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Will I Stay or Will I Go (from Brian Derby's blog)

Wed, 07/25/2012 - 7:45pm

Apparently this Blog will move to SciLogs tomorrow at lunchtime. However, I was given preview access to the site this evening and I cannot see it there. I imagine that the migration will occur seamlessly but I am mildly concerned. So this may be my last post on this vehicle.This is a quiet time in UK universities. The undergraduates have gone away for summer. The MSc students are working hard but many are in hiding to write the thesis for a September deadline. More and more staff are (suspiciously) “working from home”. It has got so bad that I had to send out an “Is anybody here” e-mail when I put the coffee on in the staff kitchen. I am taking stock and trying to get things done that I had always meant to but was too busy to do until now.Successes – getting those revisions to a paper done and submitting to a journal one week before the final deadline. Getting a multiauthor paper ready for submission about 12 months after the first draft.Dreaded tasks to do – That course on solid mechanics that I am taking over. The previous person who did it is renowned for chaotic notes so I will have to do it from scratch. – Also the 3rd year course which is being shrunk from 20 to 10 lectures.What do I leave out and who do I annoy the most by apparently downgrading their work.OK, a last post. I will blog something more interesting tomorrow if the new platform is running.

Something is going on (from Viktor Poor's blog)

Wed, 07/25/2012 - 5:13am

Something is going on behind the scenes.It’s a rather big change, but it won’t change the blog.Please, come back on Thursday for you weekly dose of Stripped Science.

Alaska creatures without us (from Liz O'Connell's blog)

Tue, 07/24/2012 - 4:07pm

Animal_BearFisher.jpgUS Forest Service : Tongassby Ned Rozell In Alan Weisman’s book, The World Without Us, the author ponders “a world from which we all suddenly vanished. Tomorrow.” In last week’s column, a few experts discussed the fate of Alaska structures if Alaskans were to disappear. This week, people who study Alaska’s wildlife donate some thought to the subject. Alaska’s lack of people has benefited many species, including caribou, which still outnumber Alaskans, and salmon, which torpedo up our rivers with a staggering, wonderful density that was once seen all over the west coast of North America.Amimal_Salmon.jpgU.S. Fish & Wildlife Service Mark Wipfli has spent many hours on salmon streams throughout Alaska, and the University of Alaska biologist has thought many times of mankind’s impact on salmon. If people were to disappear, Wipfli envisions a slow healing of damage done to salmon habitat. In Alaska, that means the recovery from logging and mining of streamside forests that provide everything from fish food in the form of insects to the contribution of dead trees to waterways (for erosion control and creation of eddies and other features good for salmon). Old-growth forests (with trees aged from 50 to 200 years) provide ideal conditions for salmon, just as those same trees have benefited us with stout building materials. The mining of minerals we use every day has also disrupted life for salmon. “If we vanished . . . there would no longer be harvesting or overharvesting,” Wipfli said. “Mining impacts to watersheds would slowly diminish, but would probably take a lot longer. And dams would eventually crumble and tumble, allowing rivers to flow like they once did.” The bottom line is salmon — and the marine, freshwater and terrestrial ecosystems that support them — would be better off without us," he said. “We continue to create barriers and stressors that collectively make it more difficult for salmon to thrive like they historically did, especially in the Lower 48.” Animal_Kinglet.jpgSongbirds like this ruby-crowned kinglet would probably do better if people flew away. / Photo by Ned Rozell.Along a robust population of salmon, Alaska also is not yet experiencing a bird shortage. “Birds from six of the seven continents come to Alaska to breed each year — that’s billions and billions of birds,” said biologist Sue Guers of the Alaska Bird Observatory in Fairbanks. “These numbers are estimates from now. Imagine what it was like before our time.” Alaska’s many million acres of unpeopled river valleys and tundra plains would continue to attract birds if we were gone, but some species would miss us, Guers said. Ravens and gray jays that pick at what we leave behind in cities and towns would revert back to following wolf packs, and the pigeons that live in Fairbanks might find life impossible at 40 below without the warm exhaust of heated buildings. “Most other species would most likely benefit from humans disappearing,” Guers said. “Think about all the habitat destruction going on in the Lower 48 and in Central and South America — loss of habitat is one of the major causes of species loss and biodiversity.” As years passed without humanity, nature will take down other bird barriers, including wind turbines, cellphone towers, and what Wiesman cited as mankind’s most damaging invention to birds, window glass. But he also wrote that housecats, the expert hunters that kill billions of songbirds worldwide each year, would do quite well without us. Large mammals like moose and caribou on far-away hilltops might not miss us at all, said biologist Tom Paragi with the Alaska Department of Fish and Game. “I don’t think the remote portions of Alaska would be much different than we see today, because of intact habitats,” Paragi said. “In contrast, if you ‘re-wilded’ Iowa or Manhattan, you’d have smaller populations of white-tailed deer and raccoons after wolves, bears and cougars come back.” Animal_Moose.jpgU.S. Fish & Wildlife Service / Photo by Ronald L. BellOne of the biggest differences between Alaska and the rest of the world is that we have cleared so little of the landscape for farming here, Paragi said. That has allowed moose their willows and caribou their lichen, as well as the space to breed and move around. Hunters and predator-control programs affect local populations of moose and caribou, but Paragi said he doesn’t think either would change much in abundance if people were to disappear. “Moose density near urban Alaska would almost certainly go down as human disturbance of vegetation ended and predators increased, but one lightning-caused fire could change the landscape in a few days more than even a large amount of logging,” he said. Each biologist in this story also mentioned the lingering affects of a warmer climate and how that may endure after people checked out. “If we generally have milder winters, species like wood bison, mule deer and fishers will likely continue to spread westward into Alaska, along with deer ticks and others along for the ride on the mammals,” Paragi said. “A huge unknown is how long human-induced climate-change effects, including ocean acidification, will linger and continue to impact and change ecosystems once we’re gone,” said Wipfli, the salmon expert. “Undoubtedly at least hundreds, more like thousands, of years.” “Problems like climate-change, pollution and introduction of exotic species all over the world means migrant birds are getting impacted by humans during all aspects of their life cycle,” Guers said..Find more on the Arctic’s Amazing Birds at Frontier ScientistsOriginally published in the Alaska Science Forum Article #2087 October 27, 2011 Alaska creatures without us by Ned Rozell"This column is provided as a public service by the Geophysical Institute, University of Alaska Fairbanks, in cooperation with the UAF research community. Ned Rozell is a science writer at the institute."

