the resulting damage taught undergraduates like myself that this brain area was the home of the personality.Kitty Genovese’s murder was tragic for a number of reasons. Her killer was actually scared off by shouts or movements from her neighbours, and she almost escaped to the safety of her building, but was thwarted by a locked door, and weakened having already been stabbed. Newspaper reports at the time painted a picture of a group of 38 neighbours who were all aware she was being attacked by did nothing to help. In fact, a recent paper (Manning et al., 2007) has documented how these newspaper reports, exaggerating the facts, have started a snowball rolling; Latané and Darley’s (1970) ‘bystander effect’ was found to be robust and compelling, and the story of Kitty’s murder inspiring these experiments is really neat, and has pervaded popular culture from graphic novels to folk songs inspired by her.But the facts about the story, presented by Manning, seem to be somewhat different from the ‘good Samaritan parable’ that is printed in Psychology textbooks. Firstly, the witnesses could not all see, some could only hear screams or a scuffle. In particular, the final attack took place in a secluded place visible only to a few people. The witnesses also claim they called the police immediately after the first attack. The figure ‘38’ came from a policeman saying “I believe that many people heard the screams…It could have been more than 38”. Manning paints a compelling picture from police reports at the time suggesting witnesses could not see the severity of the situation, and far from doing nothing, made calls to the police and succeeded in scaring her attacker away once, while not seeing him return later to murder Kitty.Now, I’ll admit, despite my youthful looking face, that this paper came out a while after I’d finished my Undergraduate course, but I’d love to know from lecturers or students whether this case study is still used.Now to Phineas, who I’ve always had a soft spot for, due to our sharing a surname. Somewhat of an older case study, his accident occurred in 1848. He was a fit, active 25 year old, and despite blasting a large iron rod through his head, he was speaking and walking within minutes, and completely conscious as he travelled to get medical attention. There’s a particularly gory description of this on Wikipedia, my favourite section being a quote from the first doctor who saw him; ‘Mr. G. got up and vomited; the effort of vomiting pressed out about half a teacupful of the brain, which fell upon the floor’. Yuk!This is where the story in text books departs from what’s known. I recall being told during my studies that Phineas became a different man after the accident. He couldn’t hold a job, he became more bawdy, had difficulty behaving appropriately for the situation that he was in, became more impulsive, less inhibited, and started lying or confabulating.The evidence appears to be somewhat less conclusive. It took Phineas a long time to recover. Despite his initial ability to walk and talk straight after the incident, his doctor’s notes suggest he was semi-comatose for a week afterwards, and was only able to return to his parents’ house after a couple of months. However, the evidence that his personality was so negatively affected is much less obvious. It is somewhat unsurprising that he didn’t go back to his work on the railway; however well he recovered, he only had one eye now, and he had a hole in his skull! Reports suggesting he mistreated his wife and child are clearly untrue, as records show Phineas did not have either.A book about inaccuracies in the reporting of Gage’s personality changes was first published in 2000, (just) before I went to University, so I can understand why this knowledge may not have made it in to text books by the time I started, but in this book there’s a report of a British psychologist Ferrier, who in 1877 expressed concern about misreporting and exaggeration in this case!Should teaching Undergraduates the facts about these cases get in the way of a good story, or is it OK to use these apocryphal examples to teach about psychological phenomena that do seem to stand up to rigorous experimentation? I can see the argument either way, these stories certainly stuck in my mind, and the underlying ‘bystander apathy’ and frontal lobe function are well known from multiple evidence sources. In these days of ubiquitous knowledge at the end of an Ethernet cable, the truth will out though, so should Psychology text books catch up? I’d love to hear your thoughts on the matter!(image From the collection of Jack and Beverly Wilgus.)

Why Can't We See Evidence of Alien Life? [video] (from Grrl Scientist's blog)

Thu, 04/26/2012 - 4:00am

SUMMARY: This video presents an animated exploration of the famous and fascinating Fermi Paradox Given the vast number of planets in the universe, many much older than Earth, why haven’t we yet seen obvious signs of alien life? The potential answers to this question are numerous and intriguing, alarming and hopeful. This video presents an animated exploration of the famous and fascinating Fermi Paradox, originally posed in 1950 by physicist Enrico Fermi, which basically states:

What to buy at homeopathic pharmacies (cartoon) (from Viktor Poor's blog)

Wed, 04/25/2012 - 8:12am

Last week I showed how should you pay for a homeopathic pharmacy.Now let’s see, what you got for your money:nothing.PNGIf you happen to have undergraduates at your lab (or you are one), you should check out this brilliant poster.

Be sceptical of the merging of faith and science (from Lee Turnpenny's blog)

Wed, 04/25/2012 - 8:01am

(or: Foot stamping) I caught this week’s Beyond Belief on BBC Radio 4, and suffered again the Christian extravasations of John Lennox. Listen (from @ 0:07:15) to his sought, considered, respected opinion as he declares…bq. “It seems to me Newton is immensely important as evidence for what we’re talking about today [Argument for first cause], because when he discovered his law of gravitation… his response was, ‘What a wonderful god he is who did it that way!’"This is evidence alright… for Newton’s zealous faith.bq. “He wrote the Principia Mathematica … with the express wish that it would convince the thinking person to believe in God."He wrote it in Latin. Unashamedly not overly-concerned with accessibility to the heathen, then.Communicating Newton’s immense scientific achievements and his impact on the scientific method is one laudable thing; but allying them to his multifarious (often crackpot) beliefs – though historically interesting from the point of view of how they imaginatively informed (or otherwise) his scientific inspiration – has no scientific merit. So, as Lennox is afforded repeat platform to mis-communicate the supernatural applicability of science, I will use my platform here to repeat my self, and alleviate my sulking irritation at the repeated ignoring of my efforts to get the Leicester Mercury to take my further re-edited, re-resubmitted and re-rejected contra-apologetic argument.Because I happen to consider it (no less) valid. Thank you for reading. ___________________________________________________________________________We are all, to some extent, ‘philosophers’, in that we tend to advocate our view of life and the world. However, most of us have neither studied philosophy, nor do we spend much time critically examining our own reasoning. We thus tend not to consider that much of the information in our minds is false and highly susceptible to our culture and belief system. Everybody likes to have their beliefs, their opinions, their prejudices confirmed, and is inclined to reject arguments against them.Yet we are often impressed when supposed pearls of wisdom emanate from public figures. Notorious Premier League footballer Joey Barton likes to tweet the occasional profound lyric or philosophical quote. This propensity seems to have partly restored his reputation in the eyes of a fickle public. But is he any more ludicrous than those who adopt the theological tactic known as apologetics?Deriving from the Greek apologia, meaning ‘reasoned defence’, apologetics is a branch of theology concerned with the defence and proof of Christianity. It becomes problematic when science gets called as witness.Christian apologists like to argue, often with cherry-picked philosophical quotations, the supernatural significance of the discoveries of great (religious) scientists, such as Isaac Newton. Science is glorified for its triumphant revealing of the workings of God’s universe. Apologetic ‘reasoning’ holds that all scientists are, wittingly or unwittingly, investigating not merely the natural world, but ’God’s plan.’ But those scientists who argue to the contrary are hypocritically reminded of the natural limitations of (their) science.It seems the capacity of science depends on the beliefs of those doing it – if you believe you are researching God’s handiwork, then it is God’s handiwork you will see. As an academic pursuit, this apologetic merging of faith and science becomes ‘philosophy’. Or theology. Whatever, it generates statements which are potentially highly misleading.Misappropriation of scientific laws as ‘evidence’ for the existence of an agent who set those laws in place does not follow scientifically. Whilst it has to be acknowledged that the religious belief of Newton and others was a driver for modern science, their pioneering of the mathematical explanation of the universe does not constitute retrospective evidence for ‘God.’ Quite right to recognise Newton’s brilliance as a scientist and mathematician. But appealing to the faith of great scientists does not a scientific argument make. Philosophical quotes, whether from pseudo-intellectuals or serious intellectual scholars, often draw admiring gasps, or approving nods of recognition. But they do not necessarily convey ‘truth’. Barton’s street philosophy makes for an occasionally refreshing change from the robotic, cliché-recycling footballer. But religious misappropriation of science is pseudoscience – a cardinal sin for any scientist.

