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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 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.

US 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.U.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.” Songbirds 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.” U.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 http://www.gi.alaska.edu/AlaskaScienceForum/article/alaska-creatures-without-us"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."

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.

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 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.

* CAVEAT LECTOR!! SPOILERS AHEAD!! *
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?

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

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:This 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:In 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. 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:Step 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. 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). And 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.So 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.

OMG, 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.

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)

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!

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:TweetLike 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:

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.