Few does not always mean insignificant (from Lee Turnpenny's blog)

Sun, 07/22/2012 - 5:44pm

Early in the week, I cut a short news clipping out of i, caught by its headline ‘Cervical cancer tests banned on religious grounds’ (differently titled online), sourced from an investigation by GP magazine. Being of the secular atheist bent, my interest was immediately piqued (even though the title is misleading – ‘tests’ ?) by reading that ‘some schools’ are not providing human papillomavirus (HPV) vaccination, as is now routinely administered to 12-13 year-old girls. Schools are not legally compelled to comply with this programme. What was most disturbing, however, was the final brief one-sentence paragraph, revealing that most of these particular schools were not informing the unvaccinated children’s GPs – in effect wilfully hindering their access to protection.Rather than seek out the other ’ churnalism ’ pieces, I wanted to read the source story, because, I presumed, it would be longer, more informative and detailed. But I was unable to access the GP story – ‘GPs not told of school HPV opt-outs’ – via its website, because I’m not a GP. However, on a visit to my GP’s surgery on Friday, I managed to blag its copy.What I was interested in, aside from the absurdity of being able to exercise an opt-out from participation in an important public health measure on ‘religious grounds’, was the names of the schools and Primary Care Trusts concerned, with the intention, if there was one in my locality, of at least bringing this to the attention of my MP.I learnt that 83 PCTs (of 152 in England) had responded to a Freedom of Information request; of these, fifteen include at least one school refusing its pupils’ inclusion in the HPV vaccination programme. The actual number of schools was unclear: of these fifteen PCTs, thirteen stated they either did not inform the relevant GPs, or were unclear on whether they had done so. Still, however, these PCTs/schools were not named.So, a couple of days after e-mailing the story’s author for more details to no effect, I conducted a bit more searching. And I landed (again) upon this anti-secularist, church and state amalgamation, which in turn directed me to the Theos take on this issue.(Both these sites also couple with comment on the Free School-creationism issue, also in the news last week, and which I won’t comment on here and now, but there is a thread over here, and a BHA-provided facility for contacting your MP and Michael Gove, should you feel driven.)Theos has managed to obtain the data (available here). And both Elizabeth Hunter of Theos and Gillan Scott, whose mouthpiece God and Politics in the UK is, rightly stress that the numbers of schools (expressly denying HPV vaccination on religious grounds) is actually very small, and also rightly decry the sensationalist nature of the newspaper headlines, which can be read as to give the misleading impression that the number of schools denying children the vaccine on religious grounds is significant. Statistically it is not. But that does not mean objection is unwarranted.Theos states:bq. ‘Some writers seem to have extrapolated from the fact that a school that didn’t give the jab was religious to the conclusion that they had refused to give the vaccine for religious reasons. There is little evidence in the Freedom of Information requests to back this up.’Aside from it not being immediately obvious why a non-HPV-vaccinating religious school would have any reasons not to vaccinate other than religious ones (unless under the influence of some general anti-vaccination wackery), it ought to be noted that the data is incomplete: 69 (45%) of the 152 PCTs did not respond to the Freedom of Information request. Whether this would affect the numbers, we don’t know. But so what?Unlike God and Politics in the UK, the Theos article avoids (despite conceding that ’… a small number of schools (are) neglecting to give important medical care to students on religious grounds…’) any actual support of the HPV vaccination programme; although both are seemingly primarily concerned with a defence of establishment religion and faith schools. And both argue that, because the number of concerned schools is small, it’s not worth making a big hullabaloo of. Well, hindering a child’s access to an important national health programme is, I would argue, contrary to their human rights, which are no less, simply because there are few of them affected. And, despite support for the programme – hence a reluctant admission of agreement with the secular argument – Gillan Scott’s God and Politics in the UK incongruously-titled article seemingly ridicules schools’ assumed promotion of, whilst simultaneously endorsing, the abstinence agenda. Just because the number of culpably irresponsible schools is small, that is not, as Scott rightly argues, an excuse to defensively sweep it under the carpet by bleating on about the media and secular groups giving religion a hard time. Such wilful inaction by schools/PCTs is ethically indefensible. Unqualifiedly.

Turbulence, by Samit Basu, a heady opus (from Kausik Datta's blog)

Sat, 07/21/2012 - 11:14am

Un-freakin’-putdownable! That’s the first thing I must say about Turbulence, the latest novel by the young (well, almost a decade younger than I am!) author Samit Basu. Ahem! In the spirit of gratuitous shoulder-rubbing, he is an alumni of my alma mater! Ahem! It is difficult to review this book without enthusiastically letting out spoilers (I am trying hard not to gush… Stay with me, people!), but I’ll try.

Basu writes with élan, making an unlikely story believable; in the universe of popular perception that is largely-dominated by American (and occasionally European) superheroes, he has made his superhero/metahuman characters, endowed with extraordinary superhuman powers, unapologetically Indian (to the extent of putting in – without explanation – regional Indian words, such as Bhajan, which may be unfamiliar to a non-Indian audience), and – what’s more – he has made it stick, too. I particularly liked the idea of these characters eventually transitioning themselves, from Indian citizens to citizens of the world, champions of humanity as a whole. Suffused with wit and charm, as well as occasional clever mentions of pop-culture references on the sly, the story takes the reader through an incredible and breathless, edge-of-the-seat, roller-coaster ride of a journey.

Basu’s strength, unarguably, lies in the narrative – a fact which jives well with his authorship of comic-book (a.k.a. graphic novel in the US) stories. In fact, he is one of the first popular Indian authors to have crossed over to the graphic novel genre and done interesting work there. In Turbulence, the whole narrative is so well illustrated with words, that the reader simply has to close one’s eyes in between, and the story elements – the locations, the characters, the events – vividly appear and unfold in glorious three-dimensional detail onto two dimensions, much like a graphic novel/comic book, providing a tongue-to-the-wind vicarious thrill. Therefore, while I don’t know if in the eyes of an intellectual (which I’m, emphatically, not) this would qualify as ‘literature’, but it’s one hell of an enjoyable and exciting story. In fact, c’est brilliant!

Turbulence, by Samit Basu

Turbulence was originally published in 2010 (Have I been living under a rock? Why did I not read this earlier?!) in India by Hatchette India (a division of Hatchette UK). Earlier this month (July 6, 2012), Titan Publications released the book in paperback and kindle formats in the UK market, with the US release slated for sometime in 2013. Why this “wicked-stepmother”-like treatment towards the US, I don’t know; apparently neither does the author. However, having breathlessly devoured, and being enthralled by, Basu’s previous fantasy-genre opus, collectively known as the Gameworld Trilogy, I couldn’t wait. Oh no. I hunted down a US seller specializing in exotic books (via Amazon US) and placed an order for the Hatchette India published edition. It took its time, finally arriving yesterday; I extracted it from our mailbox upon returning from work late in the evening, and thereafter, I was dead to the world. Dinner ate itself; my ever-favorite Rachel Maddow, Jon Stewart and Colbert on the telly came and went their sad way without finding me. Sheer exhaustion from the day dragged me to sleep at page 253; at work in the morning, I found a nice, quiet corner away from the lab, and unrepentantly immersed myself in the quest of finding out what happened to the protagonists, finally taking a breath at page 337. I heartily recommend the exhilarating experience.