Why does PLoS hate openness? (from Bob O'Hara's blog)

Wed, 04/25/2012 - 4:48am

My frustrations for the day – I’m co-author on a manuscript submitted to PLoS. We’re now trying to upload the final version but we’re hitting silly problems that are caused by PLoS seemingly being beholden to Microsoft.

Inside the AMNH Collections: Paleontology and the Big Bone Room [video] (from Grrl Scientist's blog)

Wed, 04/25/2012 - 4:00am

SUMMARY: In this video, we go on a behind-the-scenes tour of the Big Bone Room at the American Museum of Natural History to look at sauropod bones Wouldn’t you love to go on a behind-the-scenes tour of the Big Bone Room at the American Museum of Natural History? In this video, Paleontology Collections Manager Carl Mehling shows us a few fossil treasures, such as the bony beak of a triceratops, the original model of T. rex, which was used to figure out how to mount the real specimen, and one of the largest intact dinosaur bones in the world, the 650-pound thigh bone of the long-necked, plant-eating dinosaur Camarasaurus.

Alutiiq Basket Weavers Share Insight with Russian Curators. Plus, a Frontier Scientists App! (from Liz O'Connell's blog)

Tue, 04/24/2012 - 1:53pm

Fairbanks, Alaska, April 24, 2012—“The Museum of Anthropology and Ethnography (MAE) and the Russian Ethnographic Museum in St. Petersburg Russia have the earliest collections of Kodiak baskets, grass and spruce root, in the world,” said Sven Haakanson, executive director of the Alutiiq Museum and Archaeological Repository.BasketInsight_group.jpgIn 2010, Haakanson traveled with six Native weavers to St. Petersburg to study the well preserved baskets, collected by Russian explorers in the 1800’s. In turn, “the Alutiiq weavers shared with Russian museum curators what the baskets were made of, how they were made and to weave in more stories about what the baskets mean—more than just an ethnographic piece,” said Haakanson. The Frontier Scientist videos feature the weavers telling their stories in seven videos. [Frontier Scientists]BasketInsight_showcase.jpgThe videos showcasing the historic, economic and cultural value of basket weaving are the newest edition to the Frontier Scientists web site. Collecting and Curing Grass explains the price of a blade of grass from the perspective of the basket weaver. Katie Oliver, director of the Kodiak Historical Society’s Baranov Museum, and Sara Squartsoff, former education coordinator for the Alutiiq Museum, describe a brief history of Kodiak basket weaving and community participation in the video titled Teaching and Learning the Art of Basket Weaving [Alutiiq Weavers].A new app created at the University of Alaska Fairbanks (UAF) makes the Frontier Scientists (FS) web site available for the iPhone, iPad, and iPod. The free, universal app named for the website it highlights is the second app designed by UAF, but the first to make research available to the general public. “By downloading the videos onto your iOS device through the app, it gives you the freedom to watch them at your leisure, anytime, anywhere, and even without an active Internet connection,” said Bob Torgerson, UAF graduate student and one of the developers of the app. The best features of the app are 1) ability to download videos to iPhones, iPads and iPods 2) easy access to ask scientists questions 3) the possibility to locate Frontier Scientists projects on a map. [FS App Link Via iTunes] Check it out, it’s very cool!Since the April 2011 web launch, Frontier Scientists continues to share first person accounts and real time insights from leading archaeologists, grizzly bear biologists, volcano researchers, climate change specialists and other scientists.Fascinating video of current scientific discoveries in some of the Arctic’s most remote and dramatic landscapes are chronicled in short videos, Twitter feeds, blogs and web reports. The research covers these categories:

  • Grizzlies
  • Petroglyphs
  • Paleo-Eskimo
  • Cook Inlet Volcanoes
  • Computational Science
  • Alutiiq Weavers
  • Climate Change Watch
  • Arctic Winter Cruise 2011
  • Raven Bluff
  • Computational Science
“We want to let travelers, teachers, students, aspiring scientists, and anyone else interested in science feel as if they are with scientists as they track grizzlies or take the temperature of permafrost in a borehole,” explained Liz O’Connell, video director for Frontier Scientists. Visitors to Frontier Scientists can ask questions to our scientists directly; follow some of them on Twitter and Facebook, and converse with scientists on their blogs.Frontier Scientists is funded by the National Science Foundation, with additional support from the National Park Service and 360 Degrees North. Follow us!View Alaska videos at www.FrontierScientists.com.

Pure vs. Applied Research: Two outdated conceptions of science (from Tom Webb's blog)

Tue, 04/24/2012 - 11:30am

Earlier this morning, the British Ecological Society tweeted:bes tweet.jpgNow, I knew they were doing this – my department is represented at the meeting, and I was involved in our preliminary discussions regarding what we thought were important questions. But I was always uneasy about the exercise, partly because important questions don’t always come in nice even numbers; but mainly because of the single word ‘pure’. Especially as this is a centenary exercise, and if we’ve learnt one thing in 100 years of ecology, surely it’s that you can’t separate ecology from people. Or, as another ecological tweeter had put it a couple of days before:lusseau tweet.jpgTurns out @lusseau is in good company. Back in 1965, Sir Peter Medawar delivered his Henry Tizard Memorial Lecture, Two Conceptions of Science. Although the conceptions he set out were the romantic or poetic, and the rational or analytical – “the one speaking for imaginative insight and the other for the evidence of the senses”1 – and his lecture delves deeper into the philosophy of this decision than I intend to be here (subject, perhaps, for a future post) – he certainly has plenty to say on the basic versus applied division, with ‘romantic’ science “finding in scientific research its own reward” whereas ‘rational’ science calls “for a valuation in the currency of practical use.”Medawar’s particular beef is with the class distinction which he saw as having grown up around the difference between ‘pure’ and ‘applied’ science. He characterises (or rather, consciously caricatures) his two sciences in terms of their practical use, as follows (evidently Medawar’s conceptions of science didn’t extend to female scientists, but perhaps we’ll forgive him, this was nearly 50 years ago!):bq. [Romantic] science can flourish only in an atmosphere of complete freedom, protected from the nagging importunities of need and use, because the scientist must travel where his imagination leads him. Even if a man should spend five years getting nowhere, that might represent an honourable and perhaps even a noble endeavour. The patrons of science – today the Research Councils and the great Foundations – should support men, not projects, and individual men rather than teams, for the history of science is for the most part a history of men of genius.The alternative conception runs something like this… Scientific research is intended to enlarge human understanding, and its usefulness is the only objective measure of the degree to which it does so; as to freedom in science, two world wars have shown us how very well science can flourish under the pressures of necessity. Patrons of science who really know their business will support projects, not people, and most of these projects will be carried out by teams rather than by individuals, because modern science calls for a consortium of the talents and the day of the individual is almost done. If any scientist should spend five years getting nowhere, his ambitions should be turned in some other direction without delay.Medawar was well aware that these two visions of science both have elements of truth, as science involves both having an idea and testing it or trying it out. a scientist must indeed be freely imaginative and yet sceptical, creative and yet a critic. There is a sense in which he must be free, but another in which his thought must be very precisely regimented; there is poetry in science, but also a lot of bookkeeping.Tempting though it is to continue quoting Medawar at length, we’re in danger of losing the thread here: let’s return to the division between ‘pure’ and ‘applied’ science. Medawar points out that in the early days of the Royal Society, “the idea of science pursued for its own sake was regarded as frivolous or even comic”, when “the opposite of useful was not pure but – idle.” And yet somehow, during the Romantic period, this perception got turned on its head: the notion of ‘purity’ arose (despite, as Medawar notes, no scientist ever expressing admiration of a piece of work as ‘how pure!’); applied science became rather vulgar, somehow morally inferior to pure research, “and with it the dire equation Useless = Good.”It seems to me that we’ve come full circle, and now ‘pure’, ‘basic’ or ‘blue skies’ research is considered to be under attack from the dreaded impact agenda (although having claimed that science is vital to the economy, of course we are going to be asked constantly to affirm this!). But why should we be worried about the future of ‘pure’ research? “Invest in pure applied science for quick returns (the spiritual message runs), but in pure science for capital appreciation.”In other words, the idea of some future, unspecified ‘use’ is often implicit in any defence of ‘pure’ research. For example, we make a virtue (says Medawar) of encouraging pure research in medical institutes – and I could say the same about the environmental sciences – in the hope that this basic research will someday bear fruit (i.e. result in a cure, or feed the world). “But there is nothing virtuous about it! We encourage pure research in these situations because we know no other way to go about it. If we knew a direct pathway leading to the clinical problem of rheumatoid arthritis, can anyone seriously believe that we should not take it?”Medawar’s suggestion to break down this artificial division between basic and applied research is to reverse the usual process of university research, where :bq. …it is believed and hoped that something practically useful nay be come upon in the course of free-ranging enquiry, whereupon research which has hitherto shed diffuse light will now come sharply into focus. This procedure… works sometimes, and it may be the best we can do, but… [m]ight not the converse approach be equally effective, given equal opportunity and equal talent? – to start with a concrete problem, but then to allow the research to open out in the direction of greater generality, so that the more particular and special discoveries can be made to rank as theorems derived from statements of higher explanatory value… Research done in this style is always in focus, and those who carry it out, if temporarily baffled, can always retreat from the general into the particular.This, for me, is where the next century of ecological research lies: focus on the problem, use whatever means are necessary (from fundamental understanding to engineering solutions) to tackle it. Listing 100 questions in ‘pure’ ecology does not seem a sensible first step. But I’ll leave the last word to Medawar:bq. When I speak of our endeavours to make the world a better place to live in I neither say nor imply that this melioration can be achieved by purely material means, though I am quite sure it can’t be achieved without them… I believe, as many others do, that material progress is necessary for our improvement, but I do not know, and have never heard of, anybody who said that it could be sufficient… [My] general tone… may give the impression that I am an ‘optimist’, but indeed I am no such thing, though I admit to a sanguine temperament. I prefer to describe myself as a ‘meliorist’ – one who believes that the world can be improved by finding out what is wrong with it and then taking steps to put it right.1 All quotes are from the text of Medawar’s 1965 Henry Tizard Memorial Lecture, and from the Introduction to his collection of writings Pluto’s Republic.

SciBarCamb intro game (from Eva Amsen's blog)

Tue, 04/24/2012 - 6:22am

SciBarCamb is over, but it was awesome this year! I am the worst at live-tweeting, but luckily Lou and Laura and lots of other enthusiastic Twitter-users were at hand to document every single minute of it, so keep an eye on the Schemes and Memes blog for Storify collections of the whole event.I’ll just leave it to two things here. First, a massive thank-you to everyone who helped out in some way. The organisers, volunteers, sponsors, donors, the staff at our two venues, but most of all the participants – everyone who suggested or led a session, brought a demo, did stand-up, asked questions, and talked to others in the hallways in between the talks. That’s what SciBarCamb is all about!And that brings me to the second point. One of the challenges of unconferences is to get everyone comfortable enough to talk to each other and work together to create a schedule. Last year at SciBarCamb, we had interactive name badges, that created an animated image when combined in the correct way, and among 100 participants every person had five possible matches. That was a lot of fun, but we didn’t want to do the exact same thing again.This year, we started out thinking about matching keywords or phrases. For example, Watson and Crick. But you can also match both of them with DNA, and you could pair DNA with RNA, so it got rather complicated. In the end, we went with 12 sets of triplets. Each participant had one word on the back of their nametag, and on opening night they had to find two others form the same set. The first three complete sets won free drinks, and the very first team also got a T-shirt. (Three T-shirts, of course.)sbc_tags.jpgBacks of nametags_These are the sets of threes we used. macromolecules containing biological information: RNA / DNA / Proteininner layers of terrestrial planets: Core / Mantle / Crustparts of an atom: Electron / Proton / Neutrongeologic periods of the mesozoic era: Cretaceous / Jurassic / TriassicBoolean operators or logic gates: NOT / OR / ANDcurrent or recent hadron colliders: CERN: LHC / Fermilab: Tevatron/ Brookhaven: RHICflavours of neutrinos: electron neutrino / muon neutrino / tau neutrinobones of the inner ear: stirrup / anvil / hammershapes of galaxies: lenticular galaxy / elliptical galaxy / spiral galaxytrigonometric functions: sine / tangent / cosinekingdoms of multicellular life: plants / animals / fungistates of matter: gas / liquid / solidThere were doubles running around, but some people didn’t show up, so not all sets were complete. People who arrived late were scolded for not being there when there were free drinks at stake, so this had the added side effect of promoting early arrival – at least after the fact…complete_set.jpg_The second team to complete (via of people arriving late, the third team to complete was not actually complete, but I awarded them their drink for creativity. They were all neutrinos, but one person had manually changed “muon neutrino” to “electron neutrino” on their badge. The argument: this can happen in real life! There was no electron neutrino walking around the bar and they did know what the missing neutrino was, so they got their drink.SBC_drinks.jpgMe, two multicellular kingdoms and a geologic period of the mesozoic era with their free drinks. (via seemed to have worked well as an icebreaking activity, giving people an excuse to talk to each other and look at each others name tags. Feel free to use our sets at your own science event, or adapt/expand them.