If you haven’t read the book, do NOT read ahead!

Immersed deep into the glorious Marvel Universe (Go ahead, call me a geek!), I have some appreciation of comic book story lines. And therefore, I agree when author Ben Aaronovitch (of Doctor Who fame) indicates, in the blurb on the front cover, that the reader “… will demand a sequel!”

You peeked, didn’t you? This is your last chance to turn back without reading the spoilers.

I made some curious and interesting observations related to the “sequelability” of Turbulence.

  • Even with good triumphing over evil through not-so-unpredictable twists and turns, Basu has left the story open-ended. There was a clever switch of focus from the initial characters to the final ones, undoubtedly leaving the doors ajar for further character development in sequels and spin-offs. Particularly, at the very end, the nod to the possible existence of other hitherto unknown superheroes of different nationalities is quite telling, I thought (particularly since Basu is no stranger to trilogies!).
  • Contrary to the usual goody-goody-gumdrops representations of superheroes, Basu’s superheroes – formerly ordinary human beings, with special powers thrust onto them – have no qualms about obliterating supervillains without any moral or ethical quandary. I wonder if Basu’s background (same as mine), possibly steeped in the violent imagery of Indian mythologies – where anything marked ‘evil’ is fair game for the most gruesome death, made it easier to depict these scenes. It’s true that in the hectic pace of Turbulence, the superheroes and supervillains didn’t have much time to ponder over various ethics of superpowers. Would this be something to be dealt with in a future sequel, particularly since Basu lets slip an indication that anti-superhero coalitions were already forming amongst humans? Will there be, perhaps, a touch of Nietzche?
  • The indestructible, invincible supervillain was stopped finally via mind-manipulation by a superhero, rendering the villain under the heroes complete control (Basu uses the term ‘slave’, possibly to indicate that the humiliation is complete – although this may engender a feeling of discomfort amongst those non-Indian readers whose familiarity with the term stems from a different, and very real, historical context). One can’t help but wonder how complete this mind control is. Will it work like a drug to suppress the villainous impulses, while retaining other faculties? Is it permanent, or will it go away if the superhero in question dies, or disappears or loses the special powers? Or perhaps some other supervillain will be able to lift the said control in future?
Hide SPOILERS, but oh! What’s the use.

So, yes. Absolutely ripe for sequels. So when’s the next, Samit?

Eye evolution made easy (from Peter Etchells' blog)

Fri, 07/20/2012 - 12:37pm

The National Trust hit the news recently over the controversial inclusion of creationist theory in a new exhibit looking at the history of the Giant’s Causeway. The exhibit claimed that:“Like many natural phenomena around the world, the Giant’s Causeway has raised questions and prompted debate about how it was formed.This debate has ebbed and flowed since the discovery of the Causeway to science and, historically, the Causeway became part of a global debate about how the earth’s rocks were formed.This debate continues today for some people, who have an understanding of the formation of the earth which is different from that of current mainstream science.Young Earth Creationists believe that the earth was created some 6000 years ago. This is based on a specific interpretation of the Bible and in particular the account of creation in the book of Genesis.Some people around the world, and specifically here in Northern Ireland, share this perspective.Young Earth Creationists continue to debate questions about the age of the earth. As we have seen from the past, and understand today, perhaps the Giant’s Causeway will continue to prompt awe and wonder, and arouse debate and challenging questions for as long as visitors come to see it.”The good news is that the National Trust have listened to criticisms about the exhibit, and are currently reviewing it (with the hopeful conclusion that it will be removed). However, the deeper problem here, as Dr Adam Rutherford points out, is that it has allowed creationist lobby groups such as the Caleb Foundation a means through which they can appear to have a legitimate view about how the world was created. This wedge strategy is more political than religious in design; it aims, via getting a foot in the door, to slowly distort scientific facts, appeal to sentiments about freedom of speech, and peddle pseudoscience as legitimate evidence against evolution. One of the classic ways that creationists attempt to distort science is to use the example of the eye. In fact, they even quote Darwin on the matter:“…to suppose that the eye … could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree.”- On the Origin of Species, 1859If Darwin himself was stumped by the eye, it sort of undermines the whole concept of evolution, doesn’t it?Nope. In a classic case of cherry-picking, the above quote wasn’t Darwin’s last word on the matter. If you read a bit further:“…if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist … then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.”So, how do we get from ‘being blind’, to eyes as we know them today? Well, in order to answer this, we need to think a little bit about what the basic point of vision is: to provide the necessary information about our surroundings, in order for us to behave more appropriately. Certainly, if I’m something that moves, having visual information at my disposal would definitely help me to navigate around my environment properly, and avoid things that might injure or kill me. How do I get that information? From light.We know that pretty much every living thing is sensitive to light – for instance, plants have a light-sensitive hormone called auxin, which promotes cell growth and tends to collect on the darker side of a plant’s stem. Because these cells grow faster than the ones on the side that is exposed to light, then the plant ends up bending towards the light (a process called phototropism). So to begin with, we just need some simple, light-sensitive cells:Step 1: Get some photoreceptorsPhotoreceptors are specialised types of neurons that are capable of transforming light into an electrical signal. This signal can then be sent somewhere to stimulate a biological process. If you put a group of these together, you can sense light coming from a particular direction:eye1.jpgThis is handy, because it now means that you can move either towards or away from a light source, and detect in very basic terms, whether something gets in the way of your light source. You won’t be able to see what it it, but it still gives you some rudimentary knowledge of what’s going around you.Step 2: Directional sensitivityThe next step might be to figure out which direction the light is coming from. In order to get this, all you need to do is arrange the photoreceptors in a pit, like so:eye2.jpgIn step 1, our basic eye would detect light no matter where it was coming from in the 180 degree arc in front of it. By adding a little pit, we can now limit this field to an area that is (vaguely) more head-on. As this pit deepens, the direction in which light can be detected from becomes more and more specific, until eventually, a chamber is formed.Step 3: Make a pinhole cameraWhen this chamber is formed, it has an added benefit, over and above the fine directional sensitivity – it turns the eye into a pinhole camera.eye3.jpg Pinhole cameras project light that is coming in from the scene in front of it to form an inverted and reversed image on the back wall. In the case of the eye, this means that very basic shape-sensing can take place. So not only can you see whether something is blocking your light source, you can roughly see what shape it is, and in fact, you can still see this type of eye today, in the Nautilus:nautilus.pngStep 4: Close the chamberThe chamber that forms part of the pinhole camera is filled with water at the moment, but as the pinhole gets smaller, it becomes harder and harder to maintain a good flow of water through it. Ideally, we want to close off this chamber with a transparent window, in order to prevent parasitic infections or contamination with debris that either damages the photoreceptors, or blocks off incoming light.eye4.jpg This has a further benefit of allowing a specialised fluid to develop in the eye, instead of just having water in there. This specialist ‘humour’ can serve useful purposes like blocking out ultraviolet radiation, or providing a higher refractive index, or allowing the organism to see out of water.Step 5: Add a lens to improve it allWe know that lenses have evolved independently in a number of separate species. One way in which it might have happened in the case of our lineage is that the transparent window covering the eye chamber split into two layers, with a layer of liquid in between to act as a filtering system to keep the layers clean. Eventually, this secondary layer forms a lens, giving the ability to focus on near and far objects, and provide a wider viewing angle as well as higher image resolution. On top of this, a cornea eventually develops in order to passively increase the eye’s refractive power (meaning that the lens has to do less work). eye5.jpgAnd as complicated as it all sounds, it really doesn’t take that long to develop. Nilsson and Pelger showed in a 1994 paper that it would take about 364,000 generations to get from a basic eyepatch to a modern-looking eye. In the grand scheme of things, that’s no time at all.nilsson.pngSo there you go, next time a creationist bangs on about irreducible complexity, you can tell them that’s how you evolve an eye in 5 easy steps.

Twitter Archaeology (from Lowell Goldsmith's blog)

Thu, 07/19/2012 - 10:00am

Twitter Archaeology.jpgOMG, in 2514, microchip found with summary of July 2012 JID issue.Visible light (VL) induces oxygen species and enzymes & sunscreens need 2 block VL to be protective.2 doses of pachyonchia congenita gene worsens disease +s alopecia.Pemphigus vul linked with ST18 gene 4 inflammation and cell death.Stretching fibroblasts increases inflammation in DM.GTG, if this is TMI, LMK or send me your best twitter of JID.LAGImage by Kordite, downloaded from Flickr.

Are scientists still only human? (from Mike Fowler's blog)

Thu, 07/19/2012 - 8:03am

Busy, busy, busy, so here’s a link to an interesting review in the New Humanist by Jonathan Rée, of “On the Modern Cult of the Factish Gods” by agent provocateur Bruno Latour, who is somewhat notorious for pointing out the bleeding obvious. Always nice to reflect with a different perspective. I haven’t read the book (and I probably won’t. See above), but the review’s good fun.That is all. (hiss, clack)

Dynamics simulation 101 (from Nicolau Werneck's blog)

Wed, 07/18/2012 - 4:05pm

This article is an introduction to numerical methods to solve differential equations in order to simulate dynamical systems… I am studying that first of all because it’s really something I like to know well, and I think should be better known by everyone in general. I am also doing that to develop stuff for the upcoming game 0×10c!

Dictionary for lab notebooks (from Viktor Poor's blog)

Wed, 07/18/2012 - 7:04am

In lab books, you can find quite a lot of scribbles and abbreviations. Many of the abbreviations are “standardized”, but Stripped Science helps you to decipher the creative ones:lab notebook dictionary 1.PNGLike Stripped Science on Facebook if you want daily comics from the archives and the find a fine selection of the best science themed comic strips from the interwebz:

Creationist Opinion OK if you are Running a State School! (from Brian Derby's blog)

Wed, 07/18/2012 - 5:47am

I sometimes wonder if Michael Gove, the current education secretary, is more dangerous than he appears. When he arrived in government he used the Machiavellian principle of getting all the bad news (e.g. withdrawing new school building projects in poor areas) out very very fast so that they would be old news by re-election time. He also has the education politician’s knack of knowing how to teach, design syllabuses and generally tell teachers how to do their jobs with the benefit of no experience. However, he is a politician and all of them do this. He also realises that the last people you want to run schools are local councils, because they may have very different ideas from you. In addition they have the inconenience of having been elected and therefore might even be able to argue that they have a popular mandate to do thinks differently from central government. No, the best way to run a schhol is to call it a Free School, give it its own budget and get selfless people to run it with the incentive of a profit being allowed.Today a number of Free Schools have bee approve to be run bt religious organisations who actively promote creationism: see this article in the Guardian today. Remember these are state funded schools and they in principle report directly to the Secretary of State for Education (Michael Gove). This implies that teaching belief in Creationism has the approval of the Department for Education. Indeed, given that Michael Gove has a track record of micromanaging education, I have a small suspicion that he may even approve of such teaching. As the Guardian article reports, the previous government had a policy that Creationism could not be taught in any state funded school – even under the guise of religion classes are separate from science classes – and it is very worrying that the current administration is significantly altering this principle.The coalition government in the UK, in common with most previous administrations, is run by politicians who were educated in the Humanities, and there are few (I cannot think of any) who have received any scientific training beyond High School.

Meeting your deadline (from Nicolau Werneck's blog)

Tue, 07/17/2012 - 5:32pm

It finally happened. I finished writing my thesis!2012-07-05-137.jpg

Journey into the Valley of Ten Thousand Smokes (from Liz O'Connell's blog)

Tue, 07/17/2012 - 2:00pm

by Ned RozellOne hundred years after the largest volcanic eruption of the 20th century, the Valley of Ten Thousand Smokes is still a moonscape of ash and volcanic rock, without a tree or shrub in sight. The valley, located on the Alaska Peninsula where the Aleutians hook on to mainland Alaska, is a silent reminder of the power and potential of Alaska’s volcanoes.Volcano_Katmai.gifHikers trek the Valley of Ten Thousand Smokes on the Alaska Peninsula, walking on a sheet of ash and volcanic rock more than 500-feet-thick.Photo by Ned Rozell.I once visited the valley as one of a dozen people on a 10-day field trip with John Eichelberger, who then worked at the Alaska Volcano Observatory. As we approached the valley the first day on a bus ride from Brooks Camp in Katmai National Park, the story of the 1912 Katmai eruption began to unfold.A few miles before we reached the valley, we saw the skeletons of spruce trees, bone white and surrounded by green bushes. The trees have been standing dead since early June 1912, when falling ash killed them.Getting off the bus and hiking into the valley, we left Alaska for another world. As we walked deeper into the valley on rounded rocks that felt like styrofoam balls, the willows disappeared, the sparrows stopped singing, and the mosquitoes vanished. A grizzly bear had pressed a few tracks into the valley floor, but we saw no other signs of life.Botanist Robert Griggs named this desolate, beautiful place “The Valley of Ten Thousand Smokes” when he visited here on a National Geographic expedition in 1916. At the time, four years after the eruption, steam poured from vents all over the valley. Because the thick blanket of ash and volcanic rock has cooled since then, the valley no longer steams, but the dramatic landforms still inspire the feelings of Griggs and his companions in 1916. “We were overawed,” he wrote.In three days of the summer of 1912, a volcano Griggs named Novarupta (Latin for “new vent,”) transformed 40 square miles of the world’s best bear habitat into instant badlands, burying the downwind valley in more than 500 feet of ash and volcanic rock. Novarupta spewed 100 times more material than Mt. St. Helens and sent skyward a plume that probably reached 20 miles high. Sometime during the eruption, Mt. Katmai, six miles from Novarupta, was decapitated. In place of its summit today is a magnificent crater lake surrounded by 300-foot walls that echo the thunder of glaciers that now calve into lake.When Krakatoa volcano in Indonesia ejected half as much ash and rock in 1883, 35,000 people died. Because earthquakes that preceded Novarupta’s eruption scared residents of two nearby villages from the area, Novarupta’s human death toll was zero. More than one foot of ash fell on Kodiak, 100 miles away from Novarupta, in the days following the eruption. Roofs collapsed under the weight of the ash and the steady gray ashfall prevented townsfolk from seeing a lantern held at arm’s length at times.In his report for the National Geographic Society, Griggs wrote that if such an eruption occurred on Manhattan Island, those in Chicago could hear the explosions, Philadelphia residents would be buried under one foot of ash, and fumes from the eruption would tarnish brass doorknobs in Denver. On Manhattan Island, “there would be no survivors,” Griggs wrote.Much to the relief of the locals in both places, Alaska is not Manhattan; Alaska is a place with more than 100 volcanoes, 42 of which have erupted since people began writing down such observations in 1767.Today, the Alaskans who keep the closest eye on volcanoes work for the Alaska Volcano Observatory in Anchorage and Fairbanks. Scientists there take the pulse of the most active volcanoes in Alaska with networks of seismometers that detect earthquakes within volcanoes. They also check out satellite images each day, looking for ash plumes or increases in temperature on volcano surfaces that indicate activity, perhaps someday as dramatic as the eruption that created the Valley of Ten Thousand Smokes. .Find more on Cook Inlet Volcanoes at Frontier ScientistsOriginally published in the Alaska Science Forum Article #2071 July 1, 2011 Journey into the Valley of Ten Thousand Smokes by Ned Rozell"This column is provided as a public service by the Geophysical Institute, University of Alaska Fairbanks, in cooperation with the UAF research community. Ned Rozell is a science writer at the institute."