666 [video] (from Grrl Scientist's blog)

Tue, 04/24/2012 - 4:00am

SUMMARY: 666 (and sometimes 616) is the notorious Number of the Beast… what’s all that about? And what has roulette got to do with it!? I’ve always been amused by the rampant superstition associated with the number 666, particularly by religious folks. This number, famed as “the number of The Beast” or “the mark of The Beast”, is assumed by many Christians to denote Satan. But who really was “the Beast”?

Melancholia and the 'Dance of Death' (from Paige Brown's blog)

Tue, 04/24/2012 - 3:06am

Watched Melancholia tonight… Brilliant film, but I should have known what I was getting into just by the name of the movie…Although the film doesn’t live up to ‘Tree of Life’ cinematography standards for me, it is nothing short of beautiful. The film uses extreme slow motion shots to create a surreal feeling throughout the film – just brilliant. There is also the lavishness of wealth set against the impending (yet beautiful all the while) doom of planet Earth – a juxtaposition that makes the worldly lavishness look that much more trivial and trite. Melancholia is a film of contrasts and emotional arousal.melancholia.jpgJust imagine, a mysteriously entrancing blue planet called Melancholia is on a crash course for Earth, while, of course, the scientists say that Earth’s inhabitants will simply experience what’s called a ‘fly-by’ encounter. Kirsten Dunst, in an amazing performance by this actress, seems born of the same vein as Melancholia, caught in the throes of severe depression in the wake of a rather disastrous wedding night. But who can blame her? In the spirit of astrology, ‘Justine’ seems to suffer her own melancholia ever more as the planet nears Earth… only to find a rather somber peace in the face of a fateful encounter. “Trier’s initial inspiration for the film came from a depressive episode he suffered and the insight that depressed people remain calm in stressful situations.” – WikiScorpiusCC.jpg Of course, I couldn’t talk about this film without given some weight to its science – the science of Melancholia. Kiefer Sutherland, who plays the husband of Justine’s sister Claire, seems to play the part of an amateur astronomer. Telescope in hand, he excitedly, and yet anxiously in secret, tracks the approach of planet Melancholia in the days after Justine’s wedding night. The planet Melancholia is portrayed in the film as a blue gas giant, something like real-life planet Jupiter. Melancholia, previously hiding from view behind the sun, eventually eclipses the red star Antares, a red supergiant star in the Milky Way galaxy that can be seen in the real night sky as part of the constellation Scorpius. I think the Greek myth of Scorpio is intriguing here as a side note.bq. Orion went away to Crete and spent his time hunting in company with Artemis and Leto. It seems that he threatened to kill every beast there was on earth; whereupon, in her anger, Earth sent up against him a scorpion of very great size by which he was stung and so perished. After this Zeus, at one prayer of Artemis and Leto, put him among the stars, because of his manliness, and the scorpion also as a memorial of him and of what had occurred. – Fragment 4 from Pseudo-Eratosthenes Catasterismi 32. Trans. Evelyn-White. Greek epic C8th or C7th B.C.‘To kill every beast there was on the earth’… appropriate for Melancholia. Another constellation name appears in the film, in Claire’s innocent young son, Leo – the lion of the night sky.540px-Antares_System.jpg Kiefer Sutherland correctly identifies Melancholia as a blue gas giant hiding the star Antares in the film, a star that appears with a surreal red glare in the sky appropriate of its real-life appearance. The real star Antares is nearly 900x larger than our sun, with a brightness to match, making it one of the brighter stars in the night sky, and the brightest star in Scorpio: the Heart of Scorpion star. Due to its brightness and distinctive red color, this star has been the focus of many legends and astrological signs. According to Allen, R. H. (1963) and his book “Star Names: Their Lore and Meaning”, Antares is symbolic for “power, independence and a sense of danger.”Antares also has attributes fitting of melancholia and the ‘Dance of Death’.bq. Like all M-type giants and supergiants, Antares is close to the end of its lifetime. Someday soon (astronomically speaking), it will effectively run out of fuel and collapse… [The resulting] explosion, which could be tomorrow or millions of years from now, will be spectacular as seen from Earth, but we are far enough away that there likely is no danger to our planet. – EarthSkySo, how is the film not realistic, in the eyes of scientists? For one, Melancholia is hundreds of light years away from Earth… it likely is not going to ‘all of a sudden’ appear large in the night sky, jumping from ‘pin dot’ to ‘larger than moon’ size in a matter of hours or days, as the film portrays.There is also the planet’s ‘rogue’ orbit:bq. Most astrophysicists would probably reject the idea of a planet suddenly tearing itself loose from its orbit and barrelling straight across the Solar System, but to the director who once used a chalk-lined floor as a set for his films “Dogville” and “Manderlay”, such fussy objections are irrelevant. The wonders of the human psyche during a disaster, not the laws of nature, are put under the microscope in “Melancholia”. – Article by JUUL CARLSENmelancholia09.jpgAs far as the planet Melancholia’s supposed ‘boomerang’ orbit and collision with Earth in the film, and the planet’s ‘sucking’ of Earth’s atmosphere when the two planets come into close proximity, I may leave that to my astronomy scientist friends! There are some redeeming factors, however, for the producers of Melancholia in the eyes of scientists. Looking into the special effects of the movie, a recent article explains how the film’s visual effects supervisor collaborated with science advisors to make the ‘impact’ scene realistic, citing visual effect company Pixomondo’s Sven Martin: “[We learned that] in a collision with Earth, the gas planet would hardly change its shape due to its size. Shock waves and gas vortexes would wander over the surface. After extensive research, we understood that a collision of Earth with a huge gas planet would look like a raw egg, falling into a giant drop of honey.” Kudos to these guys for trying to make the impact scientifically realistic, beyond what the average audience knows!My own consensus… amazing film, you should watch with an open mind and patiently await a puzzle for both the mind and the eyes. The lack of hard science didn’t stop me from enjoying the film, and shedding a tear at the film’s depressing yet ‘ecstatic’ ending.Images from Wiki and Courtesy of Magnolia Pictures, Official Website of Melancholia.

Android n00b with a spanking new ASUS Eepad Transformer Prime (from Kausik Datta's blog)

Tue, 04/24/2012 - 2:21am

This entry is decidedly going to be rather different than the others. So… This one time, at band camp… I was angling for an Android device for the longest time in a Mac/PC household. Having played with my wife’s iPad2, I wanted the device in a Tablet form factor. I have always had a soft spot for ASUS as a technology company, and the specs of the ASUS Transformer Prime TF-201 looked highly promising; so, armed with the tax return, I took the plunge. Newegg.com of the US (bless its soul!) delivered the device in three days flat, and having charged it the mandatory 8+ hours, I am now playing with it.

ASUS Eepad Transformer Prime TF-201

The device was highly chic. Lightweight, thin, with a bright display, the TF-201 seemed, for the most part, pretty fast, as I’d expect it to be with the 1.3GHz Tegra3 dual core processor and 1GB of RAM. It came with the Ice Cream Sandwich flavor of Android (v.4.0.3), the next gen Android OS optimized for Tablets. The device connected to my home network without any hassle, and I quickly updated the firmware to the latest one, as well as the apps. The Android Marketplace was a pleasure to use, no less convenient than the iTunes store, but with an awesome feature – you purchase a paid app, and play with it. If it doesn’t suit your purpose, you can return it within 15 minutes to get a FULL refund. This is Google doing a store function right, unlike other vendors. (Yes, I am looking at you, Apple!!)

The ability to play flash-based content within the browser is a great plus, making for a much better web experience. The big sprawling keyboard that ASUS has customized from the stock Android one is very nice. With its big keys and intelligent layout of the keys, it is easy to use, and also supports the SWYPE gestures (typing by rubbing the appropriate letters in a word in sequence without lifting the finger). Without going into the vexatious autocorrect business, it provides good suggestions on a top row while typing, which helps.

I figured out how to make groups from icons (same as in iOS, it appears; drag and drop). I downloaded and installed the EEPad PC Suite (from ASUS Support) in my Windows 7 PC, which installed all the necessary USB drivers for connecting the Tablet to the PC via USB. It offers a choice to connect as a camera or as a portable file storage device, each with slightly different functions.

However, being an Android newbie, I was kinda expecting troubles with it. I just didn’t realize how much.

  1. The EEPad PC Suite that I installed in my Windows PC; I found it to be v-e-r-y slow, at least for file functions, like copying or moving.
  2. The stock browser that came with the TF-201 seemed nice. It had nice tabs, and worked pretty much like Chrome. But then I started realizing the major drawbacks. (i) It is generally rather slow. (ii) Even when I am accessing Gmail through the web interface, upon opening the compose menu and tapping the cursor into a text field (such as the ‘to’ field or the message body), the keyboard wouldn’t appear. This has happened to me several times in a row. I stopped the process, started it again, but to no avail whatsoever. And this is just one of the issues with the stock browser.
  3. In fact, the keyboard, albeit nice and big, is somehow not quite as responsive as the cramped and small keyboard of the iDevices. For many apps, there is a noticeable lag, both in its appearance and in its performance.
  4. The stock ASUS email app is… weird to say the least. I configured it to access my Gmail, Yahoo mail and Hotmail accounts. I was happy using the stock email app, until I realized everytime I was sending a message from Gmail using the email app, it created a label called ‘Imap/sent’ in my Gmail account. If I moved a message to the Spam account, it would create a label called ‘Imap/spam’; if I deleted a message, it showed up in my Gmail account with an ‘Imap/trash’ label, but is not actually deleted. None of this, incidentally, ever happened with the iOS5 email client on my iPhone 4S or my wife’s iPad2.
  5. The TF-201 is already showing noticably weird glitches, time lags, performance issues. Particularly vexing has been the clock issue. There are four clocks that show time. (i) The system time in settings. (ii) Clock in the taskbar (right bottom corner). (iii) Clock that shows up at the right top corner of the pop up menu when the taskbar is tapped. And (iv) an analog Clock widget on my homescreen. The system time (in the settings) shows the correct time. However, all the three other clocks shows completely different and arbitrary times. Check the screenshot composite that shows all of the above 4 clocks.
    time display issues with Transformer Prime
  6. The non-inclusion of a good unicode-compliant non-English Foreign Language font is cramping my style, because I use such fonts often. It’s particularly odd, since the use of this font works out rather well even in Google’s Chromebook CR-48. Not so in the TF-201, where somehow even Google’s own Transliteration IME doesn’t work. From reading at various fora, I find that this is an impossible proposition, unless I root the device and install a compatible unicode-compliant foreign language font.
  7. The apps that I was used to in the iOS platform behave slightly differently in Android, and not in a good way. For instance, the individual webmail apps (Gmail, Yahoo, Hotmail) didn’t perform as expected in the Android platform. Each of them had some design issues that made them inconvenient to use. The Yahoo mail, strangely, has no means to delete a message once I am reading the message. I have to get back to the message list in order to select the message and then delete it. It was not like this in the iOS.
  8. The Prime, sadly, doesn’t support 5GHz wireless signal. My Netgear router (dual band) does G at 2.4GHz and N at 5GHz, with two different SSIDs for each band. The Prime sees only the 2.4GHz. In addition, the Wi-fi signal drops inexplicably even when I am sitting at the same spot and not doing anything online. It keeps fluctuating when the wi-fi is actually in use. I can’t understand why.
  9. In the ASUS task manager, apps that I am not using show up when I wake the device up from sleep. Apps such as Twitter, Facebook, Keyboard, Google+, Gallery, Calendar etc.) show up, even when I haven’t used them at all; for instance, I have never opened Google+ or the Calendar on my device, and yet they show up in the task manager as running.

These problems have been so bad (especially when the comparison with iOS jumps naturally to my mind) that I am tempted to return the TF-201. A part of me wants to try rooting it and installing custom ROMs (customized and more efficient Operating Systems available from the thriving and wonderful Android community) and stuff to see if it would solve my worries. But then I probably cannot return it any more to Newegg. The process of rooting (for which ASUS has provided the tool) is supposed to invalidate the warranty, and the device is considered ‘modified’. ASUS will not even send me periodic updates for a modified device.

I have written to ASUS Tech support. If necessary, I shall call them. A lot depends on the next couple of weeks, since Newegg allows 30 days for returns. Let’s see what happens.

Views expressed in this post are exclusively mine and mine alone. It doesn’t constitute any endorsement or approbation whatsoever of the products/websites described herein by any other entity, including Nature Group of Publishers.

Why a Blog? (Or, Meet Me at the Salon (or Saloon) (from Lowell Goldsmith's blog)

Mon, 04/23/2012 - 6:31pm

Lowell-Goldsmith-photo.jpgBlogging allows freedom and elasticity that is often missing in the traditional scientific literature. This new venture will supplement the primary information published in the Journal of Investigative Dermatology (JID) and other journals publishing research related to skin, its function, and its diseases. Our aims are to 1) establish a virtual cocktail party, where readers find lively, interesting, useful conversations; as the tavern-keeper, my role will be to keep the glasses filled, conversation hopping, and brawls to a minimum; 2) provide historical context and comment on the conceptual and practical challenges related to research; and 3) broaden the reach of the JID by interesting a wide community of investigators and clinicians who care about the scientific basis of medicine and health. Ideally, I am envisioning more of a salon, than a saloon, and at my best moments I can be Gertrude Stein. No doubt our readers and commenters will enjoy riffing on that one.Original JID content will serve very often as a jumping-off point for posts, but our goal is to address larger scientific issues, such as education, funding, theory, the effects of the increasing age of funded PIs, patient care, and international differences in science funding and training. Performing outstanding science requires a social structure conducive to developing and supporting scientists and their research. We will discuss issues related to career development and governmental and industrial commitment to research, as well as new technologies and innovative ways research groups are interacting. An international perspective will be presented by writers and the comments that are offered. As Science is more and more a team effort, the role of professional societies in providing forums for the presentation and dissemination of new research and in the organization and rewarding of discovery is also anticipated to be fodder for discussion. Additional topics may be derived from professional society happenings, new events relating to scientific endeavors relating to skin, and articles published in other scientific journals of interest to the cutaneous research community. Many late-night conversations at meetings (or rather, at the hotel bar) touch on these very subjects (important, big-picture stuff), and I see this blog as a virtual forum to continue those discussions.One measure of the success of this venture will be the comments posted by our community of readers, and we welcome your full and enthusiastic participation. Commenters (and bloggers) will be expected to abide by a few basic rules: express conflicting opinions, supported with evidence (and proper citations), as they are welcome; use your real identity; take full responsibility for your words; enhance the discussion with new thoughts and questions; use appropriate language; and only throw darts at the wall (not at people). For a full set of community rules, visit http://www.nature.com/info/community-guidelines.html.