Origins of an ecological mongrel (from Tom Webb's blog)

Tue, 07/17/2012 - 11:33am

Some papers are written on a whim; others mark the completion of a huge programme of field work or the solution of a complex problem. And some are more existential, marking an emotional transition, almost a rite of passage. The couple of thousand words I’ve just published in Trends in Ecology & Evolution falls into this latter category, which perhaps explains why I’m so excited to see it come out.Of course, just seeing my name in TREE is pretty cool in and of itself – TREE’s been a consistently reliable, entertaining and useful read since my undergrad days (somewhere around vol 8, I reckon) and I think that even many of those who vehemently dislike its parent publishing company maintain a soft spot for it. So, it’s a bit of a thrill to see my work published there. (OK, I’ve published there before, but in a more destructive role; this new one is rather more constructive I hope!)But more than that, this paper feels like a validation of opinions that I’ve developed over a long time. In the paper, I argue that the separate intellectual development of marine and terrestrial ecological research has been to the detriment of both, and I make some suggestions (in particular in the fields of community ecology and macroecology) where I think greater cross-realm synthesis is likely to be especially fruitful. This is something I’ve been banging on about for a while, and having written this piece I sort of wondered why I hadn’t done so five years ago (it wouldn’t have been as good then, but would have been gathering citations…) But given that nobody else wrote it in the meantime, I thought it might be interesting to examine what it is about my background that has turned me into this sort of mongrel marine-terrestrial ecologist.My first stroke of luck was in doing my undergraduate degree at UEA in the mid 90s. At that time, the ecology syllabus was partly delivered by excellent terrestrial ecologists like Bill Sutherland, Andrew Watkinson and Bob James; but also by John Reynolds and Isabelle Côté, both of whom worked primarily on marine systems but were fully integrated into the ecological ‘mainstream’. It was natural then to learn the fundamentals of population ecology using primarily fisheries case studies, or to focus on marine protected areas in conservation lectures. Spending a year at the Centre d’Oceanologie de Marseille certainly helped; and on returning to UEA, I was able to take advantage of the close links that John had forged with CEFAS to finish my degree with a marine flourish. It never really occurred to me that marine and terrestrial ecology ought to be separated.Then chance events took me back towards terrestrial ecology – I was interviewed for a PhD in marine ecology at the British Antarctic Survey, which I didn’t get; and for one in terrestrial macroecology at Sheffield, which I did. So I spent the next 8-9 years of PhD and post-doc work gradually working my way up within the ecological mainstream, with always in the back of my mind the idea that I’d like to apply some of this stuff to marine systems one day. At one point I was interviewed by Simon Jennings for a post at CEFAS. That post went to some bloke called Dulvy (whatever happened to him?). But in rejecting me, Simon advised me that if I wanted to work in marine systems my best bet in the meantime was to do the best ecology (and work with the best ecologists) that I could, and not to worry too much about the specifics of whether it was wet or dry.My advice to you: if Simon Jennings offers you advice, listen to it. It will be wise. So after some twists and turns this strategy led me to a short post-doc with Dave Raffaelli at York. Now although that specific post had nothing to do with marine ecology, as I got talking to Dave we sort of mutually realised that we were on the same page when it came to not seeing a massive divide between marine and terrestrial systems. I guess Dave was influenced by working for such a long time on the Ythan estuary: essentially a marine ecosystem, subject to tides and so on, but with terrestrial management regimes playing an equally profound role in its ecology.One thing led to another and I found myself first coauthoring a paper with Dave and Martin Solan called ‘Do marine and terrestrial ecologists do it differently?’, part of a Theme Section in MEPS aimed at Bridging the gap between aquatic and terrestrial ecology (link to OA PDF); and then attending (at Dave’s instigation) a MarBEF workshop in Oslo trying to work out what we should do with the newly-assembled huge dataset on European marine invertebrate distributions and abundances. This workshop was hosted by John Gray. John – who has very sadly since died – had something of a reputation for not being the easiest of characters; but to me he was extremely kind, generous and encouraging, and I suddenly saw an opportunity for doing some macroecological research on a marine system.So Dave and I put together an application to NERC to do some macroecology on the MarBEF dataset. I found out the week before Christmas that it hadn’t been funded, and with my contract due to run out at the end of December things looked grim. But I managed to wangle a move back to Sheffield to work with Rob Freckleton while I tried to turn the grant application into fellowship material. First the Leverhulme Trust then, eventually, the Royal Society decided that my ideas weren’t so silly after all. I like to think that this new TREE paper marks the end of my transition into an ecological mongrel, with one wet and one dry foot.Webb, TJ (2012) Marine and terrestrial ecology: unifying concepts, revealing differences. Trends in Ecology & Evolution, doi:10.1016/j.tree.2012.06.002

Musings on Mucopolysaccharides, Mechanobiology and Eponyms (from Lowell Goldsmith's blog)

Tue, 07/17/2012 - 10:00am

Image from wikipedia.jpgMucopolysaccharides (MPS; an older term), comprise a heterogeneous group of extracellular molecules, each consisting of a core protein(a proteoglycan) with covalently joined linear carbohydrates(a glycosaminoglycan). These molecules are important biomarkers and probes for exploring disease mechanisms. At the VIII Dermatology International Congress in Copenhagen of 1930, Heinrich Adolf Gottron reported increased metachromatic staining in Dermatomyositis (DM) skin lesions. Gradually, the clinical literature has come to use Gottron’s papules (GP), red to violet plaques over the metacarpalphalangeal distal, and proximal interphalangeal joints as characteristic findings in DM. Although there are recent discussions of the sensitivity and specificity of GP and DM, the term GP has stood the test of time. Medical students are in awe when they learn that this finding can be a sign of inflammatory muscular disease and underlying internal malignancy. Now, these papules can also be a clue to the mechanisms of DM and its intriguing pathophysiology.The general concept that “structural” molecules can interact with and modify the interactions of growth factors and other molecules is now well accepted. Those interactions can involve receptors on the cell surface and bridging molecules that may be covalently or non-covalently bound to the structural molecule. Such interactions may modulate inflammatory responses.With this in mind, I refer you to Kim et al’s JID article reporting detailed studies of the MPS in GP. The glycosaminoglycan in GP is a chondroitin-4- sulfate (C4S). It interacts with both CD44 variant7 and osteopontin. Both of those latter molecules have roles in modulating immune responses, as discussed by Kim et al. A novel feature of this investigation addressed the question that has intrigued investigators for almost a century: the reason for GP’s localization to the extensor surface over hand joints. The reasons for skin disease location are often discussed but rarely approached experimentally.The role of the constant mechanical stretching of the extensor skin during ordinary circumstances was approached experimentally. Normal human fibroblasts were cultured on a tissue culture matrix, with a glass bead under their tissue culture matrix and another glass bead underneath the cell and its supporting membrane; pressure was applied above the culture. For me, this experiment recalls the fairytale princess who slept on a pea. The matrix around stretched fibroblasts was compared with non-stretched fibroblasts. The stretched cells produced increased levels of the CD 44 variant7 protein and its mRNA, which could have a role with osteopontin in contributing to inflammation and the increases in C4S.Cells interact both biochemically and physically with their environment, and the mechanical and physical interactions reported by Kim et al can be considered within the realm of “mechanobiology”. The laboratory techniques and the analyses involved may differ from those used in classical immunology and biochemistry, and no doubt they will be used in more studies of the skin. Given its potential insights, mechanobiology should be a rapidly growing science for skin biology, akin to “plastics” — as recommended to the character Benjamin in “”“>The Graduate”. I discussed the increasing importance of engineering analysis in biology in the 75th anniversary issue of JID.Your blogger has been afflicted by disease eponyms for several decades, as he has downed obscure names, drowning his neurons with eponyms for clinical syndromes since he was a resident. More recently, I have been concerned that eponyms may divide specialties and establish individual knowledge clubs. The issues related to eponyms are discussed in two articles in the British Medical Journal (Whitworth, 2007; Woywodt and Matteson, 2007). Some eponyms have been removed or de-emphasized on the basis of an individual’s notariety. Reiter and Wegener are the two most prominent examples; due to their activities related to National Socialism in Germany, The primary names of their eponymous designated diseases have been replaced with “reactive arthritis” and “idiopathic necrotizing vasculitis”, respectively (Strous and Edelman, 2007). “Gottron papules” can be a useful shorthand; instead of GP, I could have described the lesions as “symmetrical, disposed, shiny, well-delimited atrophic purplish papules on the extensor aspects of the digits, usually over joints, etc.” Even when their exact basis is known, there may not be a simple molecular name or shorthand for the overall clinical lesion. Therefore, this eponym enhances communication. But what about the man for whom they are named?Heinrich Adolf Gottron (1890-1974) was Professor and Chair of Dermatology in Breslau Germany during National Socialism and was “exonerated by the denazification committee in 1945”. He was appointed as professor and chairman in Tübingen in 1946, after Breslau was ceded to Poland after World War II. After the war he “was a notable representative of post-war dermatology”. From a brief review there seems no strong evidence that this eponym is being used inappropriately. Important academic and historical details of Gottron’s career can be found in the History of German Language Dermatology.In the over 80 years since Gottron’s report, investigative studies of the skin and immune system are increasing in DM, and further studies may lead us to understand its frequent association with muscle disease and internal malignancies.REFERENCES

  • History of German Language Dermatology edited by A. Scholz, K. Holubar, G. Burg, W. Burgdorf, H Gollnick. Wiley-VCH Verlag, 2009.
  • Strous,RD and Edelman,MC. Eponyms and the Nazi era: time to remember and time for change. IMAJ 9:207-214, 2007
  • Whitworth,JA Should eponyms be abandoned? No. BMJ 335:425, 2007.
  • Woywodt,A and Matteson, E. Should eponyms be abandoned? Yes BMJ 335:424,2007.
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Olympic Health Legacies (from Peter Etchells' blog)