Scamference (from Karen Vancampenhout's blog)

Mon, 04/23/2012 - 9:40am

Internet and email brought us global communication, with time difference being the only thing to worry about if you want to say something to someone in a far-off corner of the world. Unfortunately, it also provides almost unlimited posibilities to rip people off. Most of these attempts are pretty obvious, including bizar stories like “I am the bastard son of the king of Farfaraway and I want you to help me inherit my fathers fortune” or “Hi we are your bank/ICT department/email provider/…, our main computer exploded so please fill out all your visa details/password/user name/… so we can verify your account”. Yeah, right.

But have you ever heard of a scamference? Corporate science and the pressure to publish seems to have attracted the attention of some more sophisticated internetcriminality. Scientists are send a well writen email inviting them to an international conference in their research field, complete with actual research topics that will be discussed, a professional looking conference website and a personal invitation to submit a paper. If the  invitation is accepted, a notification of the paper’s acceptance is sent and the author is asked to pay a standard subsciption fee. All seems perfectly normal and very convincing, until people arrive on the venue, only to find that the conference never existed. 

If you have been around the scientific community for some years, you will be able to spot the trap: the typical organisations active in the research field don’t mention the conference, the letter is not signed by a famous scientist but by something like “the chairman of the scientific committee” and the timing is off (e.g. invites to submit abstracts in april when the conference is already in august). Also, these Scamferences all seem to ‘be organised’ in Toronto, Canada.

Luckily, scientists are ‘researchers’ by nature and only believe something if it has proper references. Nevertheless, it is advised not to use an ‘out of office’-reply when you’re travelling. As this service answers all email, it will tell the swindlers that your email adress is currently in use.




The fertile 'philosophy' of homeopathy (from Lee Turnpenny's blog)

Thu, 04/19/2012 - 11:15am

ResearchBlogging.orgIs it not a bit old trite hat for scientists/sceptics/freethinkers, etc, to take a swipe at homeopathy? Perhaps. Then again, while the homeopathic mindset continues with its religiously insidious self-marketing, I, for one, would argue that we should continue to guard against its cultish reach by publicly highlighting its laughable nonsense. Particularly as there are times when it isn’t actually funny.Last week (April 10-16) was World Homeopathy Awareness Week. It’s a swanky, impressive looking website, isn’t it? Slide-showing photographs of photogenic, young, middle-class couples and beautiful babies, all in glorious happy health. ( Thinks: can homeopathy make for prettier offspring?); various ethnicities emphasising its universality. This is seductive marketing. It reminds me of those photoboardings that builders erect on the periphery of their new apartment complex developments: happily laughing, successful handsome couples with perfect teeth, appealing to our desire for status. The right to happiness. Who are these people?! (Those who model for marketing agencies, I suppose.)This year’s week is themed as ‘Homeopathy and Infertility: Helping Fertility for Men and Women.’ And if you click on this label in the top right corner, you are able to download a 31-slide PowerPoint presentation, presumably as a resource you can borrow to convince any fertility-challenged friends you might have. By contrast, this slideshow is disappointingly amateurish and hurried-lookingIf you take a look, skip to slides 4 through 7. These are presented under the collective heading, ‘Philosophy’. Which they surely don’t mean in the sense of ‘love and pursuit of wisdom or truth by intellectual means’, do they? (Although it is not uncommon to come across those who profess to live by it.) Rather, it is (I prefer to think) intended in the way of doing some activity: the thinking, reasoning and evaluation of it. More apt, then, might be ethos, no?Flicking through this slideshow, it is as woolly and nonsensical to me as some Human Resources or management seminar. I don’t buy any of it – but then, I wouldn’t. Because I’m a bigoted know-all scientist who considers science the be-all and end-all, and thus incapable of recognising that science doesn’t know everything. Apparently. Is it bigoted to merely ask, “How do you know it works?”Well, have a look at a few more of these slides. Slide 21 confidently lists the (infertility relevant) ailments which homeopathy can alleviate. The one on this mis-apostrophied list that has me frowning the most is ‘Heriditary [ sic ] disposition.’ (Let’s not go there.) Then follows two blank Case Study slides, I guess left for you to fill in with examples of successful homeopathic fertility treatment from within your particular quackdom. Due to confidentiality issues, I would predict that a homeopathy-unsympathetic journalist would have difficulty getting interview access to people undergoing such treatment. So, we must take the presenters at their words.Slides 24-27 lists some examples of specific effects of certain ‘remedies’. Hey, but this looks a bit complicated and science-y now. Convinced? I mean, how could we question that? Well, let’s have a go… Sabina, it seems, is very popular, homeopathically. Because this is one all-singing, all-dancing medication – I mean, literally: aside from its menses stabilising and (presumably, if it can eliminate genital warts) anti-papilloma virus activities, it can correct an aversion to music! Maybe if I take a slug, I might even be able to tolerate Country & Western. Not quite sure how this also applies to someone who is pathogenically uncomplaining, helpful and caring, though. Complex stuff.Cimicifuga racemosa (I formatted the italics) is another seeming jack-of-all-trades. We’re not talking here of its (still contentious but nevertheless more convincing) effects as dietary supplement or herbal medicine (which do actually contain some of it). But in homeopathic doses (ie, fuck-all) it can aid in the treatment of all manner of physical and psychological maladies and, I wonder, likely make you a cup of tea in the morning to boot. And you can always slip some in your partner’s cuppa if they’re talking too much.And can cuttlefish ink actually help correct or prevent a prolapsed uterus? Can it (thus) improve your sex life, and make you better company generally? (Isn’t it an insult to a beautiful, intelligent animal to include its image in with this dross?)Importantly, skip back to slide 20, which lists the negative aspects of ‘conventional’ fertility treatments – including its limited success rate. I don’t know whether these facts and figures are accurate, but that’s not the point. Tellingly, no such data are provided for the ‘success’ rates of homeopathy on infertility. Indeed, there is no indication here of any track record whatsoever. And, despite the assertion (slides 1, 15 and 17) that homeopathy can also be applied to male infertility, there is no mention of male benefit from the exampled ‘remedies’. Is it impertinent to ask why not?This shoddy electronic pamphlet sits incongruously within the otherwise professional looking website. Or does it? Slide 28 lists ‘Reasons for using Homeopathy’, which are lifted from the website, where by clicking (near top left) ‘10 GOOD REASONS’ you will find them fleshed out (for the PowerPoint presenter to parrot). Let’s look a bit closer at one or two of these claims:bq. 1- NO HARMFUL SIDE EFFECTS‘A preparation process called potentisation removes all toxicity from each substance. It is safe for all ages and during pregnancy. However it is advised to be under the care of a qualified practitioner.’I freely confess my ignorance here. I was of the impression that ‘potentisation’ referred to the ‘activation’ of the remedy, after diluting ad infinitum and vigorous whacking and/or shaking (which always puts me in mind of tequila slammers – which are effective, by the way). But this process, then, has the doubly beneficial effect of simultaneously negating the effect of any toxins. That would explain my previous misunderstanding of water’s memory, wherein I questioned on the basis of all the other substances the water would have come into contact with. It seems water knows; can distinguish between the memory of the necessary ingredient to activate, whilst simultaneously preventing or inactivating the memories of everything else. So little remark given to something (that would be) truly remarkable. We’re left to conclude that succussion is magic.bq. 5- PREVENTATIVE‘By boosting the immune system and overall health, homeopathy improves a person’s resistance to infections and possible illnesses.’Boosting the immune system, eh. This seems to be a favourite for those who like to invoke our innate ‘healing energy’. (Just what is this energy? They never define it.) This provokes an honest open question: Where is the evidence that the immune system is boosted? How has this been quantified? After a few cosy sessions with a nice, sympathetic homeopath who listens to you and is not in any hurry to get you out of the surgery, your subsequent response to survey that you are feeling better may well be real. But how are we to know, beyond glib conjecture, that the immune system is ‘boosted’?bq. 6- NOT TESTED ON ANIMALS‘Humans respond differently to medicine than animals. All homeopathic medication is tested on healthy humans.’But what of ‘remedies’ that are used for ‘treating’ animals? This is a favourite ‘argument’ of our heir incumbent, Proper Prince Charlie, who considers it trumps scientists’ rejection of homeopathy’s efficacy because they are unable to account for the fact that it works on animals. I don’t know whether he’s considered just who scored those ‘trials’.bq. 7- EASY TO TAKE‘Homeopathic medicines are given as small pleasant tasting pellets which dissolve in the mouth, through olfaction, or in liquid form. Granules, powders & drops are also available.’Olfaction?! Uh?! What, you can sniff them? Would that be… steam?4 and 9 are funny for obvious reason.Why does homeopathy persist? Because the people who plug it are oh so nice? Who take the time to listen and show interest; to care? This is where it does its thing – not in the administering of charlatan pills, tinctures or potions, as recognised in this Southampton-based study (… so quite why the University of Southampton’s Medical School continues with this sort of thing…?). But why let that spoil a good story? The WHAW site bigs itself up thus:bq. ‘During this week homeopaths and friends of homeopathy will come together to share with the world the miracles of homeopathy.’The ‘miracles’? Actually very apt use of the word, because if it did work, it would certainly defy the known natural order. Personally, I don’t find such religious language surprising. Yes, I am aware of my flippancy here. (Here’s one: With water restrictions in place due to officially declared drought, I suggest, along with hosepipes, that the preparation of homeopathic remedies be banned in the UK.) And I am also aware that I am woefully ignorant of much to do with homeopathy. “Just because we don’t know how it works, doesn’t mean it doesn’t work. Keep an open mind”, I’m told. Well, I do keep an open mind – sufficient to spot the gaping flaw in the first part of that statement; and I am learning more. But until you’ve ever had someone tell you with a straight face that shaking/whacking some water activates (its memory of) some substance that has been diluted out of it, you perhaps don’t let it bother you so much. And, the thing is, the more I learn of it, the more un-convinced I become. So, outraged homeopaths, spare me the ad hominem-isms. And that other logical fallacy – the appeal to the natural_. If some people want comfort for their bruises and headaches and itches (there, there), then who am I to object? However, (aside from the seriously problematic issues of claimed treatments for cancers, or malaria, which I’m not addressing here), infertility can be a highly emotive matter, requiring considerable levels of competency and responsibility. If those purporting to treat it are giving false hope, their ethos is unethical. dat=bpr3.included=1;bpr3.tags=Biology%2CMedicine%2CPhilosophy%2CSocial+Science%2CResearch+%2F+Scholarship%2COther%2CHealth%2CHomeopathy%2C+Ethics%2C+Science+Communication%2C+Medical+Ethics%2C+Reproductive+Health%2C+Reproduction">Brien, S., Lachance, L., Prescott, P., McDermott, C., & Lewith, G. (2010). Homeopathy has clinical benefits in rheumatoid arthritis patients that are attributable to the consultation process but not the homeopathic remedy: a randomized controlled clinical trial Rheumatology, 50 (6), 1070-1082 DOI: 10.1093/rheumatology/keq234