Tue, 07/17/2012 - 7:25am

jat-team.jpgOver the course of 17 days this summer, an estimated 14,000 athletes will take part in over 300 Olympic events in the UK, mostly centered on London. Such a mammoth event takes time to plan, and while we hear lots in the news about stadiums being built, controversial security plans being put into action, and athletes being trained, we don’t hear much about a less obvious, yet hugely important factor in any major event – how to keep everyone healthy and safe. With some 10 million tickets having been allocated, making sure that health hazards are monitored, outbreaks are contained and people are kept healthy is no small feat. We can’t predict everything that will happen in London this year, but we can draw upon a vast amount of experience from people involved in previous Olympics.One such veteran is Dr Jat Sandhu, the Regional Director for the Public Health Surveillance Unit in Vancouver, Canada. The unit is part of Vancouver Coastal Health Authority, the host health jurisdiction for the 2010 Winter Olympic and Paralympic Games. Two years ago his team was tasked with monitoring public health during the Games, and responding quickly to any issues that came up. I recently caught up with him, and asked him about his work.PE: What was your role in the organisation of the Winter Olympics?JS: I was involved with different aspects of planning and preparedness of health services including public health for the Games, both inside and outside the fence. Specifically during the games, my team was responsible for a daily public health status report for VANOC (the Vancouver Organizing Committee), the IOC, and various, regional, national and international public health partners.Did anything unexpected health incidents actually happen during the Games?While some far-fetched scenarios were put forward during tabletop exercises and discussions, thankfully the Games were largely a public health success with no major, or unforeseen, issues needing to be dealt with. In actual fact, things like seasonal influenza activity were below seasonal norms, despite the circulation of the H1N1 pandemic strain. We did have a norovirus outbreak in a temporary housing facility for the Olympic workforce, and we saw some increased reports of injuries relating to public intoxication, assaults and falls, but nothing that couldn’t be handled by our routine protocols. Food safety was a critical component of preparations and monitoring during the Games, and ensuring the compliance with food safety regulations was another contributor to a healthy and memorable experience for athletes, officials, media and the general public. Being the sole hosting health jurisdiction was a real blessing, which meant we could primarily rely on routine protocols and procedures for the Games – having to coordinate response protocols across multiple jurisdictions would have been challenging!Part of your job included collecting lots of public health data during the Games. How did you deal with all of that information? Vancouver was the largest city to host a Winter Olympics, but aside from that, it’s a major tourist destination. So while our health care system has good experience with large numbers of visitors, it was a good chance to improve some of our surveillance techniques and procedures. During the Games, we produced daily Health Watch status reports on things like disease surveillance, food service closures, air and water quality indicators, emergency management advisories and health promotion messages. We produced 41 of these altogether, so it was important that each one contained just the essential information presented in an easy-to-understand way for the public, public health partners and the IOC. The format of the bulletins was always one or two key summary points, with the third point being a health promotion message. During the Games, our team got together at 7 in the morning to produce a summary for the day. This would get to my desk for review at about 9am, and if I found something unusual that I thought needed to be investigated further, I’d flag it for the team, say what indicator it was, and then one of the epidemiologists would investigate it further. It was a really intense process, in that information was coming in thick and fast from all the different surveillance systems. A daily situation report (SitRep) would then be reviewed by the public health senior leadership team at noon. By the end of the meeting, we would have determined what the key messages were for the day, what needed to be highlighted, and what health promotion messages would be included. Alongside the SitRep, we’d also have another document containing graphs and visuals, so if we wanted to visualise a particular health indicator, that could be done as well. Everything would get pulled together into the draft bulletin by 3pm, with the aim of getting the final document out at 4pm.HWmarch.pngThis sounds like a really useful system – tough to set up, but once it’s up and running, much easier to manage?This was the first time that such a comprehensive bulletin was done for an Olympic Games – we really raised the bar. The whole point is that at a big event like this, you’re under the microscope a little bit, so you want to have your finger on the pulse. At previous mass gatherings, there was a tendency to be reliant on manual data – having people on the ground at various venue or hospital locations, manually collecting data and feeding data back that has to be edited does not sound anything like having your finger on the pulse.HWdec.pngThe majority of our data was electronic. In the lead-up to the event, we had written statistical algorithms for data to be analysed and summarised. The summary data files were linked automatically to an Excel workbook where graphs and tables would be automatically populated. The statistical algorithms also help you look for patterns, say in the last 7 days, or in the same period last year, but the trick comes in setting the sensitivity – do you want to overreact to things, or do you want to miss things? The emergency rooms at hospitals we were monitoring had information systems to capture every single visit that they get. We worked with our IT team to define what were some of the fields that they could pull out and inform situational awareness. An extract was established for every day at around 5am that would extract info out of the various systems and send it to our secure servers at 6am every day. The system was so successful that we actually won an innovation award last year at the Canadian Injury Prevention and Safety Promotion Conference.Have these improvements helped in any way in the aftermath?We’re now very good at monitoring acute events in the community since the Games. The system’s not perfect, but does provide some insight into what’s going on. For example in April of 2011, from our emergency room data we were able to observe a signal that indicated increased overdose visits and this coincided with the detection of more potent street heroin being in circulation. Towards the end of 2011, we also noticed an increase in some ecstasy-related visits to hospitals, and this time it was a result of tainted ecstasy that was considerably more toxic. There were other things like during the Stanley-Cup playoffs in 2011 we noticed higher visits related to alcohol intoxication and assaults, which supported the decision to close Vancouver liquor stores for the final two games of the playoffs. Unfortunately this did not prevent the riot that followed but alcohol misuse was identified in the subsequent inquiry as a contributor to the riot. (PE: You can check out the Health Watch bulletin from the playoffs here.)So do you think what you learned from the Games helped you when the riot broke out?It was a completely different atmosphere and set of circumstances. With the Olympics we had large crowds gathering in the downtown areas as well, except it was more of a family atmosphere, spread throughout the day with all ages and a very international nature to the crowd. Whereas during the hockey games, we had a greater number of younger adults with many fueled by alcohol consumed in a relatively short period in the early evenings. One of the things that came out of the Stanley Cup riot review was the recommendation to develop a municipal alcohol policy to discourage binge drinking, and that resulted in a recently launched website to raise public awareness. What public health challenges do you think the London Games face this year? How are they different to those that Vancouver (or Beijing) faced?Generally speaking communicable diseases have not been a significant issue at previous Olympics, but mass gatherings can be conducive to the introduction or spread of disease. However, this is an area that most health jurisdictions have experience with and the UK is no exception. The geopolitical climate for the Summer Games is very different, given the much larger number of countries involved and the greater global attention. I would imagine there would have been many scenarios being planned for, especially after the unfortunate experiences of 7/7 and the Litvinenko incident. Fortunately, I would say the public health command and control structure is more robust in the UK and the HPA (Health Protection Agency) has a good working relationship with different parts of local (boroughs) and national (e.g. COBRA committee) governments. The key is ensuring that clear lines of communication are maintained between different agencies and for the co-ordination of multi-jurisdictional issues. Have you been involved in any big events since the Games?Unfortunately, not directly but I’m part of the WHO virtual advisory group on mass gatherings so often hear about other events. This is a multidisciplinary professional group that comprises a number of different people from various past host jurisdictions, as well as future ones, involved in disaster and emergency management, risk assessment, global health security, public health and surveillance. This is a great expert group to connect with for hosts of mass gathering events if you are not already aware of them, or heard from a member! For those interested, the Lancet had a commentary piece out recently on mass gatherings and about creating a lasting legacy in the form of improved and advanced healthcare systems, it’s well worth checking out. What were your favourite things about being involved with the Olympics?It’s a difficult question but so many different aspects were rewarding. We were so intensely involved in doing our part for the Games, that we could have easily missed out on them actually occurring. I guess, thinking about it, it was good to actually get through it all unscathed – and knowing that we did a good job and set a new standard for future events. The camaraderie amidst the long days was a highlight. Everyone worked really hard, and knowing you’ve got a good team around you, where everyone understands their role, you know that they won’t let you down. So yeah, if you ask me about what things I’m really happy about, it was just seeing how well our team performed in making sure (at least from a public health point of view) the Games were a success. When you hear about public health in the news, it usually means that something’s gone wrong. If the staff are doing a good job, you never get to hear about them. The public health workforce are one of the many unsung heroes of the Games.About Dr SandhuDr Jat Sandhu, is the Regional Director of the Public Health Surveillance Unit at Vancouver Coastal Health Authority. The Unit was established in 2007 to support regional public health practice in the areas of health assessment, disease surveillance, epidemiological investigations and knowledge exchange. The Unit was recognised as a national leading practice for public health by Accreditation Canada in November 2010.Dr Sandhu has training and work experience that has encompassed British Military Hospital Pathology; WHO regional training centre for Medical Education in Sydney, Australia; the Australian Red Cross; the Provincial Laboratory for Public Health in Alberta; faculty at the University of Bristol in England, and work with various public health agencies of the National Health Service in the United Kingdom.Dr Sandhu contributes to public health capacity development through his faculty appointments at the University of British Columbia and Simon Fraser University, as well as being primary placement supervisor for field epidemiologists with the Canadian Field Epidemiology Program of the Public Health Agency of Canada.

Where is the Wonder? (from Brian Derby's blog)

Mon, 07/16/2012 - 6:21pm

I spent this morning interviewing students for PhD positions. We have a policy of interviewing all students so that we can fairly distribute PhD awards to the best students. A good common question to ask is whether they can discuss some science related topic they may have picked up from news reports in the recent past. Maybe it is because they are nervous, or possibly they are trying too hard to impress us with their focus, but it is surprising how many prospective students appear to be unable to talk about any topic that is not related to their underrgraduate research project or the Ph.D. they hope to pursue.I expected there to be a large number of students keen to apply for PhDs this year because of the recession and presumably fewer jobs for graduates. However, there seems to be little difference in the number of students from the UK and Europe who are applying this year when compared with last year’s figures. However, there seem to be a larger number of Chinese, Mexican and Brazilian students. A surprising comparison as I had thought their economies to be in better health than Europe.

Tarot Woman (from Lee Turnpenny's blog)

Mon, 07/16/2012 - 4:12pm

(or: Foot stamping III)For anyone who visits and reads this blog from time to time, and is familiar with my various disaffections with an apparent ‘black-listing’ by the Leicester Mercury_, take a look, if you will, at this recent example of what it considers sufficient topical relevance for communication to the citizens of Leicester – the awarding of business funding to a dreaming tarot reader.Its author’s apparent appeal for support for an organisation called "_Leicester Business Women": seems laudable enough. Got no argument with empowering women to get fledgling business ideas off the ground, particularly in these economically dire times in what is (whether we’re reluctant to admit it or not) a (fucked-up-by) ’man’s world.’ Fair play. Except what the author is obviously doing is exploiting an opportunity to also market her wares. I know, I know, it is better for the blood pressure to just ignore; each to their own, and all those relativist platitudes. And, flabbergasted as I was/am, I have not used the Leicester Mercury‘s online portal to ’examine.’ There, I merely appended the not unreasonable comment as to LBW_’s apparent profligate lavishing of scarce resources on the funding of such a ridiculous enterprise.However, I couldn’t resist hunting out the business’s own website. So, give yourself a treat and take a look at "_Pure & Blessed Tarot": As its owner makes more information publicly available there, I will here claim the right to publicly offer up comment and opinion on the assorted claims and services therein.I was (and still am) largely ignorant of what its practitioners claim Tarot can do for anybody, but it seems to me, from what I read there, that it is not unconnected with that whole ‘positive’ thing that crops up ubiquitously, couched in that woolly kind of language that all reads very nice, but actually says nothing. The Home page quickly employs an interesting disclaiming tactic:bq. ‘I help open minded people’ [sic]This is potential genius. If, after you’ve shelled out your coffers, you find yourself curiously unaffected, well, I’m afraid that will be because you were not simple-minded enough simply were not open-minded enough. I’m not sure whether being open-minded is here considered an either/or logic state; or the attainment of some point on a gradient ranging from lead-dense bigotry to vacuum-skulled self-oblivion. Whatever, it appears that prior credulousness is a necessary pre-requisite. (Yes, I’m aware of the tautology in that last sentence; it is deliberate.)So, what else is on offer there?Well, being a member of the Federation of Holistic Therapies, the possibilities are seemingly endless. As a diversion, take yourself to the FHT search facility, which is, I have to say, fascinating in its scope. Here, you will find a quite bewildering list of ‘therapies’, including, along with the usual suspects (eg, Crystal Therapy, Homeopathy, Reflexology), stuff that would seem to be not ‘therapy’, but cosmetic, or fitness; along with some bizarre stuff I’d never heard of (eg, Iridology, Moxibustion, Zero Balancing). Despair not: clicking on a selection may provide a small adjacent boxed description. It is well worth a browse. And I confess that some of these read quite pleasurable. But let’s not get side-tracked. Instead, back to our subject, who is proud to declare among her skills a sub-set of that listing, including: Reflexology, Reiki, and… in case you needed confirmation of how stupid human beings being stupid can be… Thermal-Auricular Therapy (Ear candle) – yes, lighting candles in your ears.Of these, the one allocated a tabbed page of its own – and thus, we might presume, a skill the site’s author is particularly proud of – is Reiki. I think all I need do here is quote the words provided:bq. ‘The Reiki system of healing uses universal life-force energy. This is an energy, which is safe, gentle, natural and intelligent. The energy is channelled through the practitioner and knows where to go and what to do, to help restore harmony and balance to the body. Reiki is easy to learn and generally split into three levels. Reiki is used by people of all faiths and belief systems, as a system of relaxation and healing. You can receive and practice Reiki, no matter what your religion.’Unless you, reader, are completely devoid of sceptical bones, I really do not think I need go to work on that paragraph of pseudoscholastic piffle.But it gets worse better: scroll down, and you are offered ‘House Blessings’:bq. ‘Bringing harmonious energies to your home with rituals and blessing inspired and developed through the knowledge and understanding of Reiki and Crystal energies.’This old ‘energy’ thing again. Combined with the religious-lite/spiritual thing for cuddlesome universality. Of course if you are tempted but require convincing, there are always those positive Testimonials. Don’t expect any negative ones – after all, it is not a place for negativity.Why do I do this? Why am I criticising the online activity of someone I don’t know and have never met? Is it really worth the expenditure of my time and energy? Is it a channelling of ‘positive energy’ to take umbrage with umbrage?bq. Tarot woman, I don’t knowI don’t knowI don’t knowHey, I don’t know

Sparrow [Book Review] (from Grrl Scientist's blog)

Mon, 07/16/2012 - 12:00pm

SUMMARY: A lovely exploration of sparrows, the scientific insights they inspire and how they influence human culture Regardless of where you go, there they are. In bushes, in parking lots, on sidewalks, underfoot. They’re chirping, eating, hopping, quarreling, fornicating. “Little brown jobs,” bird watchers murmur dismissively. Sparrows. They’re seemingly everywhere. In the opening sentence in her new book, Sparrow [Reaktion Books; 2012: Guardian Bookshop; Amazon UK; Amazon US], environment writer Kim Todd immediately captures her readers’ attention by stating; “The sparrow is a slight bird, small and dun-coloured, easily crushed.”Easily crushed?

Abusing a Prior: some slides (from Bob O'Hara's blog)

Mon, 07/16/2012 - 6:31am

Here are the slides for my talk today about Bayesian variable selection. It’s mainly of interest to other statisticians, my excuse is that I’m talking at a statistical meeting (and I’m a keynote speaker! Wooo!).