Impact, like a drop in the ocean. (from Peter Etchells' blog)

Thu, 04/19/2012 - 10:30am

Impact EventI really disliked exams, and I’m really glad I don’t have to do another one (well, as far as I know). I used to get really nervous, even in the weeks before when I was revising, and I seemed to have blanked the actual experience of sitting in an exam hall from my memory. I think the holy grail for students of all ages, especially at this time of year, is an easy and innocuous quick fix to increase your exam performance. Well, according a news release on Wednesday, the answer has been with us all this time. “”http://www.alphagalileo.org/ViewItem.aspx?ItemId=119335&CultureCode=en">Bring water into exams to improve your grade“, proclaims research presented at the British Psychological Society Annual Conference this week.The observational study looked at 447 students across a number of years taking their exams at the University of East London. The results suggested that around a quarter of the students took bottles of water into exams with them, and after taking into account academic ability, these students showed an improvement of around 5% in their exam grades. While the researchers admitted that they didn’t know precisely why this might have occurred, suggestions included ”http://www.dailymail.co.uk/sciencetech/article-2131276/How-better-exams-Drinking-glass-water-boost-results-grade.html">“theory is that information flows more freely between brain cells when they are well hydrated” and that “water consumption may also alleviate anxiety, which is known to have a negative effect on exam performance”.Compelling stuff, but there are a few things that bother me about this report. For one, I think the PR machine has jumped the gun this time – the results haven’t been published in a peer-reviewed journal yet, they’re just from a conference presentation. As such, it isn’t clear what precisely was controlled for. Given that the study was observational, the answer to that question is probably ‘not much’. Which means that any speculation about psychopathological and physiological interactions and effects is a bit pointless really; we don’t know that such effects explain the results any more than saying that people who are generally more prepared for exams will probably be more likely to bring water with them. It’s also worth pointing out that nowhere in any of the press releases does it say that the students actually drank the water. Just that they brought a bottle in with them. Hmmm.Perhaps I’m being unfair – it’s quite clearly a PR gaff and they should have waited until the full study was published. Normally, I would have let it slip, but something in the final paragraphs in the BBC article raised my hackles. Not the old “Future research is needed to tease apart these explanations” gambit (really? I thought we’d done with all that testing and science malarky now). Nope, it was the point that “There are also implications for policy makers in terms of the availability of water on campuses”. Impact statement: tick.Now, don’t get me wrong – I’m all for thinking about how your research might actually contribute something meaningful to a population broader than your scientific readership. But aren’t things getting a bit ridiculous now? Do we have to justify absolutely every piece of research in terms of immediate and direct impact on policy? What does that even mean any more? We’ve got a case in point right here – what are the implications for policy makers, exactly (and who are these policy makers)? Making water more widely available on campus doesn’t necessarily mean that students are going to bring more of it into exams. Or do we need to start forcing water bottles into their hands as they walking in to the exam room? Perhaps a little water fountain at each desk, or an intravenous drip?I’m probably being a bit over-grumpy about it all; I just worry that in the drive to tick more boxes to get funding, scientists are having to come up with meaningless statements to justify their research in a wider context, and really, that doesn’t benefit anybody.

Mendelian Randomisation and the Prevention of Spurious Findings (from Suzi Gage's blog)

Thu, 04/19/2012 - 8:05am

Epidemiology uses statistical methods to investigate patterns in public health. Or, if you believe certain news articles, it splits every possible life influence into things that either cause or cure cancer (or occasionally do both). Epidemiologists investigate health outcomes in a number of different ways, ranging from looking at changes in whole populations to conducting randomised controlled trials (RCTs), testing one intervention against another, or against the placebo effect. RCTs are the ‘Gold Standard’ of Epidemiological research, as their design means they can provide the strongest evidence for or against a hypothesis. Other epidemiological methods involve observation, rather than manipulation, and this can be problematic.One week there may be a paper suggesting vitamin pills protect against heart disease, and the next week evidence emerges that they don’t. This is often because of misleading findings from observational studies. People who decide to take vitamin supplements are likely to be different in a number of ways from people who don’t take them. They might lead a more healthy lifestyle, exercise more, smoke less, and eat more vegetables. These differences are likely to impact on their chance of getting heart disease. Epidemiologists call these differences confounding variables, and although it’s possible to take them into account in various statistical ways, the scientist has to know what they are in order to control for them. Miss one confounder out of your analysis, and it may inflate any relationship between the two factors you’re interested in, so you’ve got a spurious finding. One way of getting round this problem is to conduct RCTs, so different types of people are randomly distributed across your intervention condition. Although this may be fine to do with a vitamin pill, it’s sometimes not ethical or even possible. If withholding the intervention being investigated is thought to lead to harm, it is unethical to do so, and if the intervention is something like drinking alcohol, it’s impractical to get people to either drink or not drink for an experiment. Investigating alcohol in observational studies has the same problems mentioned above; people who drink are different to people who don’t. Socioeconomic status, likelihood to smoke and education level may all affect the relationship you’re interested in. There are added complications in that people may have stopped drinking because they are unwell, so instead of drinking affecting the disease, the disease is changing alcohol use. This is called reverse causation, and may explain why we hear that a glass of wine is good for you (sorry to be the bringer of bad news).But advances in the understanding of genetics can help. Everyone has 23 pairs of chromosomes, and coded in these are genes; the building blocks for who we are. My genes are practically identical to yours, but there are some key genes which have different DNA code in different people. Some of these differences can lead to diseases, such as Cystic Fibrosis, caused by a faulty gene not properly making an important protein. Some have less extreme, but still very interesting, effects. There has been a gene variation found, common in East Asian populations, which means a protein needed to break down a metabolite of alcohol is not produced. People with this variation get unpleasant symptoms when they drink due to a build up of acetaldehyde in their blood, so very often they avoid alcohol. By looking at someone’s DNA in the location known here, we can investigate the effect of alcohol use on whatever we’re interested in, using the gene as a proxy variable instead of directly analysing alcohol intake, as people with the unusual variation will be less likely to drink. All well and good, but surely this is still just observing, so how do we stop the interference of confounding?It turns out that our genes have some very useful properties which make them perfect for this task. The genes that you have are all unrelated to environment, as you got them before you were born, so environmental confounders should be randomly distributed between your gene categories. Also, when your parents’ chromosomes divided to create the egg or sperm that contained the genes you inherited from them, each gene splits independently of all the others, so you have a random chance of also inheriting a genetic confounder. Because of these neat properties, you can assume that your proxy gene will be independent of any confounding variable affecting the exposure you’re interested in, and therefore where confounder levels would have been uneven across people grouped by alcohol consumption, they will be randomly distributed across gene variation. Results using this technique have shown evidence against alcohol being a gateway drug leading to illicit drug use, as the gene variation was not associated with illicit drug use.Of course, nothing’s perfect. There are a few conditions where this technique will fall down, but as long as you’re aware of them, you should be able to avoid the problems. Firstly, occasionally ‘linkage disequilibrium’ occurs. Certain genes are more likely to move together during meiosis, meaning they are not inherited independently. If your proxy gene travels with a gene which affects your outcome of interest, this will impact on your findings. There is a method to check for linkage disequilibrium, so you can ensure it’s not a problem. Also, there are certain genes which have an impact on a number of different traits (this is called pleiotropy), so if your gene has a direct effect on the outcome you are interested in, it is unsuitable for Mendelian Randomisation. Finally, the technique fails to work effectively if there are systematic differences in the genetics of the population you are investigating. For example, if a population is made up of two groups of peoples that used to live separately, but now live together, there will be non random genetic differences between the groups due to selective mating over the time when they were separate. This may mean other differences between the groups will not be randomly distributed across the gene you’re interested in, making the population unsuitable. However, although this technique can only be used in very specific circumstances, where a gene is known to affect the intervention you’re interested in, and doesn’t suffer from the limitations mentioned above, it is a really elegant technique which will hopefully stop the spurious results from observational studies becoming newspaper fodder. Check this article out for an overview of MR.

Does Abnormal NREM Sleep Impair Declarative Memory Consolidation? (from William Lu's blog)

Wed, 04/18/2012 - 7:37pm

Finally got to uploading the review paper Robert Goder and I had written not too long ago on sleep and memory. You can download it at http://tinyurl.com/c2xd35n. Essentially, we proposed that abnormal NREM sleep processes (i.e. reduced slow-wave sleep and sleep spindles) contributed to declarative memory impairment and sleep disruption in certain neuropsychiatric disorders including Alzheimer’s, schizophrenia, and fibromyalgia. Underneath, I posted what the tentative model looks like (click to enlarge). Would love to hear your thoughts. Untitled.pngFig. 1. During NREM sleep, abnormal thalamocortical structures may be unable to generate sufficient slow oscillations to drive the reactivation of hippocampal memory traces. These same structures may also be unable to facilitate normal spindle activity, preventing efficient declarative memory consolidation due to an absence in cortical plastic changes. Decreases in spindle activity lead to failure in inhibiting sensory information from reaching the neocortex. Thus, the individual is awakened and kept awake by sensory information, consequently experiencing disturbed NREM sleep.Reference:Lu, W., & Göder, R. (2011). Does abnormal non-rapid eye movement sleep impair declarative memory consolidation? Sleep Medicine Reviews DOI: 10.1016/j.smrv.2011.08.001

The price of homeopathy (cartoon) (from Viktor Poor's blog)

Wed, 04/18/2012 - 7:53am

This week is Homeopathy Awareness Week!On Stripped Science, you can figure it out, how much should you pay for a homeopathic remedy:homeopathic wallet.PNGThen read this brilliant compilation by Martin Robbins: Homeopaths on Homeopathy